{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I assume that you want to e.g. express fluorescent proteins for doing some kind of experimental study of Salmonella, as opposed to industrial protein production.</p>\n<p>I would suggest looking into prior work that uses Salmonella as a model. For example, I found <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1230934/\" rel=\"nofollow noreferrer\">this paper</a> somewhat at random that uses several vectors in Salmonella to do experiments. <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148252/\" rel=\"nofollow noreferrer\">Here</a> is another. And <a href=\"https://www.nature.com/articles/srep30591\" rel=\"nofollow noreferrer\">here</a> is another. Several of these appear to share authors, I don't know if that's Google SEO or a small research community.</p>\n","answer_id":112860,"answer_text":"I assume that you want to e.g. express fluorescent proteins for doing some kind of experimental study of Salmonella, as opposed to industrial protein production.\n\n\n\n\nI would suggest looking into prior work that uses Salmonella as a model. For example, I found this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1230934/) somewhat at random that uses several vectors in Salmonella to do experiments. Here (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148252/) is another. And here (https://www.nature.com/articles/srep30591) is another. Several of these appear to share authors, I don't know if that's Google SEO or a small research community.","answer_url":"https://biology.stackexchange.com/a/112860","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2023-08-23T23:34:46+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:38.885561+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/a145de97eabc007745b45919875489a41261075cbdf33d916d9640ba4ad0bd35_0.json","raw_sha256":"e7d8d4315eef8e039a452d2811869cbe305575c6ff8a6bef8f80d6dfb58c5bfd","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/112982;112980;112979;112977;112972;112967;112962;112956;112952;112948;112941;112938;112937;112936;112927;112925;112923;112919;112909;112905;112904;112898;112895;112893;112884;112881;112880;112879;112873;112872;112870;112869;112867;112850;112849;112848;112841;112835;112831;112824;112818;112811;112808;112807;112790;112789;112785;112777;112773;112770;112762;112759;112757;112756;112746;112739;112738;112737;112731;112705;112703;112700;112699;112698;112693;112691;112687;112685;112677;112671;112667;112663;112659;112653;112647;112646;112645;112636;112625;112621;112615;112614;112613;112610;112598;112593;112592;112586;112580;112575;112574;112564;112558;112552;112550;112549;112544;112539;112535;112531/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":112848,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2023-08-23T23:34:46+00:00","raw_file":"raw/codex_api_v1/9b8fea4e5df4051aa25c1aa90b42eca7481ee703f92ba25aeabed3d0b53e7a04_1790824026598483100_0.json","raw_sha256":"f252fc1b154815b8794116efb3b685202eda8dddb2cd870ae32ee5e82716c300","revision_guid":"924D87E9-4094-4AE1-A1E6-1208DFE16664","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/924D87E9-4094-4AE1-A1E6-1208DFE16664/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"John Appleseed","author_url":"https://biology.stackexchange.com/users/76665/john-appleseed","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"John Appleseed","profile_url":"https://biology.stackexchange.com/users/76665/john-appleseed","user_type":"registered"},"created_at":"2023-08-22T01:38:00+00:00","raw_file":"raw/codex_api_v1/9b8fea4e5df4051aa25c1aa90b42eca7481ee703f92ba25aeabed3d0b53e7a04_1790824026598483100_0.json","raw_sha256":"f252fc1b154815b8794116efb3b685202eda8dddb2cd870ae32ee5e82716c300","revision_guid":"DCF88F7D-806A-43EA-89F1-8DE13B79EBA9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DCF88F7D-806A-43EA-89F1-8DE13B79EBA9/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2023-09-23T01:06:05+00:00","raw_file":"raw/codex_api_v1/276704dec9e06f92cc8145549f11d289b09416db9510f3666cf41802c4fac079_1790824013419814500_0.json","raw_sha256":"062895378f6d877b905162e2e8855c08fb76517235f50b72affe2d1d54cb9ced","revision_guid":"A7856B8E-0876-45EE-8251-5540F0DC7551","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/A7856B8E-0876-45EE-8251-5540F0DC7551/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2024-01-21T02:07:35+00:00","raw_file":"raw/codex_api_v1/276704dec9e06f92cc8145549f11d289b09416db9510f3666cf41802c4fac079_1790824013419814500_0.json","raw_sha256":"062895378f6d877b905162e2e8855c08fb76517235f50b72affe2d1d54cb9ced","revision_guid":"6D741F30-7C13-42E4-BDAE-AB8EBB416841","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/6D741F30-7C13-42E4-BDAE-AB8EBB416841/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2024-05-20T03:07:40+00:00","raw_file":"raw/codex_api_v1/276704dec9e06f92cc8145549f11d289b09416db9510f3666cf41802c4fac079_1790824013419814500_0.json","raw_sha256":"062895378f6d877b905162e2e8855c08fb76517235f50b72affe2d1d54cb9ced","revision_guid":"0C2B5E60-7F44-42BD-99F9-5662C7C1CAF8","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/0C2B5E60-7F44-42BD-99F9-5662C7C1CAF8/view-source"}],"url":"https://biology.stackexchange.com/questions/112848/what-is-a-good-expression-vector-for-salmonella-enterica-subsp-enterica-serovar"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"112860","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2023-08-23T23:34:46+00:00","raw_file":"raw/codex_api_v1/9b8fea4e5df4051aa25c1aa90b42eca7481ee703f92ba25aeabed3d0b53e7a04_1790824026598483100_0.json","raw_sha256":"f252fc1b154815b8794116efb3b685202eda8dddb2cd870ae32ee5e82716c300","revision_guid":"924D87E9-4094-4AE1-A1E6-1208DFE16664","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/924D87E9-4094-4AE1-A1E6-1208DFE16664/view-source"}],"url":"https://biology.stackexchange.com/a/112860"}],"contexts":[{"context_id":"question","html":"<p>I am interested in expressing custom proteins in a Salmonella strain, however I am facing difficulties in finding the appropriate expression vector for it. It seems that most of the resources provide for E. coli expression. Does anyone have any recommendations?</p>\n<p>Thanks in advance.</p>\n","text":"I am interested in expressing custom proteins in a Salmonella strain, however I am facing difficulties in finding the appropriate expression vector for it. It seems that most of the resources provide for E. coli expression. Does anyone have any recommendations?\n\n\n\n\nThanks in advance."},{"context_id":"112860","html":"<p>I assume that you want to e.g. express fluorescent proteins for doing some kind of experimental study of Salmonella, as opposed to industrial protein production.</p>\n<p>I would suggest looking into prior work that uses Salmonella as a model. For example, I found <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1230934/\" rel=\"nofollow noreferrer\">this paper</a> somewhat at random that uses several vectors in Salmonella to do experiments. <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148252/\" rel=\"nofollow noreferrer\">Here</a> is another. And <a href=\"https://www.nature.com/articles/srep30591\" rel=\"nofollow noreferrer\">here</a> is another. Several of these appear to share authors, I don't know if that's Google SEO or a small research community.</p>\n","text":"I assume that you want to e.g. express fluorescent proteins for doing some kind of experimental study of Salmonella, as opposed to industrial protein production.\n\n\n\n\nI would suggest looking into prior work that uses Salmonella as a model. For example, I found this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1230934/) somewhat at random that uses several vectors in Salmonella to do experiments. Here (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148252/) is another. And here (https://www.nature.com/articles/srep30591) is another. Several of these appear to share authors, I don't know if that's Google SEO or a small research community."}],"domain":"biology","external_citations":["https://www.nature.com/articles/srep30591","https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1230934/","https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148252/"],"ground_truth_type":"metadata_grounded","group_id":"a7760a6818f7146d164b518e53d673e11325be77442ca0933062aefd8a3bc440","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-f547d12922cb9e75d101d079","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:12.794960+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/01e5186067e30dc1b8d7a145670ab7edd6b017797b271a481af8b7b7f55f13c2_0.json","raw_sha256":"6c3960de7e1d3d7920bb88d02e2184614c219b391f39d9bddc2a582fdc9a71e7","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=10&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"John Appleseed","profile_url":"https://biology.stackexchange.com/users/76665/john-appleseed","user_type":"registered"},"created_at":"2023-08-22T01:38:00+00:00","raw_file":"raw/codex_api_v1/9b8fea4e5df4051aa25c1aa90b42eca7481ee703f92ba25aeabed3d0b53e7a04_1790824026598483100_0.json","raw_sha256":"f252fc1b154815b8794116efb3b685202eda8dddb2cd870ae32ee5e82716c300","revision_guid":"DCF88F7D-806A-43EA-89F1-8DE13B79EBA9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DCF88F7D-806A-43EA-89F1-8DE13B79EBA9/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2023-09-23T01:06:05+00:00","raw_file":"raw/codex_api_v1/276704dec9e06f92cc8145549f11d289b09416db9510f3666cf41802c4fac079_1790824013419814500_0.json","raw_sha256":"062895378f6d877b905162e2e8855c08fb76517235f50b72affe2d1d54cb9ced","revision_guid":"A7856B8E-0876-45EE-8251-5540F0DC7551","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/A7856B8E-0876-45EE-8251-5540F0DC7551/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2024-01-21T02:07:35+00:00","raw_file":"raw/codex_api_v1/276704dec9e06f92cc8145549f11d289b09416db9510f3666cf41802c4fac079_1790824013419814500_0.json","raw_sha256":"062895378f6d877b905162e2e8855c08fb76517235f50b72affe2d1d54cb9ced","revision_guid":"6D741F30-7C13-42E4-BDAE-AB8EBB416841","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/6D741F30-7C13-42E4-BDAE-AB8EBB416841/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2024-05-20T03:07:40+00:00","raw_file":"raw/codex_api_v1/276704dec9e06f92cc8145549f11d289b09416db9510f3666cf41802c4fac079_1790824013419814500_0.json","raw_sha256":"062895378f6d877b905162e2e8855c08fb76517235f50b72affe2d1d54cb9ced","revision_guid":"0C2B5E60-7F44-42BD-99F9-5662C7C1CAF8","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/0C2B5E60-7F44-42BD-99F9-5662C7C1CAF8/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"112848","source_record_sha256":"99e17528a030a5dc0ebc7a49348cef390f7febcab05ba6b22cc3d79f190556ad","source_url":"https://biology.stackexchange.com/questions/112848/what-is-a-good-expression-vector-for-salmonella-enterica-subsp-enterica-serovar","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What is a good expression vector for Salmonella enterica subsp. enterica serovar typhimurium\nI am interested in expressing custom proteins in a Salmonella strain, however I am facing difficulties in finding the appropriate expression vector for it. It seems that most of the resources provide for E. coli expression. Does anyone have any recommendations?\n\n\n\n\nThanks in advance.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":112860,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":113002,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>This <a href=\"https://academic.oup.com/plphys/article/167/4/1554/6113757?login=false\" rel=\"nofollow noreferrer\">article</a> states that in plants at 15-25% relative water content (RWC), the PSII density is around ~700 complexes/µm<span class=\"math-container\">$^2$</span>, and in hydrated plants ~1500 complexes/µm<span class=\"math-container\">$^2$</span>.</p>\n<p><a href=\"https://i.sstatic.net/mTwk1.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/mTwk1.png\" alt=\"PSII complexes/RWC\" /></a></p>\n<p>They also have some nice Cryo-SEM images of grana membranes and the changes in PSII complexes density depending on their RWC. Which is also an important aspect of the question, since the amount of PSI and PSII complexes will vary depending on the environmental stimuli.</p>\n<p><a href=\"https://i.sstatic.net/ekOQw.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/ekOQw.png\" alt=\"changes in PSII density through de- and rehydration\" /></a></p>\n<p>Additionally, given that biological material is variable even within the same species (different tolerances might have a different effect on the amount of complexes/µm<span class=\"math-container\">$^2$</span>), I would expect variability in the complexes density among different species of plants too.</p>\n<p>Regarding PSI, I found an <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699766/\" rel=\"nofollow noreferrer\">article</a> where mass spectrometry analysis approximates the average of PSI in the thylakoid of a <em>Prochlorococcus</em> MED4 ecotype to 4303/μm<span class=\"math-container\">$^2$</span>. However, the thylakoids of another ecotype had more densely PSI organizations of crystalline pseudo-hexagonal arrays and the average was estimated at 5583/μm<span class=\"math-container\">$^2$</span>. In fact, the article tested growth under different conditions (low-light, high-light, poor-nutrient) of the different ecotypes and supports the hypothesis that the second ecotype adapted to low-light conditions (by maximizing the amount of pigments in its thylakoid membrane) while the first one adapted to high-light conditions. In this case, the observed part of the membrane with cryo-EM tomography was ~6 μm<span class=\"math-container\">$^2$</span>and ~22 μm<span class=\"math-container\">$^2$</span> of thylakoid membrane area for the first and the second ecotype.</p>\n<p>I think the right answer is that there are many factors affecting the distribution of PSI and PSII that are still unknown and a better approximation cannot be made.</p>\n<hr/>\n<p>References</p>\n<p>Charuvi, Dana &amp; Nevo, Reinat &amp; Shimoni, Eyal &amp; Naveh, Leah &amp; Zia, Ahmad &amp; Adam, Zach &amp; Farrant, Jill &amp; Kirchhoff, Helmut &amp; Reich, Ziv. (2015). Photoprotection Conferred by Changes in Photosynthetic Protein Levels and Organization during Dehydration of a Homoiochlorophyllous Resurrection Plant. Plant physiology. 167. 10.1104/pp.114.255794.</p>\n<p>MacGregor-Chatwin C, Jackson PJ, Sener M, Chidgey JW, Hitchcock A, Qian P, Mayneord GE, Johnson MP, Luthey-Schulten Z, Dickman MJ, Scanlan DJ, Hunter CN. Membrane organization of photosystem I complexes in the most abundant phototroph on Earth. Nat Plants. 2019 Aug;5(8):879-889. doi: 10.1038/s41477-019-0475-z. Epub 2019 Jul 22. PMID: 31332310; PMCID: PMC6699766.</p>\n","answer_id":113002,"answer_text":"This article (https://academic.oup.com/plphys/article/167/4/1554/6113757?login=false) states that in plants at 15-25% relative water content (RWC), the PSII density is around ~700 complexes/µm$^2$, and in hydrated plants ~1500 complexes/µm$^2$.\n\n\n\n\n[image: PSII complexes/RWC; source: https://i.sstatic.net/mTwk1.png] (https://i.sstatic.net/mTwk1.png)\n\n\n\n\nThey also have some nice Cryo-SEM images of grana membranes and the changes in PSII complexes density depending on their RWC. Which is also an important aspect of the question, since the amount of PSI and PSII complexes will vary depending on the environmental stimuli.\n\n\n\n\n[image: changes in PSII density through de- and rehydration; source: https://i.sstatic.net/ekOQw.png] (https://i.sstatic.net/ekOQw.png)\n\n\n\n\nAdditionally, given that biological material is variable even within the same species (different tolerances might have a different effect on the amount of complexes/µm$^2$), I would expect variability in the complexes density among different species of plants too.\n\n\n\n\nRegarding PSI, I found an article (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699766/) where mass spectrometry analysis approximates the average of PSI in the thylakoid of a Prochlorococcus MED4 ecotype to 4303/μm$^2$. However, the thylakoids of another ecotype had more densely PSI organizations of crystalline pseudo-hexagonal arrays and the average was estimated at 5583/μm$^2$. In fact, the article tested growth under different conditions (low-light, high-light, poor-nutrient) of the different ecotypes and supports the hypothesis that the second ecotype adapted to low-light conditions (by maximizing the amount of pigments in its thylakoid membrane) while the first one adapted to high-light conditions. In this case, the observed part of the membrane with cryo-EM tomography was ~6 μm$^2$and ~22 μm$^2$ of thylakoid membrane area for the first and the second ecotype.\n\n\n\n\nI think the right answer is that there are many factors affecting the distribution of PSI and PSII that are still unknown and a better approximation cannot be made.\n\n\n\n\n\n\n\nReferences\n\n\n\n\nCharuvi, Dana & Nevo, Reinat & Shimoni, Eyal & Naveh, Leah & Zia, Ahmad & Adam, Zach & Farrant, Jill & Kirchhoff, Helmut & Reich, Ziv. (2015). Photoprotection Conferred by Changes in Photosynthetic Protein Levels and Organization during Dehydration of a Homoiochlorophyllous Resurrection Plant. Plant physiology. 167. 10.1104/pp.114.255794.\n\n\n\n\nMacGregor-Chatwin C, Jackson PJ, Sener M, Chidgey JW, Hitchcock A, Qian P, Mayneord GE, Johnson MP, Luthey-Schulten Z, Dickman MJ, Scanlan DJ, Hunter CN. Membrane organization of photosystem I complexes in the most abundant phototroph on Earth. Nat Plants. 2019 Aug;5(8):879-889. doi: 10.1038/s41477-019-0475-z. Epub 2019 Jul 22. 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know whether there are say hundreds of complexes or millions. Is there any published data on this?</p>\n","text":"I haven't been able to find any good order-of-magnitude estimates for how many photosystems (e.g. how many PSII complexes, how many PSI complexes) are in an average chloroplast (or perhaps per area of thylakoid membrane).\n\n\n\n\nTextbooks always just show a small area of membrane, and I'm interested to know whether there are say hundreds of complexes or millions. Is there any published data on this?"},{"context_id":"113002","html":"<p>This <a href=\"https://academic.oup.com/plphys/article/167/4/1554/6113757?login=false\" rel=\"nofollow noreferrer\">article</a> states that in plants at 15-25% relative water content (RWC), the PSII density is around ~700 complexes/µm<span class=\"math-container\">$^2$</span>, and in hydrated plants ~1500 complexes/µm<span class=\"math-container\">$^2$</span>.</p>\n<p><a href=\"https://i.sstatic.net/mTwk1.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/mTwk1.png\" alt=\"PSII complexes/RWC\" /></a></p>\n<p>They also have some nice Cryo-SEM images of grana membranes and the changes in PSII complexes density depending on their RWC. Which is also an important aspect of the question, since the amount of PSI and PSII complexes will vary depending on the environmental stimuli.</p>\n<p><a href=\"https://i.sstatic.net/ekOQw.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/ekOQw.png\" alt=\"changes in PSII density through de- and rehydration\" /></a></p>\n<p>Additionally, given that biological material is variable even within the same species (different tolerances might have a different effect on the amount of complexes/µm<span class=\"math-container\">$^2$</span>), I would expect variability in the complexes density among different species of plants too.</p>\n<p>Regarding PSI, I found an <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699766/\" rel=\"nofollow noreferrer\">article</a> where mass spectrometry analysis approximates the average of PSI in the thylakoid of a <em>Prochlorococcus</em> MED4 ecotype to 4303/μm<span class=\"math-container\">$^2$</span>. However, the thylakoids of another ecotype had more densely PSI organizations of crystalline pseudo-hexagonal arrays and the average was estimated at 5583/μm<span class=\"math-container\">$^2$</span>. In fact, the article tested growth under different conditions (low-light, high-light, poor-nutrient) of the different ecotypes and supports the hypothesis that the second ecotype adapted to low-light conditions (by maximizing the amount of pigments in its thylakoid membrane) while the first one adapted to high-light conditions. In this case, the observed part of the membrane with cryo-EM tomography was ~6 μm<span class=\"math-container\">$^2$</span>and ~22 μm<span class=\"math-container\">$^2$</span> of thylakoid membrane area for the first and the second ecotype.</p>\n<p>I think the right answer is that there are many factors affecting the distribution of PSI and PSII that are still unknown and a better approximation cannot be made.</p>\n<hr/>\n<p>References</p>\n<p>Charuvi, Dana &amp; Nevo, Reinat &amp; Shimoni, Eyal &amp; Naveh, Leah &amp; Zia, Ahmad &amp; Adam, Zach &amp; Farrant, Jill &amp; Kirchhoff, Helmut &amp; Reich, Ziv. (2015). Photoprotection Conferred by Changes in Photosynthetic Protein Levels and Organization during Dehydration of a Homoiochlorophyllous Resurrection Plant. Plant physiology. 167. 10.1104/pp.114.255794.</p>\n<p>MacGregor-Chatwin C, Jackson PJ, Sener M, Chidgey JW, Hitchcock A, Qian P, Mayneord GE, Johnson MP, Luthey-Schulten Z, Dickman MJ, Scanlan DJ, Hunter CN. Membrane organization of photosystem I complexes in the most abundant phototroph on Earth. Nat Plants. 2019 Aug;5(8):879-889. doi: 10.1038/s41477-019-0475-z. Epub 2019 Jul 22. PMID: 31332310; PMCID: PMC6699766.</p>\n","text":"This article (https://academic.oup.com/plphys/article/167/4/1554/6113757?login=false) states that in plants at 15-25% relative water content (RWC), the PSII density is around ~700 complexes/µm$^2$, and in hydrated plants ~1500 complexes/µm$^2$.\n\n\n\n\n[image: PSII complexes/RWC; source: https://i.sstatic.net/mTwk1.png] (https://i.sstatic.net/mTwk1.png)\n\n\n\n\nThey also have some nice Cryo-SEM images of grana membranes and the changes in PSII complexes density depending on their RWC. Which is also an important aspect of the question, since the amount of PSI and PSII complexes will vary depending on the environmental stimuli.\n\n\n\n\n[image: changes in PSII density through de- and rehydration; source: https://i.sstatic.net/ekOQw.png] (https://i.sstatic.net/ekOQw.png)\n\n\n\n\nAdditionally, given that biological material is variable even within the same species (different tolerances might have a different effect on the amount of complexes/µm$^2$), I would expect variability in the complexes density among different species of plants too.\n\n\n\n\nRegarding PSI, I found an article (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699766/) where mass spectrometry analysis approximates the average of PSI in the thylakoid of a Prochlorococcus MED4 ecotype to 4303/μm$^2$. However, the thylakoids of another ecotype had more densely PSI organizations of crystalline pseudo-hexagonal arrays and the average was estimated at 5583/μm$^2$. In fact, the article tested growth under different conditions (low-light, high-light, poor-nutrient) of the different ecotypes and supports the hypothesis that the second ecotype adapted to low-light conditions (by maximizing the amount of pigments in its thylakoid membrane) while the first one adapted to high-light conditions. In this case, the observed part of the membrane with cryo-EM tomography was ~6 μm$^2$and ~22 μm$^2$ of thylakoid membrane area for the first and the second ecotype.\n\n\n\n\nI think the right answer is that there are many factors affecting the distribution of PSI and PSII that are still unknown and a better approximation cannot be made.\n\n\n\n\n\n\n\nReferences\n\n\n\n\nCharuvi, Dana & Nevo, Reinat & Shimoni, Eyal & Naveh, Leah & Zia, Ahmad & Adam, Zach & Farrant, Jill & Kirchhoff, Helmut & Reich, Ziv. (2015). Photoprotection Conferred by Changes in Photosynthetic Protein Levels and Organization during Dehydration of a Homoiochlorophyllous Resurrection Plant. Plant physiology. 167. 10.1104/pp.114.255794.\n\n\n\n\nMacGregor-Chatwin C, Jackson PJ, Sener M, Chidgey JW, Hitchcock A, Qian P, Mayneord GE, Johnson MP, Luthey-Schulten Z, Dickman MJ, Scanlan DJ, Hunter CN. Membrane organization of photosystem I complexes in the most abundant phototroph on Earth. Nat Plants. 2019 Aug;5(8):879-889. doi: 10.1038/s41477-019-0475-z. Epub 2019 Jul 22. PMID: 31332310; PMCID: PMC6699766."}],"domain":"biology","external_citations":["https://academic.oup.com/plphys/article/167/4/1554/6113757?login=false","https://i.sstatic.net/ekOQw.png","https://i.sstatic.net/mTwk1.png","https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699766/"],"ground_truth_type":"metadata_grounded","group_id":"8385fa69dac5b90fdecf44cc37d062dbd3a67ad5e775dca4a500ea26e29d87a6","hard_case_family":["multiple_sources"],"id":"RHM-6871edca8f181b6e243ef3e3","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:12.794960+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/01e5186067e30dc1b8d7a145670ab7edd6b017797b271a481af8b7b7f55f13c2_0.json","raw_sha256":"6c3960de7e1d3d7920bb88d02e2184614c219b391f39d9bddc2a582fdc9a71e7","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=10&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user265902","profile_url":"https://biology.stackexchange.com/users/13384/user265902","user_type":"registered"},"created_at":"2023-09-12T10:26:46+00:00","raw_file":"raw/codex_api_v1/276704dec9e06f92cc8145549f11d289b09416db9510f3666cf41802c4fac079_1790824013419814500_0.json","raw_sha256":"062895378f6d877b905162e2e8855c08fb76517235f50b72affe2d1d54cb9ced","revision_guid":"846B1DAF-31F5-4E3C-903F-4ED7D74E7B4D","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/846B1DAF-31F5-4E3C-903F-4ED7D74E7B4D/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"112977","source_record_sha256":"99695a967b3f8c43f4ea7ac133f735444bffbf67dad89a4b650a43e34721c2bc","source_url":"https://biology.stackexchange.com/questions/112977/how-many-photosystems-in-a-chloroplast","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How many photosystems in a chloroplast?\nI haven't been able to find any good order-of-magnitude estimates for how many photosystems (e.g. how many PSII complexes, how many PSI complexes) are in an average chloroplast (or perhaps per area of thylakoid membrane).\n\n\n\n\nTextbooks always just show a small area of membrane, and I'm interested to know whether there are say hundreds of complexes or millions. Is there any published data on this?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113002,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Against my better nature (I think that this is a question about software, not biology), I offer:</p>\n<p><a href=\"https://www.tbi.univie.ac.at/RNA/#download\" rel=\"nofollow noreferrer\">https://www.tbi.univie.ac.at/RNA/#download</a></p>\n<p><a href=\"https://i.sstatic.net/dLUbu.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/dLUbu.png\" alt=\"Download screenshot\" /></a></p>\n<p>This download works for me to get the precompiled packages.</p>\n<p>You could also try here (for a few days): davidleader.net/Wienershnitzel/index.html</p>\n","answer_id":113011,"answer_text":"Against my better nature (I think that this is a question about software, not biology), I offer:\n\n\n\n\nhttps://www.tbi.univie.ac.at/RNA/#download (https://www.tbi.univie.ac.at/RNA/#download)\n\n\n\n\n[image: Download screenshot; source: https://i.sstatic.net/dLUbu.png] (https://i.sstatic.net/dLUbu.png)\n\n\n\n\nThis download works for me to get the precompiled packages.\n\n\n\n\nYou could also try here (for a few days): davidleader.net/Wienershnitzel/index.html","answer_url":"https://biology.stackexchange.com/a/113011","author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","created_at":"2023-09-15T08:40:37+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:36.208962+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/ce9de3cf6525f1e283f75a76c7c279c0bd53024cf8e6597abc34f072e18cfbf7_0.json","raw_sha256":"c65c49a81e92972be3758d3b220c036300d85c38ce4d9079a6203d2eeac0d96d","source_api":"Stack Exchange API 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Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2023-09-15T12:10:33+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"B454E72F-FBBC-44C5-845D-4EBAEF410B37","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B454E72F-FBBC-44C5-845D-4EBAEF410B37/view-source"},{"content_license":"CC BY-SA 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4.0","contributor":{"display_name":"biohacker","profile_url":"https://biology.stackexchange.com/users/53247/biohacker","user_type":"registered"},"created_at":"2023-09-15T03:52:48+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"9BBD96A3-A148-4051-8862-A5AAFB156019","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9BBD96A3-A148-4051-8862-A5AAFB156019/view-source"}],"url":"https://biology.stackexchange.com/questions/113009/is-there-no-good-way-to-run-the-vienna-rna-tools-on-windows"},{"author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","context_id":"113011","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2023-09-15T08:40:37+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"16C73AF5-8D69-4CA4-B0D6-A28DFA5C1EF5","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/16C73AF5-8D69-4CA4-B0D6-A28DFA5C1EF5/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2023-09-15T12:10:33+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"B454E72F-FBBC-44C5-845D-4EBAEF410B37","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B454E72F-FBBC-44C5-845D-4EBAEF410B37/view-source"},{"content_license":"CC BY-SA 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4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2023-09-15T21:47:53+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"8F75788F-3754-4C09-AC34-107D24DAD84B","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8F75788F-3754-4C09-AC34-107D24DAD84B/view-source"}],"url":"https://biology.stackexchange.com/a/113011"}],"contexts":[{"context_id":"question","html":"<p>I'm trying to get the Vienna RNA tools (particularly RNAfold) running locally (as opposed to using the web interface--because I have lots of sequences I wish to process in batch mode). On the website, it mentions that there are pre-compiled versions of the software available for all major operating systems, however the site seems to be down. All that's still accessible is the GitHub page with source code access.</p>\n<p>From my experience, trying to get large C/C++ projects, that often have quite a few third party dependencies, to compile is a huge pain. And even the Python &quot;version&quot; (really a Python wrapper around the C++ code) doesn't install with pip, despite having a compiler available (and found by pip), there are quite some header files that aren't on my Windows system that it complains about--and I've generally never had a problem with pip not being able to install other Python packages, even ones that are internally mostly C/C++. Even installing Anaconda, then bioconda, and then trying to install &quot;viennarna&quot;, it isn't found. I'm beginning to think that these tools are just broken other than on the sorts of workstations on which they were developed, which already have all the necessary dependencies and headers.</p>\n<p>Has anyone else managed to get a local install of these tools working?</p>\n","text":"I'm trying to get the Vienna RNA tools (particularly RNAfold) running locally (as opposed to using the web interface--because I have lots of sequences I wish to process in batch mode). On the website, it mentions that there are pre-compiled versions of the software available for all major operating systems, however the site seems to be down. All that's still accessible is the GitHub page with source code access.\n\n\n\n\nFrom my experience, trying to get large C/C++ projects, that often have quite a few third party dependencies, to compile is a huge pain. And even the Python \"version\" (really a Python wrapper around the C++ code) doesn't install with pip, despite having a compiler available (and found by pip), there are quite some header files that aren't on my Windows system that it complains about--and I've generally never had a problem with pip not being able to install other Python packages, even ones that are internally mostly C/C++. Even installing Anaconda, then bioconda, and then trying to install \"viennarna\", it isn't found. I'm beginning to think that these tools are just broken other than on the sorts of workstations on which they were developed, which already have all the necessary dependencies and headers.\n\n\n\n\nHas anyone else managed to get a local install of these tools working?"},{"context_id":"113011","html":"<p>Against my better nature (I think that this is a question about software, not biology), I offer:</p>\n<p><a href=\"https://www.tbi.univie.ac.at/RNA/#download\" rel=\"nofollow noreferrer\">https://www.tbi.univie.ac.at/RNA/#download</a></p>\n<p><a href=\"https://i.sstatic.net/dLUbu.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/dLUbu.png\" alt=\"Download screenshot\" /></a></p>\n<p>This download works for me to get the precompiled packages.</p>\n<p>You could also try here (for a few days): davidleader.net/Wienershnitzel/index.html</p>\n","text":"Against my better nature (I think that this is a question about software, not biology), I offer:\n\n\n\n\nhttps://www.tbi.univie.ac.at/RNA/#download (https://www.tbi.univie.ac.at/RNA/#download)\n\n\n\n\n[image: Download screenshot; source: https://i.sstatic.net/dLUbu.png] (https://i.sstatic.net/dLUbu.png)\n\n\n\n\nThis download works for me to get the precompiled packages.\n\n\n\n\nYou could also try here (for a few days): davidleader.net/Wienershnitzel/index.html"}],"domain":"biology","external_citations":["https://i.sstatic.net/dLUbu.png","https://www.tbi.univie.ac.at/RNA/#download"],"ground_truth_type":"metadata_grounded","group_id":"c1bc4541f38587c852e6beb4333a09b573a47d8cd6afdf88667a73a5ea3c051d","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-5e4ce2655cbcaf989a374efd","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:11.333206+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/3e71d6afdfe444c721dbb1321f43c14066813d2fd740fb255123cf87e737d071_0.json","raw_sha256":"84992ad678a40907dca3af99f849ee653142b680281a54e02542dc7f47d30773","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=9&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"biohacker","profile_url":"https://biology.stackexchange.com/users/53247/biohacker","user_type":"registered"},"created_at":"2023-09-15T03:52:48+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"9BBD96A3-A148-4051-8862-A5AAFB156019","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9BBD96A3-A148-4051-8862-A5AAFB156019/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113009","source_record_sha256":"55e285449e5bb7b5f3b9185f2b80320a06624c1d18eecfeea45102be6adb2e4a","source_url":"https://biology.stackexchange.com/questions/113009/is-there-no-good-way-to-run-the-vienna-rna-tools-on-windows","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Is there no good way to run the Vienna RNA tools on Windows?\nI'm trying to get the Vienna RNA tools (particularly RNAfold) running locally (as opposed to using the web interface--because I have lots of sequences I wish to process in batch mode). On the website, it mentions that there are pre-compiled versions of the software available for all major operating systems, however the site seems to be down. All that's still accessible is the GitHub page with source code access.\n\n\n\n\nFrom my experience, trying to get large C/C++ projects, that often have quite a few third party dependencies, to compile is a huge pain. And even the Python \"version\" (really a Python wrapper around the C++ code) doesn't install with pip, despite having a compiler available (and found by pip), there are quite some header files that aren't on my Windows system that it complains about--and I've generally never had a problem with pip not being able to install other Python packages, even ones that are internally mostly C/C++. Even installing Anaconda, then bioconda, and then trying to install \"viennarna\", it isn't found. I'm beginning to think that these tools are just broken other than on the sorts of workstations on which they were developed, which already have all the necessary dependencies and headers.\n\n\n\n\nHas anyone else managed to get a local install of these tools working?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113011,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>There are many ways to divide and sort peripheral and spinal cord nerves and axons.</p>\n<p>One division is into &quot;autonomic&quot; (further divided into sympathetic and parasympathetic) and &quot;somatic&quot; nervous system; the <a href=\"https://en.wikipedia.org/wiki/Somatic_nervous_system\" rel=\"nofollow noreferrer\">somatic nervous system</a> is the part controlling the skeletal muscles and also involving the somatosensory system: touch/pressure/etc, as well as proprioception and proprioceptive reflexes.</p>\n<p>Another division is directional: afferent versus efferent. Afferent nerves/fibers transmit information towards the central nervous system; efferent nerves/fibers transmit information away from the central nervous system, such as to control muscles.</p>\n<p><em>Usually</em>, when I hear &quot;sensory&quot; and &quot;motor&quot; I would assume someone is talking about <em>afferent and efferent parts of the somatic nervous system</em>. They're not necessarily considering the autonomic system at all (there's a bit of a tradition in some subfields in biology/physiology to forget that others exist). But there are also some sources that seem to prefer avoiding introducing the terms afferent and efferent for students and still use sensory and motor. I can't know what is being done in the specific text you're reading.</p>\n<p>That doesn't mean that the autonomic part of the nervous system doesn't involve sensory or motor functions, just that &quot;sensory&quot; is often shorthand for &quot;somatosensory&quot; and &quot;motor&quot; shorthand for &quot;skeletal motor&quot;.</p>\n<p>If you want to talk about nerves within the parasympathetic system (or autonomic more generally) are carrying information into the CNS or out of the CNS, I'd recommend using the words &quot;afferent&quot; or &quot;efferent&quot;, though nothing is wrong about calling them sensory and motor, you just want to be clear you are not talking about somatic nervous system functions. Using those terms, <a href=\"https://en.wikipedia.org/wiki/Vagus_nerve\" rel=\"nofollow noreferrer\">cranial nerve X/vagus nerve</a> is primarily made up of both afferent and efferent fibers of the autonomic nervous system.</p>\n<p><strong>However,</strong> nothing is quite so simple in biology, and the vagus also carries some skeletal muscle efferent fibers and sensory afferents.</p>\n<p>For the cranial nerves more generally, I think it's important to recognize that the cranial nerves are not all homologous even though they're numbered in sequence - someone just naively counted all the &quot;pipes&quot; coming out of the brain and ordered them. I would not attempt to generalize among them besides that feature (and even the simple idea that &quot;cranial nerves leave the brain&quot; is a bit suspect!).</p>\n<p>Some of the cranial nerves are really no different from the somatic nerves coming out of the spinal cord, they just happen to come out really close to the brain. Others, like the olfactory nerve and optic nerve, are quite special: they don't come out of the brainstem but rather the cerebrum, and arguably the optic nerve doesn't even really leave the brain if you consider that the retina is embryonically brain tissue.</p>\n<p>For a quick summary from <a href=\"https://www.ncbi.nlm.nih.gov/books/NBK470353/\" rel=\"nofollow noreferrer\">Sonne J, Lopez-Ojeda W. Neuroanatomy, Cranial Nerve.</a>:</p>\n<blockquote>\n<p>Cranial nerves I (olfactory), II (optic), and VIII (vestibulocochlear) are considered purely afferent. Cranial nerves III (oculomotor), IV (trochlear), VI (abducens), XI (spinal accessory), and XII (hypoglossal) are purely efferent. The remaining cranial nerves, V (trigeminal), VII (facial), IX (glossopharyngeal), and X (vagus), are functionally mixed (sensory and motor).</p>\n</blockquote>\n","answer_id":113035,"answer_text":"There are many ways to divide and sort peripheral and spinal cord nerves and axons.\n\n\n\n\nOne division is into \"autonomic\" (further divided into sympathetic and parasympathetic) and \"somatic\" nervous system; the somatic nervous system (https://en.wikipedia.org/wiki/Somatic_nervous_system) is the part controlling the skeletal muscles and also involving the somatosensory system: touch/pressure/etc, as well as proprioception and proprioceptive reflexes.\n\n\n\n\nAnother division is directional: afferent versus efferent. Afferent nerves/fibers transmit information towards the central nervous system; efferent nerves/fibers transmit information away from the central nervous system, such as to control muscles.\n\n\n\n\nUsually, when I hear \"sensory\" and \"motor\" I would assume someone is talking about afferent and efferent parts of the somatic nervous system. They're not necessarily considering the autonomic system at all (there's a bit of a tradition in some subfields in biology/physiology to forget that others exist). But there are also some sources that seem to prefer avoiding introducing the terms afferent and efferent for students and still use sensory and motor. I can't know what is being done in the specific text you're reading.\n\n\n\n\nThat doesn't mean that the autonomic part of the nervous system doesn't involve sensory or motor functions, just that \"sensory\" is often shorthand for \"somatosensory\" and \"motor\" shorthand for \"skeletal motor\".\n\n\n\n\nIf you want to talk about nerves within the parasympathetic system (or autonomic more generally) are carrying information into the CNS or out of the CNS, I'd recommend using the words \"afferent\" or \"efferent\", though nothing is wrong about calling them sensory and motor, you just want to be clear you are not talking about somatic nervous system functions. Using those terms, cranial nerve X/vagus nerve (https://en.wikipedia.org/wiki/Vagus_nerve) is primarily made up of both afferent and efferent fibers of the autonomic nervous system.\n\n\n\n\nHowever, nothing is quite so simple in biology, and the vagus also carries some skeletal muscle efferent fibers and sensory afferents.\n\n\n\n\nFor the cranial nerves more generally, I think it's important to recognize that the cranial nerves are not all homologous even though they're numbered in sequence - someone just naively counted all the \"pipes\" coming out of the brain and ordered them. I would not attempt to generalize among them besides that feature (and even the simple idea that \"cranial nerves leave the brain\" is a bit suspect!).\n\n\n\n\nSome of the cranial nerves are really no different from the somatic nerves coming out of the spinal cord, they just happen to come out really close to the brain. Others, like the olfactory nerve and optic nerve, are quite special: they don't come out of the brainstem but rather the cerebrum, and arguably the optic nerve doesn't even really leave the brain if you consider that the retina is embryonically brain tissue.\n\n\n\n\nFor a quick summary from Sonne J, Lopez-Ojeda W. Neuroanatomy, Cranial Nerve. (https://www.ncbi.nlm.nih.gov/books/NBK470353/):\n\n\n\n\n\n\n\nCranial nerves I (olfactory), II (optic), and VIII (vestibulocochlear) are considered purely afferent. Cranial nerves III (oculomotor), IV (trochlear), VI (abducens), XI (spinal accessory), and XII (hypoglossal) are purely efferent. The remaining cranial nerves, V (trigeminal), VII (facial), IX (glossopharyngeal), and X (vagus), are functionally mixed (sensory and motor).","answer_url":"https://biology.stackexchange.com/a/113035","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2023-09-18T15:00:51+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:36.208962+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/ce9de3cf6525f1e283f75a76c7c279c0bd53024cf8e6597abc34f072e18cfbf7_0.json","raw_sha256":"c65c49a81e92972be3758d3b220c036300d85c38ce4d9079a6203d2eeac0d96d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113468;113465;113459;113453;113451;113449;113442;113437;113425;113421;113416;113415;113413;113406;113400;113398;113386;113378;113364;113363;113347;113340;113333;113324;113317;113315;113310;113303;113307;113299;113293;113291;113284;113282;113279;113277;113275;113274;113263;113253;113252;113243;113239;113235;113231;113229;113223;113221;113218;113216;113210;113198;113191;113183;113180;113175;113164;113158;113153;113146;113141;113118;113116;113115;113113;113110;113109;113106;113104;113101;113095;113089;113086;113081;113080;113077;113076;113075;113070;113067;113064;113053;113046;113043;113039;113031;113030;113028;113027;113024;113017;113016;113015;113014;113009;113008;113007;113005;112998;112984/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113027,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2023-09-18T15:00:51+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"5E91C7EE-E24D-4440-91DD-8427311DF0FE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5E91C7EE-E24D-4440-91DD-8427311DF0FE/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Drita Raci","author_url":"https://biology.stackexchange.com/users/70297/drita-raci","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Drita Raci","profile_url":"https://biology.stackexchange.com/users/70297/drita-raci","user_type":"registered"},"created_at":"2023-09-16T16:56:39+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"C74AA9B3-A200-423B-86CE-1EB8CF3C4CB9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C74AA9B3-A200-423B-86CE-1EB8CF3C4CB9/view-source"}],"url":"https://biology.stackexchange.com/questions/113027/are-parasympathetic-nerves-different-from-motor-and-sensory-nerves"},{"author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","context_id":"113035","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2023-09-18T15:00:51+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"5E91C7EE-E24D-4440-91DD-8427311DF0FE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5E91C7EE-E24D-4440-91DD-8427311DF0FE/view-source"}],"url":"https://biology.stackexchange.com/a/113035"}],"contexts":[{"context_id":"question","html":"<p>So the nerves leaving the spinal cord are either motor or sensory (only?). But what about the cranial nerves? For example, the cranial nerve vagus is a parasympathetic nerve. Are parasympathetic nerves divided into categories of motor or sensory? Or is it just a parasympathetic nerve?</p>\n<p>If it is indeed composed of motor and sensory nerves, then what about these nerves coming from the spinal cord? Should they not be of a broader name? Just like nerve vagus is of the parasympathetic nervous system.</p>\n<p>So, it goes like this: parasympathetic -&gt; n. vagus -&gt; motor or sensory, right?</p>\n<p>What about: ? -&gt; n. median -&gt; motor or sensory</p>\n","text":"So the nerves leaving the spinal cord are either motor or sensory (only?). But what about the cranial nerves? For example, the cranial nerve vagus is a parasympathetic nerve. Are parasympathetic nerves divided into categories of motor or sensory? Or is it just a parasympathetic nerve?\n\n\n\n\nIf it is indeed composed of motor and sensory nerves, then what about these nerves coming from the spinal cord? Should they not be of a broader name? Just like nerve vagus is of the parasympathetic nervous system.\n\n\n\n\nSo, it goes like this: parasympathetic -> n. vagus -> motor or sensory, right?\n\n\n\n\nWhat about: ? -> n. median -> motor or sensory"},{"context_id":"113035","html":"<p>There are many ways to divide and sort peripheral and spinal cord nerves and axons.</p>\n<p>One division is into &quot;autonomic&quot; (further divided into sympathetic and parasympathetic) and &quot;somatic&quot; nervous system; the <a href=\"https://en.wikipedia.org/wiki/Somatic_nervous_system\" rel=\"nofollow noreferrer\">somatic nervous system</a> is the part controlling the skeletal muscles and also involving the somatosensory system: touch/pressure/etc, as well as proprioception and proprioceptive reflexes.</p>\n<p>Another division is directional: afferent versus efferent. Afferent nerves/fibers transmit information towards the central nervous system; efferent nerves/fibers transmit information away from the central nervous system, such as to control muscles.</p>\n<p><em>Usually</em>, when I hear &quot;sensory&quot; and &quot;motor&quot; I would assume someone is talking about <em>afferent and efferent parts of the somatic nervous system</em>. They're not necessarily considering the autonomic system at all (there's a bit of a tradition in some subfields in biology/physiology to forget that others exist). But there are also some sources that seem to prefer avoiding introducing the terms afferent and efferent for students and still use sensory and motor. I can't know what is being done in the specific text you're reading.</p>\n<p>That doesn't mean that the autonomic part of the nervous system doesn't involve sensory or motor functions, just that &quot;sensory&quot; is often shorthand for &quot;somatosensory&quot; and &quot;motor&quot; shorthand for &quot;skeletal motor&quot;.</p>\n<p>If you want to talk about nerves within the parasympathetic system (or autonomic more generally) are carrying information into the CNS or out of the CNS, I'd recommend using the words &quot;afferent&quot; or &quot;efferent&quot;, though nothing is wrong about calling them sensory and motor, you just want to be clear you are not talking about somatic nervous system functions. Using those terms, <a href=\"https://en.wikipedia.org/wiki/Vagus_nerve\" rel=\"nofollow noreferrer\">cranial nerve X/vagus nerve</a> is primarily made up of both afferent and efferent fibers of the autonomic nervous system.</p>\n<p><strong>However,</strong> nothing is quite so simple in biology, and the vagus also carries some skeletal muscle efferent fibers and sensory afferents.</p>\n<p>For the cranial nerves more generally, I think it's important to recognize that the cranial nerves are not all homologous even though they're numbered in sequence - someone just naively counted all the &quot;pipes&quot; coming out of the brain and ordered them. I would not attempt to generalize among them besides that feature (and even the simple idea that &quot;cranial nerves leave the brain&quot; is a bit suspect!).</p>\n<p>Some of the cranial nerves are really no different from the somatic nerves coming out of the spinal cord, they just happen to come out really close to the brain. Others, like the olfactory nerve and optic nerve, are quite special: they don't come out of the brainstem but rather the cerebrum, and arguably the optic nerve doesn't even really leave the brain if you consider that the retina is embryonically brain tissue.</p>\n<p>For a quick summary from <a href=\"https://www.ncbi.nlm.nih.gov/books/NBK470353/\" rel=\"nofollow noreferrer\">Sonne J, Lopez-Ojeda W. Neuroanatomy, Cranial Nerve.</a>:</p>\n<blockquote>\n<p>Cranial nerves I (olfactory), II (optic), and VIII (vestibulocochlear) are considered purely afferent. Cranial nerves III (oculomotor), IV (trochlear), VI (abducens), XI (spinal accessory), and XII (hypoglossal) are purely efferent. The remaining cranial nerves, V (trigeminal), VII (facial), IX (glossopharyngeal), and X (vagus), are functionally mixed (sensory and motor).</p>\n</blockquote>\n","text":"There are many ways to divide and sort peripheral and spinal cord nerves and axons.\n\n\n\n\nOne division is into \"autonomic\" (further divided into sympathetic and parasympathetic) and \"somatic\" nervous system; the somatic nervous system (https://en.wikipedia.org/wiki/Somatic_nervous_system) is the part controlling the skeletal muscles and also involving the somatosensory system: touch/pressure/etc, as well as proprioception and proprioceptive reflexes.\n\n\n\n\nAnother division is directional: afferent versus efferent. Afferent nerves/fibers transmit information towards the central nervous system; efferent nerves/fibers transmit information away from the central nervous system, such as to control muscles.\n\n\n\n\nUsually, when I hear \"sensory\" and \"motor\" I would assume someone is talking about afferent and efferent parts of the somatic nervous system. They're not necessarily considering the autonomic system at all (there's a bit of a tradition in some subfields in biology/physiology to forget that others exist). But there are also some sources that seem to prefer avoiding introducing the terms afferent and efferent for students and still use sensory and motor. I can't know what is being done in the specific text you're reading.\n\n\n\n\nThat doesn't mean that the autonomic part of the nervous system doesn't involve sensory or motor functions, just that \"sensory\" is often shorthand for \"somatosensory\" and \"motor\" shorthand for \"skeletal motor\".\n\n\n\n\nIf you want to talk about nerves within the parasympathetic system (or autonomic more generally) are carrying information into the CNS or out of the CNS, I'd recommend using the words \"afferent\" or \"efferent\", though nothing is wrong about calling them sensory and motor, you just want to be clear you are not talking about somatic nervous system functions. Using those terms, cranial nerve X/vagus nerve (https://en.wikipedia.org/wiki/Vagus_nerve) is primarily made up of both afferent and efferent fibers of the autonomic nervous system.\n\n\n\n\nHowever, nothing is quite so simple in biology, and the vagus also carries some skeletal muscle efferent fibers and sensory afferents.\n\n\n\n\nFor the cranial nerves more generally, I think it's important to recognize that the cranial nerves are not all homologous even though they're numbered in sequence - someone just naively counted all the \"pipes\" coming out of the brain and ordered them. I would not attempt to generalize among them besides that feature (and even the simple idea that \"cranial nerves leave the brain\" is a bit suspect!).\n\n\n\n\nSome of the cranial nerves are really no different from the somatic nerves coming out of the spinal cord, they just happen to come out really close to the brain. Others, like the olfactory nerve and optic nerve, are quite special: they don't come out of the brainstem but rather the cerebrum, and arguably the optic nerve doesn't even really leave the brain if you consider that the retina is embryonically brain tissue.\n\n\n\n\nFor a quick summary from Sonne J, Lopez-Ojeda W. Neuroanatomy, Cranial Nerve. (https://www.ncbi.nlm.nih.gov/books/NBK470353/):\n\n\n\n\n\n\n\nCranial nerves I (olfactory), II (optic), and VIII (vestibulocochlear) are considered purely afferent. Cranial nerves III (oculomotor), IV (trochlear), VI (abducens), XI (spinal accessory), and XII (hypoglossal) are purely efferent. The remaining cranial nerves, V (trigeminal), VII (facial), IX (glossopharyngeal), and X (vagus), are functionally mixed (sensory and motor)."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Somatic_nervous_system","https://en.wikipedia.org/wiki/Vagus_nerve","https://www.ncbi.nlm.nih.gov/books/NBK470353/"],"ground_truth_type":"metadata_grounded","group_id":"eafddc1014c97aff49ec3a8d1de3506ad9d584a49298d302a5c9607e07a92c56","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-9cf04006c4f76779377fe6aa","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:11.333206+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/3e71d6afdfe444c721dbb1321f43c14066813d2fd740fb255123cf87e737d071_0.json","raw_sha256":"84992ad678a40907dca3af99f849ee653142b680281a54e02542dc7f47d30773","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=9&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Drita Raci","profile_url":"https://biology.stackexchange.com/users/70297/drita-raci","user_type":"registered"},"created_at":"2023-09-16T16:56:39+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"C74AA9B3-A200-423B-86CE-1EB8CF3C4CB9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C74AA9B3-A200-423B-86CE-1EB8CF3C4CB9/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113027","source_record_sha256":"a4822e019a5ea9364b90563a2f5697942e4970b973b22071d93489292ccf0f0b","source_url":"https://biology.stackexchange.com/questions/113027/are-parasympathetic-nerves-different-from-motor-and-sensory-nerves","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Are parasympathetic nerves different from motor and sensory nerves?\nSo the nerves leaving the spinal cord are either motor or sensory (only?). But what about the cranial nerves? For example, the cranial nerve vagus is a parasympathetic nerve. Are parasympathetic nerves divided into categories of motor or sensory? Or is it just a parasympathetic nerve?\n\n\n\n\nIf it is indeed composed of motor and sensory nerves, then what about these nerves coming from the spinal cord? Should they not be of a broader name? Just like nerve vagus is of the parasympathetic nervous system.\n\n\n\n\nSo, it goes like this: parasympathetic -> n. vagus -> motor or sensory, right?\n\n\n\n\nWhat about: ? -> n. median -> motor or sensory","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113035,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>AlphaFold defines these measures in the <a href=\"https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03819-2/MediaObjects/41586_2021_3819_MOESM1_ESM.pdf\" rel=\"nofollow noreferrer\">supplementary information of the paper</a>, as referenced in the main text.</p>\n<p>Generally speaking, a lot of information for these highly condensed papers goes into the supplementary information, and that's the first place to look for more explanation.</p>\n<h2>MSA depth</h2>\n<p>Figure S10 legend:</p>\n<blockquote>\n<p>MSA depth is computed by counting the number of non-gap residues for each position in the MSA (using the Neff weighting scheme with a threshold of 80% identity measured on the region that is non-gap in either sequence) and taking the median across residues.</p>\n</blockquote>\n<p>This is not a standard measure, just to be clear.</p>\n<h2>MSA clustering</h2>\n<p>There is a section &quot;1.2.7 MSA clustering&quot; in the paper supplement that describes the clustering procedure at some length.</p>\n<p>MSA clustering is a fairly standard thing to do, but there are many possible algorithms for deriving clusters, and a large family of implementations of each algorithm. I suggest looking into the field of <a href=\"https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwjZxoz5lreBAxWlOH0KHaU7B-wQFnoECBQQAQ&amp;url=https%3A%2F%2Fplato.stanford.edu%2Fentries%2Fphylogenetic-inference%2F&amp;usg=AOvVaw2kMNvfnjpTGHX50FzWv2Cb&amp;opi=89978449\" rel=\"nofollow noreferrer\">phylogenetic inference</a> for other examples.</p>\n","answer_id":113044,"answer_text":"AlphaFold defines these measures in the supplementary information of the paper (https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03819-2/MediaObjects/41586_2021_3819_MOESM1_ESM.pdf), as referenced in the main text.\n\n\n\n\nGenerally speaking, a lot of information for these highly condensed papers goes into the supplementary information, and that's the first place to look for more explanation.\n\n\n\n\nMSA depth\n\n\n\n\nFigure S10 legend:\n\n\n\n\n\n\n\nMSA depth is computed by counting the number of non-gap residues for each position in the MSA (using the Neff weighting scheme with a threshold of 80% identity measured on the region that is non-gap in either sequence) and taking the median across residues.\n\n\n\n\n\n\n\nThis is not a standard measure, just to be clear.\n\n\n\n\nMSA clustering\n\n\n\n\nThere is a section \"1.2.7 MSA clustering\" in the paper supplement that describes the clustering procedure at some length.\n\n\n\n\nMSA clustering is a fairly standard thing to do, but there are many possible algorithms for deriving clusters, and a large family of implementations of each algorithm. I suggest looking into the field of phylogenetic inference (https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjZxoz5lreBAxWlOH0KHaU7B-wQFnoECBQQAQ&url=https%3A%2F%2Fplato.stanford.edu%2Fentries%2Fphylogenetic-inference%2F&usg=AOvVaw2kMNvfnjpTGHX50FzWv2Cb&opi=89978449) for other examples.","answer_url":"https://biology.stackexchange.com/a/113044","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2023-09-19T17:19:31+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:36.208962+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/ce9de3cf6525f1e283f75a76c7c279c0bd53024cf8e6597abc34f072e18cfbf7_0.json","raw_sha256":"c65c49a81e92972be3758d3b220c036300d85c38ce4d9079a6203d2eeac0d96d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113468;113465;113459;113453;113451;113449;113442;113437;113425;113421;113416;113415;113413;113406;113400;113398;113386;113378;113364;113363;113347;113340;113333;113324;113317;113315;113310;113303;113307;113299;113293;113291;113284;113282;113279;113277;113275;113274;113263;113253;113252;113243;113239;113235;113231;113229;113223;113221;113218;113216;113210;113198;113191;113183;113180;113175;113164;113158;113153;113146;113141;113118;113116;113115;113113;113110;113109;113106;113104;113101;113095;113089;113086;113081;113080;113077;113076;113075;113070;113067;113064;113053;113046;113043;113039;113031;113030;113028;113027;113024;113017;113016;113015;113014;113009;113008;113007;113005;112998;112984/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113031,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2023-09-19T17:19:31+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"335FF2FD-512C-4E17-96FE-910F706E9E7D","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/335FF2FD-512C-4E17-96FE-910F706E9E7D/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Jack","author_url":"https://biology.stackexchange.com/users/76986/jack","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Jack","profile_url":"https://biology.stackexchange.com/users/76986/jack","user_type":"registered"},"created_at":"2023-09-18T09:19:43+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"97E2DDD6-FFD0-4055-9C8A-AFC8CFC373DE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/97E2DDD6-FFD0-4055-9C8A-AFC8CFC373DE/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2023-09-19T17:21:11+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"35B72ACD-424F-4D43-8A5A-683BD89E3182","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/35B72ACD-424F-4D43-8A5A-683BD89E3182/view-source"}],"url":"https://biology.stackexchange.com/questions/113031/msa-cluster-and-msa-depth"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"113044","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2023-09-19T17:19:31+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"335FF2FD-512C-4E17-96FE-910F706E9E7D","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/335FF2FD-512C-4E17-96FE-910F706E9E7D/view-source"}],"url":"https://biology.stackexchange.com/a/113044"}],"contexts":[{"context_id":"question","html":"<p>I was reading the <a href=\"https://www.nature.com/articles/s41586-021-03819-2\" rel=\"nofollow noreferrer\">AlphaFold paper</a> and had difficulty with a couple of terms introduced in the main text of the paper. I asked ChatGPT what these were but I'm not sure that it's accurate.</p>\n<p>I had a hard time finding the definitions of an MSA (multiple sequence alignment) cluster and MSA depth. GPT-4 explains that an MSA cluster is a subset of sequences from an overall MSA that are closely related to each other, which seems to be simply the results from clustering analysis on MSA. GPT-4 also defines the MSA depth as the number of sequences in MSA. However, I want to make sure that these definitions are correct and are not just hallucinations from GPT-4.</p>\n","text":"I was reading the AlphaFold paper (https://www.nature.com/articles/s41586-021-03819-2) and had difficulty with a couple of terms introduced in the main text of the paper. I asked ChatGPT what these were but I'm not sure that it's accurate.\n\n\n\n\nI had a hard time finding the definitions of an MSA (multiple sequence alignment) cluster and MSA depth. GPT-4 explains that an MSA cluster is a subset of sequences from an overall MSA that are closely related to each other, which seems to be simply the results from clustering analysis on MSA. GPT-4 also defines the MSA depth as the number of sequences in MSA. However, I want to make sure that these definitions are correct and are not just hallucinations from GPT-4."},{"context_id":"113044","html":"<p>AlphaFold defines these measures in the <a href=\"https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03819-2/MediaObjects/41586_2021_3819_MOESM1_ESM.pdf\" rel=\"nofollow noreferrer\">supplementary information of the paper</a>, as referenced in the main text.</p>\n<p>Generally speaking, a lot of information for these highly condensed papers goes into the supplementary information, and that's the first place to look for more explanation.</p>\n<h2>MSA depth</h2>\n<p>Figure S10 legend:</p>\n<blockquote>\n<p>MSA depth is computed by counting the number of non-gap residues for each position in the MSA (using the Neff weighting scheme with a threshold of 80% identity measured on the region that is non-gap in either sequence) and taking the median across residues.</p>\n</blockquote>\n<p>This is not a standard measure, just to be clear.</p>\n<h2>MSA clustering</h2>\n<p>There is a section &quot;1.2.7 MSA clustering&quot; in the paper supplement that describes the clustering procedure at some length.</p>\n<p>MSA clustering is a fairly standard thing to do, but there are many possible algorithms for deriving clusters, and a large family of implementations of each algorithm. I suggest looking into the field of <a href=\"https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwjZxoz5lreBAxWlOH0KHaU7B-wQFnoECBQQAQ&amp;url=https%3A%2F%2Fplato.stanford.edu%2Fentries%2Fphylogenetic-inference%2F&amp;usg=AOvVaw2kMNvfnjpTGHX50FzWv2Cb&amp;opi=89978449\" rel=\"nofollow noreferrer\">phylogenetic inference</a> for other examples.</p>\n","text":"AlphaFold defines these measures in the supplementary information of the paper (https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03819-2/MediaObjects/41586_2021_3819_MOESM1_ESM.pdf), as referenced in the main text.\n\n\n\n\nGenerally speaking, a lot of information for these highly condensed papers goes into the supplementary information, and that's the first place to look for more explanation.\n\n\n\n\nMSA depth\n\n\n\n\nFigure S10 legend:\n\n\n\n\n\n\n\nMSA depth is computed by counting the number of non-gap residues for each position in the MSA (using the Neff weighting scheme with a threshold of 80% identity measured on the region that is non-gap in either sequence) and taking the median across residues.\n\n\n\n\n\n\n\nThis is not a standard measure, just to be clear.\n\n\n\n\nMSA clustering\n\n\n\n\nThere is a section \"1.2.7 MSA clustering\" in the paper supplement that describes the clustering procedure at some length.\n\n\n\n\nMSA clustering is a fairly standard thing to do, but there are many possible algorithms for deriving clusters, and a large family of implementations of each algorithm. I suggest looking into the field of phylogenetic inference (https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjZxoz5lreBAxWlOH0KHaU7B-wQFnoECBQQAQ&url=https%3A%2F%2Fplato.stanford.edu%2Fentries%2Fphylogenetic-inference%2F&usg=AOvVaw2kMNvfnjpTGHX50FzWv2Cb&opi=89978449) for other examples."}],"domain":"biology","external_citations":["https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03819-2/MediaObjects/41586_2021_3819_MOESM1_ESM.pdf","https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjZxoz5lreBAxWlOH0KHaU7B-wQFnoECBQQAQ&url=https%3A%2F%2Fplato.stanford.edu%2Fentries%2Fphylogenetic-inference%2F&usg=AOvVaw2kMNvfnjpTGHX50FzWv2Cb&opi=89978449","https://www.nature.com/articles/s41586-021-03819-2"],"ground_truth_type":"metadata_grounded","group_id":"8b08181fb19115c76d059eb9c106d72ebe08f508eb2a01f901e2e5b5ce591be1","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-dba756fe45c923077428f569","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:11.333206+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/3e71d6afdfe444c721dbb1321f43c14066813d2fd740fb255123cf87e737d071_0.json","raw_sha256":"84992ad678a40907dca3af99f849ee653142b680281a54e02542dc7f47d30773","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=9&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Jack","profile_url":"https://biology.stackexchange.com/users/76986/jack","user_type":"registered"},"created_at":"2023-09-18T09:19:43+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"97E2DDD6-FFD0-4055-9C8A-AFC8CFC373DE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/97E2DDD6-FFD0-4055-9C8A-AFC8CFC373DE/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2023-09-19T17:21:11+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"35B72ACD-424F-4D43-8A5A-683BD89E3182","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/35B72ACD-424F-4D43-8A5A-683BD89E3182/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113031","source_record_sha256":"4eb929ea56236ff172bb8dcefb151bafaac450ec13c279683c7194322d3e6e36","source_url":"https://biology.stackexchange.com/questions/113031/msa-cluster-and-msa-depth","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"MSA cluster and MSA depth\nI was reading the AlphaFold paper (https://www.nature.com/articles/s41586-021-03819-2) and had difficulty with a couple of terms introduced in the main text of the paper. I asked ChatGPT what these were but I'm not sure that it's accurate.\n\n\n\n\nI had a hard time finding the definitions of an MSA (multiple sequence alignment) cluster and MSA depth. GPT-4 explains that an MSA cluster is a subset of sequences from an overall MSA that are closely related to each other, which seems to be simply the results from clustering analysis on MSA. GPT-4 also defines the MSA depth as the number of sequences in MSA. However, I want to make sure that these definitions are correct and are not just hallucinations from GPT-4.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113044,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Even with lightening your photo:\n<a href=\"https://i.sstatic.net/HyDIc.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/HyDIc.png\" alt=\"enter image description here\" /></a></p>\n<p>It is difficult to ID this to genus. If you are only interested in knowing whether it is a medically significant spider, you can rest assured that it is not. The (few) markings and shape of it are enough to rule out widows and recluses.</p>\n<p>From its shape and habitus, it is likely a cobweb weaver of some kind (family Theridiidae), but there are many possible choices for genus unless you can get a clearer photo. While black widows are also Theridiidae, the medically-significant female widows have solid black legs while we can see leg banding in this specimen. As @anongoodnurse points out in the comments, the legs here are shorter than a black widow's legs, so I would even rule out a male widow. The abdomen here is rounder shape than the tear-drop abdomen with a tapered end that a widow has. (Similarly, recluses do not have banded legs and do not hang in webs like this Araneoid is. And there are no other medically significant spiders you need to worry about in your geographic area).</p>\n<p>The leg banding, general shape, and the slight white marking on the abdomen we can see in the lightened photo make this a little reminiscent of Enoplognatha marmorata (like this one <a href=\"https://bugguide.net/node/view/646186/bgimage\" rel=\"nofollow noreferrer\">https://bugguide.net/node/view/646186/bgimage</a>). It is very rare to find Enoplognatha indoors.</p>\n<p>Here is an example of an E. marmorata found in Indiana: <a href=\"https://www.inaturalist.org/observations/107343897\" rel=\"nofollow noreferrer\">https://www.inaturalist.org/observations/107343897</a></p>\n","answer_id":113066,"answer_text":"Even with lightening your photo:\n[image: enter image description here; source: https://i.sstatic.net/HyDIc.png] (https://i.sstatic.net/HyDIc.png)\n\n\n\n\nIt is difficult to ID this to genus. If you are only interested in knowing whether it is a medically significant spider, you can rest assured that it is not. The (few) markings and shape of it are enough to rule out widows and recluses.\n\n\n\n\nFrom its shape and habitus, it is likely a cobweb weaver of some kind (family Theridiidae), but there are many possible choices for genus unless you can get a clearer photo. While black widows are also Theridiidae, the medically-significant female widows have solid black legs while we can see leg banding in this specimen. As @anongoodnurse points out in the comments, the legs here are shorter than a black widow's legs, so I would even rule out a male widow. The abdomen here is rounder shape than the tear-drop abdomen with a tapered end that a widow has. (Similarly, recluses do not have banded legs and do not hang in webs like this Araneoid is. And there are no other medically significant spiders you need to worry about in your geographic area).\n\n\n\n\nThe leg banding, general shape, and the slight white marking on the abdomen we can see in the lightened photo make this a little reminiscent of Enoplognatha marmorata (like this one https://bugguide.net/node/view/646186/bgimage (https://bugguide.net/node/view/646186/bgimage)). It is very rare to find Enoplognatha indoors.\n\n\n\n\nHere is an example of an E. marmorata found in Indiana: https://www.inaturalist.org/observations/107343897 (https://www.inaturalist.org/observations/107343897)","answer_url":"https://biology.stackexchange.com/a/113066","author":"JimN","author_url":"https://biology.stackexchange.com/users/61490/jimn","content_license":"CC BY-SA 4.0","created_at":"2023-09-23T11:48:10+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:36.208962+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/ce9de3cf6525f1e283f75a76c7c279c0bd53024cf8e6597abc34f072e18cfbf7_0.json","raw_sha256":"c65c49a81e92972be3758d3b220c036300d85c38ce4d9079a6203d2eeac0d96d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113468;113465;113459;113453;113451;113449;113442;113437;113425;113421;113416;113415;113413;113406;113400;113398;113386;113378;113364;113363;113347;113340;113333;113324;113317;113315;113310;113303;113307;113299;113293;113291;113284;113282;113279;113277;113275;113274;113263;113253;113252;113243;113239;113235;113231;113229;113223;113221;113218;113216;113210;113198;113191;113183;113180;113175;113164;113158;113153;113146;113141;113118;113116;113115;113113;113110;113109;113106;113104;113101;113095;113089;113086;113081;113080;113077;113076;113075;113070;113067;113064;113053;113046;113043;113039;113031;113030;113028;113027;113024;113017;113016;113015;113014;113009;113008;113007;113005;112998;112984/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113064,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"JimN","profile_url":"https://biology.stackexchange.com/users/61490/jimn","user_type":"registered"},"created_at":"2023-09-23T11:48:10+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"D40E1E6B-A577-47E0-87C5-8E092A5E30F8","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D40E1E6B-A577-47E0-87C5-8E092A5E30F8/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"JimN","profile_url":"https://biology.stackexchange.com/users/61490/jimn","user_type":"registered"},"created_at":"2023-09-23T14:30:46+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"76D45C7D-E652-4ED0-8AA6-D9700A54034B","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/76D45C7D-E652-4ED0-8AA6-D9700A54034B/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"JimN","profile_url":"https://biology.stackexchange.com/users/61490/jimn","user_type":"registered"},"created_at":"2023-09-23T18:04:53+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"7B5F6340-4225-4676-8A8B-063918CC665C","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7B5F6340-4225-4676-8A8B-063918CC665C/view-source"}],"score":1},{"answer_html":"<p>The globular abdomen, posture in the web and general shape certainly suggest a Theridiid.  The glossy black body and banded legs are consistent with both the pretty harmless Steatoda species of &quot;False Widows&quot;and their more problematic cousins the Black Widows.  In both cases, the abdominal stripes and leg bands fade to black as the female matures, and while it would be unusual, I bet that having an all-black abdomen and still have traces of the brown banding on the legs is not too uncommon. However, Latrodectus mactans, which I think is the more likely Black Widow species in Indiana, would be expected to still show some of the red spots on the abdomen at this point in its growth. So I'm leaning toward a Steatoda.  Both are noted for strong webs, with the real Widows having a particularly strong silk; the simple ID solution is to check the underside - a real Widow will have the classic red &quot;hourglass&quot; marking, while a Steatoda will not.</p>\n<p>The image below is Steatoda grossa, the bigger of the common &quot;False Widows&quot;.  Steatoda borealis females commonly feature a white midline on the back, but I'm not sure if the photograph shows a real feature or just an artifact of the flash.</p>\n<p><a href=\"https://i.sstatic.net/L9IJE.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/L9IJE.jpg\" alt=\"enter image description here\" /></a></p>\n","answer_id":113802,"answer_text":"The globular abdomen, posture in the web and general shape certainly suggest a Theridiid.  The glossy black body and banded legs are consistent with both the pretty harmless Steatoda species of \"False Widows\"and their more problematic cousins the Black Widows.  In both cases, the abdominal stripes and leg bands fade to black as the female matures, and while it would be unusual, I bet that having an all-black abdomen and still have traces of the brown banding on the legs is not too uncommon. However, Latrodectus mactans, which I think is the more likely Black Widow species in Indiana, would be expected to still show some of the red spots on the abdomen at this point in its growth. So I'm leaning toward a Steatoda.  Both are noted for strong webs, with the real Widows having a particularly strong silk; the simple ID solution is to check the underside - a real Widow will have the classic red \"hourglass\" marking, while a Steatoda will not.\n\n\n\n\nThe image below is Steatoda grossa, the bigger of the common \"False Widows\".  Steatoda borealis females commonly feature a white midline on the back, but I'm not sure if the photograph shows a real feature or just an artifact of the flash.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/L9IJE.jpg] (https://i.sstatic.net/L9IJE.jpg)","answer_url":"https://biology.stackexchange.com/a/113802","author":"John Robinson","author_url":"https://biology.stackexchange.com/users/38079/john-robinson","content_license":"CC BY-SA 4.0","created_at":"2024-01-05T20:43:49+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:37.585395+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/d8f0ba725c7d7cdce167507177cd9e8c354e0409a9f0824b4ba8dffcb28b6eed_0.json","raw_sha256":"7275599cd4dfa07c5d9ad8953eeb29f56ff2d11403ea7cd58a0dd6a1c9b3b64c","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113468;113465;113459;113453;113451;113449;113442;113437;113425;113421;113416;113415;113413;113406;113400;113398;113386;113378;113364;113363;113347;113340;113333;113324;113317;113315;113310;113303;113307;113299;113293;113291;113284;113282;113279;113277;113275;113274;113263;113253;113252;113243;113239;113235;113231;113229;113223;113221;113218;113216;113210;113198;113191;113183;113180;113175;113164;113158;113153;113146;113141;113118;113116;113115;113113;113110;113109;113106;113104;113101;113095;113089;113086;113081;113080;113077;113076;113075;113070;113067;113064;113053;113046;113043;113039;113031;113030;113028;113027;113024;113017;113016;113015;113014;113009;113008;113007;113005;112998;112984/answers?filter=withbody&order=asc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113064,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"John Robinson","profile_url":"https://biology.stackexchange.com/users/38079/john-robinson","user_type":"registered"},"created_at":"2024-01-05T20:43:49+00:00","raw_file":"raw/codex_api_v1/85b5645347f81712378316d7ce101572df9f33b4b1773526e317a302b1f0b138_1790824051913889100_0.json","raw_sha256":"6c01c074c3b6604e944aeb1c481e22bdf0b7c0a7082c18421dfbb8bc6388be2e","revision_guid":"CD260D1F-9AC2-4FCB-B3A5-84A68F59459E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CD260D1F-9AC2-4FCB-B3A5-84A68F59459E/view-source"}],"score":0}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Epiphany","author_url":"https://biology.stackexchange.com/users/77046/epiphany","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Epiphany","profile_url":"https://biology.stackexchange.com/users/77046/epiphany","user_type":"registered"},"created_at":"2023-09-23T04:36:30+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"1A6A2B6F-8790-46CA-9C8F-38586533980C","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/1A6A2B6F-8790-46CA-9C8F-38586533980C/view-source"}],"url":"https://biology.stackexchange.com/questions/113064/what-kind-of-spider-is-this-please-southern-indiana-very-strong-web"},{"author":"JimN","author_url":"https://biology.stackexchange.com/users/61490/jimn","content_license":"CC BY-SA 4.0","context_id":"113066","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"JimN","profile_url":"https://biology.stackexchange.com/users/61490/jimn","user_type":"registered"},"created_at":"2023-09-23T11:48:10+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"D40E1E6B-A577-47E0-87C5-8E092A5E30F8","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D40E1E6B-A577-47E0-87C5-8E092A5E30F8/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"JimN","profile_url":"https://biology.stackexchange.com/users/61490/jimn","user_type":"registered"},"created_at":"2023-09-23T14:30:46+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"76D45C7D-E652-4ED0-8AA6-D9700A54034B","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/76D45C7D-E652-4ED0-8AA6-D9700A54034B/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"JimN","profile_url":"https://biology.stackexchange.com/users/61490/jimn","user_type":"registered"},"created_at":"2023-09-23T18:04:53+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"7B5F6340-4225-4676-8A8B-063918CC665C","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7B5F6340-4225-4676-8A8B-063918CC665C/view-source"}],"url":"https://biology.stackexchange.com/a/113066"},{"author":"John Robinson","author_url":"https://biology.stackexchange.com/users/38079/john-robinson","content_license":"CC BY-SA 4.0","context_id":"113802","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"John Robinson","profile_url":"https://biology.stackexchange.com/users/38079/john-robinson","user_type":"registered"},"created_at":"2024-01-05T20:43:49+00:00","raw_file":"raw/codex_api_v1/85b5645347f81712378316d7ce101572df9f33b4b1773526e317a302b1f0b138_1790824051913889100_0.json","raw_sha256":"6c01c074c3b6604e944aeb1c481e22bdf0b7c0a7082c18421dfbb8bc6388be2e","revision_guid":"CD260D1F-9AC2-4FCB-B3A5-84A68F59459E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CD260D1F-9AC2-4FCB-B3A5-84A68F59459E/view-source"}],"url":"https://biology.stackexchange.com/a/113802"}],"contexts":[{"context_id":"question","html":"<p><a href=\"https://i.sstatic.net/a7OWF.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/a7OWF.jpg\" alt=\"enter image description here\" /></a>\nIt never comes out during the day so it's been hard to get a decent picture. We have been battling over ownership of my mailbox. It's a house box and every morning it's covered in cobweb from it to the siding or across the top of it if the lid was left up. Very strong web, it takes effort to get it off. I was going to put up a new one with a sealed lid but would kind of like to know if it's poisonous before I go messing about the battle grounds.<a href=\"https://i.sstatic.net/IpnyJ.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/IpnyJ.jpg\" alt=\"enter image description here\" /></a></p>\n","text":"[image: enter image description here; source: https://i.sstatic.net/a7OWF.jpg] (https://i.sstatic.net/a7OWF.jpg)\nIt never comes out during the day so it's been hard to get a decent picture. We have been battling over ownership of my mailbox. It's a house box and every morning it's covered in cobweb from it to the siding or across the top of it if the lid was left up. Very strong web, it takes effort to get it off. I was going to put up a new one with a sealed lid but would kind of like to know if it's poisonous before I go messing about the battle grounds.[image: enter image description here; source: https://i.sstatic.net/IpnyJ.jpg] (https://i.sstatic.net/IpnyJ.jpg)"},{"context_id":"113066","html":"<p>Even with lightening your photo:\n<a href=\"https://i.sstatic.net/HyDIc.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/HyDIc.png\" alt=\"enter image description here\" /></a></p>\n<p>It is difficult to ID this to genus. If you are only interested in knowing whether it is a medically significant spider, you can rest assured that it is not. The (few) markings and shape of it are enough to rule out widows and recluses.</p>\n<p>From its shape and habitus, it is likely a cobweb weaver of some kind (family Theridiidae), but there are many possible choices for genus unless you can get a clearer photo. While black widows are also Theridiidae, the medically-significant female widows have solid black legs while we can see leg banding in this specimen. As @anongoodnurse points out in the comments, the legs here are shorter than a black widow's legs, so I would even rule out a male widow. The abdomen here is rounder shape than the tear-drop abdomen with a tapered end that a widow has. (Similarly, recluses do not have banded legs and do not hang in webs like this Araneoid is. And there are no other medically significant spiders you need to worry about in your geographic area).</p>\n<p>The leg banding, general shape, and the slight white marking on the abdomen we can see in the lightened photo make this a little reminiscent of Enoplognatha marmorata (like this one <a href=\"https://bugguide.net/node/view/646186/bgimage\" rel=\"nofollow noreferrer\">https://bugguide.net/node/view/646186/bgimage</a>). It is very rare to find Enoplognatha indoors.</p>\n<p>Here is an example of an E. marmorata found in Indiana: <a href=\"https://www.inaturalist.org/observations/107343897\" rel=\"nofollow noreferrer\">https://www.inaturalist.org/observations/107343897</a></p>\n","text":"Even with lightening your photo:\n[image: enter image description here; source: https://i.sstatic.net/HyDIc.png] (https://i.sstatic.net/HyDIc.png)\n\n\n\n\nIt is difficult to ID this to genus. If you are only interested in knowing whether it is a medically significant spider, you can rest assured that it is not. The (few) markings and shape of it are enough to rule out widows and recluses.\n\n\n\n\nFrom its shape and habitus, it is likely a cobweb weaver of some kind (family Theridiidae), but there are many possible choices for genus unless you can get a clearer photo. While black widows are also Theridiidae, the medically-significant female widows have solid black legs while we can see leg banding in this specimen. As @anongoodnurse points out in the comments, the legs here are shorter than a black widow's legs, so I would even rule out a male widow. The abdomen here is rounder shape than the tear-drop abdomen with a tapered end that a widow has. (Similarly, recluses do not have banded legs and do not hang in webs like this Araneoid is. And there are no other medically significant spiders you need to worry about in your geographic area).\n\n\n\n\nThe leg banding, general shape, and the slight white marking on the abdomen we can see in the lightened photo make this a little reminiscent of Enoplognatha marmorata (like this one https://bugguide.net/node/view/646186/bgimage (https://bugguide.net/node/view/646186/bgimage)). It is very rare to find Enoplognatha indoors.\n\n\n\n\nHere is an example of an E. marmorata found in Indiana: https://www.inaturalist.org/observations/107343897 (https://www.inaturalist.org/observations/107343897)"},{"context_id":"113802","html":"<p>The globular abdomen, posture in the web and general shape certainly suggest a Theridiid.  The glossy black body and banded legs are consistent with both the pretty harmless Steatoda species of &quot;False Widows&quot;and their more problematic cousins the Black Widows.  In both cases, the abdominal stripes and leg bands fade to black as the female matures, and while it would be unusual, I bet that having an all-black abdomen and still have traces of the brown banding on the legs is not too uncommon. However, Latrodectus mactans, which I think is the more likely Black Widow species in Indiana, would be expected to still show some of the red spots on the abdomen at this point in its growth. So I'm leaning toward a Steatoda.  Both are noted for strong webs, with the real Widows having a particularly strong silk; the simple ID solution is to check the underside - a real Widow will have the classic red &quot;hourglass&quot; marking, while a Steatoda will not.</p>\n<p>The image below is Steatoda grossa, the bigger of the common &quot;False Widows&quot;.  Steatoda borealis females commonly feature a white midline on the back, but I'm not sure if the photograph shows a real feature or just an artifact of the flash.</p>\n<p><a href=\"https://i.sstatic.net/L9IJE.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/L9IJE.jpg\" alt=\"enter image description here\" /></a></p>\n","text":"The globular abdomen, posture in the web and general shape certainly suggest a Theridiid.  The glossy black body and banded legs are consistent with both the pretty harmless Steatoda species of \"False Widows\"and their more problematic cousins the Black Widows.  In both cases, the abdominal stripes and leg bands fade to black as the female matures, and while it would be unusual, I bet that having an all-black abdomen and still have traces of the brown banding on the legs is not too uncommon. However, Latrodectus mactans, which I think is the more likely Black Widow species in Indiana, would be expected to still show some of the red spots on the abdomen at this point in its growth. So I'm leaning toward a Steatoda.  Both are noted for strong webs, with the real Widows having a particularly strong silk; the simple ID solution is to check the underside - a real Widow will have the classic red \"hourglass\" marking, while a Steatoda will not.\n\n\n\n\nThe image below is Steatoda grossa, the bigger of the common \"False Widows\".  Steatoda borealis females commonly feature a white midline on the back, but I'm not sure if the photograph shows a real feature or just an artifact of the flash.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/L9IJE.jpg] (https://i.sstatic.net/L9IJE.jpg)"}],"domain":"biology","external_citations":["https://bugguide.net/node/view/646186/bgimage","https://i.sstatic.net/HyDIc.png","https://i.sstatic.net/IpnyJ.jpg","https://i.sstatic.net/L9IJE.jpg","https://i.sstatic.net/a7OWF.jpg","https://www.inaturalist.org/observations/107343897"],"ground_truth_type":"metadata_grounded","group_id":"4583c523c9b7305e33fc77bf6ed3ed4b05ff54b75b807a8c8f9e5d3bc2588cc2","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-aa0811b432d3c5ce93e7fe7b","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:11.333206+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/3e71d6afdfe444c721dbb1321f43c14066813d2fd740fb255123cf87e737d071_0.json","raw_sha256":"84992ad678a40907dca3af99f849ee653142b680281a54e02542dc7f47d30773","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=9&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Epiphany","profile_url":"https://biology.stackexchange.com/users/77046/epiphany","user_type":"registered"},"created_at":"2023-09-23T04:36:30+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"1A6A2B6F-8790-46CA-9C8F-38586533980C","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/1A6A2B6F-8790-46CA-9C8F-38586533980C/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113064","source_record_sha256":"f1852e99e59fb985367a5447fef51cb25fb7b714d2df86a9f025f0d58ae93f04","source_url":"https://biology.stackexchange.com/questions/113064/what-kind-of-spider-is-this-please-southern-indiana-very-strong-web","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What kind of spider is this please? Southern Indiana. Very strong web\n[image: enter image description here; source: https://i.sstatic.net/a7OWF.jpg] (https://i.sstatic.net/a7OWF.jpg)\nIt never comes out during the day so it's been hard to get a decent picture. We have been battling over ownership of my mailbox. It's a house box and every morning it's covered in cobweb from it to the siding or across the top of it if the lid was left up. Very strong web, it takes effort to get it off. I was going to put up a new one with a sealed lid but would kind of like to know if it's poisonous before I go messing about the battle grounds.[image: enter image description here; source: https://i.sstatic.net/IpnyJ.jpg] (https://i.sstatic.net/IpnyJ.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113066,"score":1},{"answer_id":113802,"score":0}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Since kleptoparasitism, that is, stealing food from other entities that have procured that food earlier for themselves, is a widespread strategy in animals, it is no surprise that birds also engage in this kind of behavior (up to 856 accounts of some sort of interspecific thievery). Food stealing skills is even related to parental quality in <em>Sterna dougallii</em>. Honest parents had lower productivity. Additionally, in parrot-owner behavioral problems dynamics, stealing human food got a 2.34 in a 5-point Likert scale where 5 = <em>always</em>.</p>\n<p>On top of that, theoretical ecology tells us that behavioral dynamics are characterized by a cooperation/conflict tension where a behavior such as theft may thrive (while also depending on many other factors, e.g.: larger thieves tended to get the highest payoff, and bear in mind size is but one factor). So I think a bird will maximize stealing if the opportunity is present to it and whether it's physically capable of doing it.</p>\n<p>In <em>Larus argentatus</em>, head turns, approaches, and angular body position were three behavioral markers identified in an ethogram to measure attention to anthropogenic food-based contexts. I think this article is the one that is key to your question, considering how difficult it is to find statistics for how often thievery from anthropogenic sources happens. It is key, because combined with theoretical ecology, and the amount of bird intelligence research nowadays, it shows intuitively that birds will probably steal from human fish traps 1) if they have knowledge about it, and 2) as much as they can.</p>\n<p>Anecdotally, birds, (both known and unknown to me) have also stolen from me several times in varied environments (many of them could be considered &quot;traps&quot; or at least &quot;food containers that require a certain degree of skill to operate or get to&quot;), but not fish traps.</p>\n<hr />\n<p>References</p>\n<p>Anne Tygesen &amp; Björn Forkman (2023) The Parrot–Owner Relationship and Problem Behaviors in Parrots, Anthrozoös, DOI: 10.1080/08927936.2023.2238434</p>\n<p>David A. Shealer, Jeffrey A. Spendelow, Jeff S. Hatfield, Ian C. T. Nisbet, The adaptive significance of stealing in a marine bird and its relationship to parental quality, Behavioral Ecology, Volume 16, Issue 2, Mar./Apr. 2005, Pages 371–376, <a href=\"https://doi.org/10.1093/beheco/ari008\" rel=\"nofollow noreferrer\">https://doi.org/10.1093/beheco/ari008</a></p>\n<p>Feist F, Graham P. An ethogram identifies behavioural markers of attention to humans in European herring gulls (Larus argentatus). Biol Open. 2023 Jun 15;12(6):bio060016. doi: 10.1242/bio.060016. Epub 2023 Jun 13. PMID: 37309817; PMCID: PMC10281265.</p>\n<p>Hadjichrysanthou C, Broom M, Rychtář J. Models of kleptoparasitism on networks: the effect of population structure on food stealing behaviour. J Math Biol. 2018 May;76(6):1465-1488. doi: 10.1007/s00285-017-1177-7. Epub 2017 Sep 18. PMID: 28921258; PMCID: PMC5840298.</p>\n<p>Morand-Ferron J, Sol D. and Lefebvre L (2007) Food stealing in birds: brain or brawn? <em>Animal Behaviour</em>, 74, 6, 1725-1734. <a href=\"https://doi.org/10.1016/j.anbehav.2007.04.031\" rel=\"nofollow noreferrer\">https://doi.org/10.1016/j.anbehav.2007.04.031</a></p>\n<p>Phillips JA, Peacock SJ, Bateman A, Bartlett M, Lewis MA, Krkošek M. An asymmetric producer-scrounger game: body size and the social foraging behavior of coho salmon. Theor Ecol. 2018;11(4):417-431. doi: 10.1007/s12080-018-0375-2. Epub 2018 May 1. PMID: 30931016; PMCID: PMC6405016.</p>\n","answer_id":113136,"answer_text":"Since kleptoparasitism, that is, stealing food from other entities that have procured that food earlier for themselves, is a widespread strategy in animals, it is no surprise that birds also engage in this kind of behavior (up to 856 accounts of some sort of interspecific thievery). Food stealing skills is even related to parental quality in Sterna dougallii. Honest parents had lower productivity. Additionally, in parrot-owner behavioral problems dynamics, stealing human food got a 2.34 in a 5-point Likert scale where 5 = always.\n\n\n\n\nOn top of that, theoretical ecology tells us that behavioral dynamics are characterized by a cooperation/conflict tension where a behavior such as theft may thrive (while also depending on many other factors, e.g.: larger thieves tended to get the highest payoff, and bear in mind size is but one factor). So I think a bird will maximize stealing if the opportunity is present to it and whether it's physically capable of doing it.\n\n\n\n\nIn Larus argentatus, head turns, approaches, and angular body position were three behavioral markers identified in an ethogram to measure attention to anthropogenic food-based contexts. I think this article is the one that is key to your question, considering how difficult it is to find statistics for how often thievery from anthropogenic sources happens. It is key, because combined with theoretical ecology, and the amount of bird intelligence research nowadays, it shows intuitively that birds will probably steal from human fish traps 1) if they have knowledge about it, and 2) as much as they can.\n\n\n\n\nAnecdotally, birds, (both known and unknown to me) have also stolen from me several times in varied environments (many of them could be considered \"traps\" or at least \"food containers that require a certain degree of skill to operate or get to\"), but not fish traps.\n\n\n\n\n\n\n\nReferences\n\n\n\n\nAnne Tygesen & Björn Forkman (2023) The Parrot–Owner Relationship and Problem Behaviors in Parrots, Anthrozoös, DOI: 10.1080/08927936.2023.2238434\n\n\n\n\nDavid A. Shealer, Jeffrey A. Spendelow, Jeff S. Hatfield, Ian C. T. Nisbet, The adaptive significance of stealing in a marine bird and its relationship to parental quality, Behavioral Ecology, Volume 16, Issue 2, Mar./Apr. 2005, Pages 371–376, https://doi.org/10.1093/beheco/ari008 (https://doi.org/10.1093/beheco/ari008)\n\n\n\n\nFeist F, Graham P. An ethogram identifies behavioural markers of attention to humans in European herring gulls (Larus argentatus). Biol Open. 2023 Jun 15;12(6):bio060016. doi: 10.1242/bio.060016. Epub 2023 Jun 13. PMID: 37309817; PMCID: PMC10281265.\n\n\n\n\nHadjichrysanthou C, Broom M, Rychtář J. Models of kleptoparasitism on networks: the effect of population structure on food stealing behaviour. J Math Biol. 2018 May;76(6):1465-1488. doi: 10.1007/s00285-017-1177-7. Epub 2017 Sep 18. PMID: 28921258; PMCID: PMC5840298.\n\n\n\n\nMorand-Ferron J, Sol D. and Lefebvre L (2007) Food stealing in birds: brain or brawn? Animal Behaviour, 74, 6, 1725-1734. https://doi.org/10.1016/j.anbehav.2007.04.031 (https://doi.org/10.1016/j.anbehav.2007.04.031)\n\n\n\n\nPhillips JA, Peacock SJ, Bateman A, Bartlett M, Lewis MA, Krkošek M. An asymmetric producer-scrounger game: body size and the social foraging behavior of coho salmon. Theor Ecol. 2018;11(4):417-431. doi: 10.1007/s12080-018-0375-2. Epub 2018 May 1. PMID: 30931016; PMCID: PMC6405016.","answer_url":"https://biology.stackexchange.com/a/113136","author":"zzzp","author_url":"https://biology.stackexchange.com/users/52933/zzzp","content_license":"CC BY-SA 4.0","created_at":"2023-10-01T11:44:27+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:36.208962+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/ce9de3cf6525f1e283f75a76c7c279c0bd53024cf8e6597abc34f072e18cfbf7_0.json","raw_sha256":"c65c49a81e92972be3758d3b220c036300d85c38ce4d9079a6203d2eeac0d96d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113468;113465;113459;113453;113451;113449;113442;113437;113425;113421;113416;113415;113413;113406;113400;113398;113386;113378;113364;113363;113347;113340;113333;113324;113317;113315;113310;113303;113307;113299;113293;113291;113284;113282;113279;113277;113275;113274;113263;113253;113252;113243;113239;113235;113231;113229;113223;113221;113218;113216;113210;113198;113191;113183;113180;113175;113164;113158;113153;113146;113141;113118;113116;113115;113113;113110;113109;113106;113104;113101;113095;113089;113086;113081;113080;113077;113076;113075;113070;113067;113064;113053;113046;113043;113039;113031;113030;113028;113027;113024;113017;113016;113015;113014;113009;113008;113007;113005;112998;112984/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113080,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"zzzp","profile_url":"https://biology.stackexchange.com/users/52933/zzzp","user_type":"registered"},"created_at":"2023-10-01T11:44:27+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"FDC1B0EE-2C42-4275-90C1-EE108ABBFB03","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FDC1B0EE-2C42-4275-90C1-EE108ABBFB03/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"JuhaniH","author_url":"https://biology.stackexchange.com/users/77070/juhanih","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"JuhaniH","profile_url":"https://biology.stackexchange.com/users/77070/juhanih","user_type":"registered"},"created_at":"2023-09-25T12:50:12+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"55C26FE7-4C9C-4BCC-A9F3-FEF8AD48D723","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/55C26FE7-4C9C-4BCC-A9F3-FEF8AD48D723/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"zzzp","profile_url":"https://biology.stackexchange.com/users/52933/zzzp","user_type":"registered"},"created_at":"2023-09-25T18:15:00+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"038327C1-00C8-4E7D-A85E-7185CC9CF780","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/038327C1-00C8-4E7D-A85E-7185CC9CF780/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2023-10-31T12:07:56+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"A153C73E-9A21-443D-97FC-D504C85BF29F","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/A153C73E-9A21-443D-97FC-D504C85BF29F/view-source"}],"url":"https://biology.stackexchange.com/questions/113080/how-often-do-birds-steal-from-fish-traps"},{"author":"zzzp","author_url":"https://biology.stackexchange.com/users/52933/zzzp","content_license":"CC BY-SA 4.0","context_id":"113136","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"zzzp","profile_url":"https://biology.stackexchange.com/users/52933/zzzp","user_type":"registered"},"created_at":"2023-10-01T11:44:27+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"FDC1B0EE-2C42-4275-90C1-EE108ABBFB03","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FDC1B0EE-2C42-4275-90C1-EE108ABBFB03/view-source"}],"url":"https://biology.stackexchange.com/a/113136"}],"contexts":[{"context_id":"question","html":"<p>Does anyone have any solid information about how often birds (e.g. cormorants, mergansers, gulls etc) steal fish from any sort of fish trap? Fish traps include, but are not limited to, fyke nets, pound nets, gill nets etc. I'm not looking for info on birds getting caught in the traps, rather any cases where the birds actually take the fish in the trap.</p>\n<p>Ideally I'm looking for published articles, but grey literature or any reports are useful.</p>\n<p>If you can think of anything more or less suitable, please let me know.</p>\n","text":"Does anyone have any solid information about how often birds (e.g. cormorants, mergansers, gulls etc) steal fish from any sort of fish trap? Fish traps include, but are not limited to, fyke nets, pound nets, gill nets etc. I'm not looking for info on birds getting caught in the traps, rather any cases where the birds actually take the fish in the trap.\n\n\n\n\nIdeally I'm looking for published articles, but grey literature or any reports are useful.\n\n\n\n\nIf you can think of anything more or less suitable, please let me know."},{"context_id":"113136","html":"<p>Since kleptoparasitism, that is, stealing food from other entities that have procured that food earlier for themselves, is a widespread strategy in animals, it is no surprise that birds also engage in this kind of behavior (up to 856 accounts of some sort of interspecific thievery). Food stealing skills is even related to parental quality in <em>Sterna dougallii</em>. Honest parents had lower productivity. Additionally, in parrot-owner behavioral problems dynamics, stealing human food got a 2.34 in a 5-point Likert scale where 5 = <em>always</em>.</p>\n<p>On top of that, theoretical ecology tells us that behavioral dynamics are characterized by a cooperation/conflict tension where a behavior such as theft may thrive (while also depending on many other factors, e.g.: larger thieves tended to get the highest payoff, and bear in mind size is but one factor). So I think a bird will maximize stealing if the opportunity is present to it and whether it's physically capable of doing it.</p>\n<p>In <em>Larus argentatus</em>, head turns, approaches, and angular body position were three behavioral markers identified in an ethogram to measure attention to anthropogenic food-based contexts. I think this article is the one that is key to your question, considering how difficult it is to find statistics for how often thievery from anthropogenic sources happens. It is key, because combined with theoretical ecology, and the amount of bird intelligence research nowadays, it shows intuitively that birds will probably steal from human fish traps 1) if they have knowledge about it, and 2) as much as they can.</p>\n<p>Anecdotally, birds, (both known and unknown to me) have also stolen from me several times in varied environments (many of them could be considered &quot;traps&quot; or at least &quot;food containers that require a certain degree of skill to operate or get to&quot;), but not fish traps.</p>\n<hr />\n<p>References</p>\n<p>Anne Tygesen &amp; Björn Forkman (2023) The Parrot–Owner Relationship and Problem Behaviors in Parrots, Anthrozoös, DOI: 10.1080/08927936.2023.2238434</p>\n<p>David A. Shealer, Jeffrey A. Spendelow, Jeff S. Hatfield, Ian C. T. Nisbet, The adaptive significance of stealing in a marine bird and its relationship to parental quality, Behavioral Ecology, Volume 16, Issue 2, Mar./Apr. 2005, Pages 371–376, <a href=\"https://doi.org/10.1093/beheco/ari008\" rel=\"nofollow noreferrer\">https://doi.org/10.1093/beheco/ari008</a></p>\n<p>Feist F, Graham P. An ethogram identifies behavioural markers of attention to humans in European herring gulls (Larus argentatus). Biol Open. 2023 Jun 15;12(6):bio060016. doi: 10.1242/bio.060016. Epub 2023 Jun 13. PMID: 37309817; PMCID: PMC10281265.</p>\n<p>Hadjichrysanthou C, Broom M, Rychtář J. Models of kleptoparasitism on networks: the effect of population structure on food stealing behaviour. J Math Biol. 2018 May;76(6):1465-1488. doi: 10.1007/s00285-017-1177-7. Epub 2017 Sep 18. PMID: 28921258; PMCID: PMC5840298.</p>\n<p>Morand-Ferron J, Sol D. and Lefebvre L (2007) Food stealing in birds: brain or brawn? <em>Animal Behaviour</em>, 74, 6, 1725-1734. <a href=\"https://doi.org/10.1016/j.anbehav.2007.04.031\" rel=\"nofollow noreferrer\">https://doi.org/10.1016/j.anbehav.2007.04.031</a></p>\n<p>Phillips JA, Peacock SJ, Bateman A, Bartlett M, Lewis MA, Krkošek M. An asymmetric producer-scrounger game: body size and the social foraging behavior of coho salmon. Theor Ecol. 2018;11(4):417-431. doi: 10.1007/s12080-018-0375-2. Epub 2018 May 1. PMID: 30931016; PMCID: PMC6405016.</p>\n","text":"Since kleptoparasitism, that is, stealing food from other entities that have procured that food earlier for themselves, is a widespread strategy in animals, it is no surprise that birds also engage in this kind of behavior (up to 856 accounts of some sort of interspecific thievery). Food stealing skills is even related to parental quality in Sterna dougallii. Honest parents had lower productivity. Additionally, in parrot-owner behavioral problems dynamics, stealing human food got a 2.34 in a 5-point Likert scale where 5 = always.\n\n\n\n\nOn top of that, theoretical ecology tells us that behavioral dynamics are characterized by a cooperation/conflict tension where a behavior such as theft may thrive (while also depending on many other factors, e.g.: larger thieves tended to get the highest payoff, and bear in mind size is but one factor). So I think a bird will maximize stealing if the opportunity is present to it and whether it's physically capable of doing it.\n\n\n\n\nIn Larus argentatus, head turns, approaches, and angular body position were three behavioral markers identified in an ethogram to measure attention to anthropogenic food-based contexts. I think this article is the one that is key to your question, considering how difficult it is to find statistics for how often thievery from anthropogenic sources happens. It is key, because combined with theoretical ecology, and the amount of bird intelligence research nowadays, it shows intuitively that birds will probably steal from human fish traps 1) if they have knowledge about it, and 2) as much as they can.\n\n\n\n\nAnecdotally, birds, (both known and unknown to me) have also stolen from me several times in varied environments (many of them could be considered \"traps\" or at least \"food containers that require a certain degree of skill to operate or get to\"), but not fish traps.\n\n\n\n\n\n\n\nReferences\n\n\n\n\nAnne Tygesen & Björn Forkman (2023) The Parrot–Owner Relationship and Problem Behaviors in Parrots, Anthrozoös, DOI: 10.1080/08927936.2023.2238434\n\n\n\n\nDavid A. Shealer, Jeffrey A. Spendelow, Jeff S. Hatfield, Ian C. T. Nisbet, The adaptive significance of stealing in a marine bird and its relationship to parental quality, Behavioral Ecology, Volume 16, Issue 2, Mar./Apr. 2005, Pages 371–376, https://doi.org/10.1093/beheco/ari008 (https://doi.org/10.1093/beheco/ari008)\n\n\n\n\nFeist F, Graham P. An ethogram identifies behavioural markers of attention to humans in European herring gulls (Larus argentatus). Biol Open. 2023 Jun 15;12(6):bio060016. doi: 10.1242/bio.060016. Epub 2023 Jun 13. PMID: 37309817; PMCID: PMC10281265.\n\n\n\n\nHadjichrysanthou C, Broom M, Rychtář J. Models of kleptoparasitism on networks: the effect of population structure on food stealing behaviour. J Math Biol. 2018 May;76(6):1465-1488. doi: 10.1007/s00285-017-1177-7. Epub 2017 Sep 18. PMID: 28921258; PMCID: PMC5840298.\n\n\n\n\nMorand-Ferron J, Sol D. and Lefebvre L (2007) Food stealing in birds: brain or brawn? Animal Behaviour, 74, 6, 1725-1734. https://doi.org/10.1016/j.anbehav.2007.04.031 (https://doi.org/10.1016/j.anbehav.2007.04.031)\n\n\n\n\nPhillips JA, Peacock SJ, Bateman A, Bartlett M, Lewis MA, Krkošek M. An asymmetric producer-scrounger game: body size and the social foraging behavior of coho salmon. Theor Ecol. 2018;11(4):417-431. doi: 10.1007/s12080-018-0375-2. Epub 2018 May 1. PMID: 30931016; PMCID: PMC6405016."}],"domain":"biology","external_citations":["https://doi.org/10.1016/j.anbehav.2007.04.031","https://doi.org/10.1093/beheco/ari008"],"ground_truth_type":"metadata_grounded","group_id":"b67bf0c8c995074db6528d403b0bc059880f6d557b415ad0be4fa502b6368caa","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-44ab72a120e5e6d7acbd872a","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:11.333206+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/3e71d6afdfe444c721dbb1321f43c14066813d2fd740fb255123cf87e737d071_0.json","raw_sha256":"84992ad678a40907dca3af99f849ee653142b680281a54e02542dc7f47d30773","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=9&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"JuhaniH","profile_url":"https://biology.stackexchange.com/users/77070/juhanih","user_type":"registered"},"created_at":"2023-09-25T12:50:12+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"55C26FE7-4C9C-4BCC-A9F3-FEF8AD48D723","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/55C26FE7-4C9C-4BCC-A9F3-FEF8AD48D723/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"zzzp","profile_url":"https://biology.stackexchange.com/users/52933/zzzp","user_type":"registered"},"created_at":"2023-09-25T18:15:00+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"038327C1-00C8-4E7D-A85E-7185CC9CF780","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/038327C1-00C8-4E7D-A85E-7185CC9CF780/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2023-10-31T12:07:56+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"A153C73E-9A21-443D-97FC-D504C85BF29F","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/A153C73E-9A21-443D-97FC-D504C85BF29F/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113080","source_record_sha256":"c87a9bd1f65ea2b2439309f8ebfad4ffa6e2d2d6fece189d0692da0c019bd180","source_url":"https://biology.stackexchange.com/questions/113080/how-often-do-birds-steal-from-fish-traps","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How often do birds steal from fish traps?\nDoes anyone have any solid information about how often birds (e.g. cormorants, mergansers, gulls etc) steal fish from any sort of fish trap? Fish traps include, but are not limited to, fyke nets, pound nets, gill nets etc. I'm not looking for info on birds getting caught in the traps, rather any cases where the birds actually take the fish in the trap.\n\n\n\n\nIdeally I'm looking for published articles, but grey literature or any reports are useful.\n\n\n\n\nIf you can think of anything more or less suitable, please let me know.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113136,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>All the plexus system in our body is just like electrical wiring. In case if fibres from different spinal segments are coming together to form a single nerve they donot get mixed up . In their further course they may get separate. Though there may be fibres other than of c5 and c6 in posterior cord the fibres that forms the axillary nerve is c5 and c6 fibres. There are other examples of these kind of seperation where though fibers come together and looks like a single nerve but in their further course they are seperated . One of the example is superior root of ansa cervicalis.🙂</p>\n","answer_id":115148,"answer_text":"All the plexus system in our body is just like electrical wiring. In case if fibres from different spinal segments are coming together to form a single nerve they donot get mixed up . In their further course they may get separate. Though there may be fibres other than of c5 and c6 in posterior cord the fibres that forms the axillary nerve is c5 and c6 fibres. There are other examples of these kind of seperation where though fibers come together and looks like a single nerve but in their further course they are seperated . One of the example is superior root of ansa cervicalis.🙂","answer_url":"https://biology.stackexchange.com/a/115148","author":"Sabyasachi Pramanik","author_url":"https://biology.stackexchange.com/users/84994/sabyasachi-pramanik","content_license":"CC BY-SA 4.0","created_at":"2024-08-09T10:16:47+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:37.585395+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/d8f0ba725c7d7cdce167507177cd9e8c354e0409a9f0824b4ba8dffcb28b6eed_0.json","raw_sha256":"7275599cd4dfa07c5d9ad8953eeb29f56ff2d11403ea7cd58a0dd6a1c9b3b64c","source_api":"Stack Exchange API 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so shouldn't the root value be all the spinal nerves of the brachial plexus which is the case for radial nerve?</p>\n","text":"Posterior cord is formed by the posterior division of all the three trunks, so shouldn't the root value be all the spinal nerves of the brachial plexus which is the case for radial nerve?"},{"context_id":"115148","html":"<p>All the plexus system in our body is just like electrical wiring. In case if fibres from different spinal segments are coming together to form a single nerve they donot get mixed up . In their further course they may get separate. Though there may be fibres other than of c5 and c6 in posterior cord the fibres that forms the axillary nerve is c5 and c6 fibres. There are other examples of these kind of seperation where though fibers come together and looks like a single nerve but in their further course they are seperated . One of the example is superior root of ansa cervicalis.🙂</p>\n","text":"All the plexus system in our body is just like electrical wiring. In case if fibres from different spinal segments are coming together to form a single nerve they donot get mixed up . In their further course they may get separate. Though there may be fibres other than of c5 and c6 in posterior cord the fibres that forms the axillary nerve is c5 and c6 fibres. There are other examples of these kind of seperation where though fibers come together and looks like a single nerve but in their further course they are seperated . One of the example is superior root of ansa cervicalis.🙂"}],"domain":"biology","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"d9491a1cd1ba315e856355b81a078a932c777292cc733a200e0ec46f30bcd56b","hard_case_family":["no_accepted_answer"],"id":"RHM-7bd2fda46cac0a5fe0e96832","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:11.333206+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/3e71d6afdfe444c721dbb1321f43c14066813d2fd740fb255123cf87e737d071_0.json","raw_sha256":"84992ad678a40907dca3af99f849ee653142b680281a54e02542dc7f47d30773","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=9&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical 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I know that with pre-labelled plates and disposable loops, I can sub ~100 plates in about an hour.</p>\n<p>For longer term storage of species, it is best to keep a <a href=\"https://www.addgene.org/protocols/create-glycerol-stock/\" rel=\"nofollow noreferrer\">glycerol stock</a>. These are stored at -80 C (ultracold freezer) and can be used indefinitely. If you wanted to work from glycerol stock (to be sure of getting the right species), add maybe another 5 min to look up location in the freezer and get them out for streaking. There is no need to thaw a glycerol stock (in fact it is detrimental to thaw them) - just use a cooled flamed loop, or a clean disposable loop to scrape a tiny amount of the stock from the top of the tube and streak this out.</p>\n","answer_id":113289,"answer_text":"Aside from MikeyC's commented suggestion, which I think is a good idea and they should write it up as an answer.\n\n\n\n\nIn my experience, most species of bacteria you might use as controls for Gram staining will easily last 2-4 weeks in the fridge on a plate and still be usable as controls.  These will be genera like Staphylococcus and Escherichia, well known, readily available and well characterized.\n\n\n\n\nFor fairly minimal effort, one can simply take a plate of the organism wanted and re-streak/sub-culture once a week or once every two weeks. The streaking itself should only take you a minute or two, adding in time for labelling of plates and general fluffing around in the lab (opening incubator, placing plate in incubator etc.), maybe a maximum of 5-10 min per plate. I know that with pre-labelled plates and disposable loops, I can sub ~100 plates in about an hour.\n\n\n\n\nFor longer term storage of species, it is best to keep a glycerol stock (https://www.addgene.org/protocols/create-glycerol-stock/). These are stored at -80 C (ultracold freezer) and can be used indefinitely. If you wanted to work from glycerol stock (to be sure of getting the right species), add maybe another 5 min to look up location in the freezer and get them out for streaking. There is no need to thaw a glycerol stock (in fact it is detrimental to thaw them) - just use a cooled flamed loop, or a clean disposable loop to scrape a tiny amount of the stock from the top of the tube and streak this out.","answer_url":"https://biology.stackexchange.com/a/113289","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2023-10-22T03:52:58+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:36.208962+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/ce9de3cf6525f1e283f75a76c7c279c0bd53024cf8e6597abc34f072e18cfbf7_0.json","raw_sha256":"c65c49a81e92972be3758d3b220c036300d85c38ce4d9079a6203d2eeac0d96d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113468;113465;113459;113453;113451;113449;113442;113437;113425;113421;113416;113415;113413;113406;113400;113398;113386;113378;113364;113363;113347;113340;113333;113324;113317;113315;113310;113303;113307;113299;113293;113291;113284;113282;113279;113277;113275;113274;113263;113253;113252;113243;113239;113235;113231;113229;113223;113221;113218;113216;113210;113198;113191;113183;113180;113175;113164;113158;113153;113146;113141;113118;113116;113115;113113;113110;113109;113106;113104;113101;113095;113089;113086;113081;113080;113077;113076;113075;113070;113067;113064;113053;113046;113043;113039;113031;113030;113028;113027;113024;113017;113016;113015;113014;113009;113008;113007;113005;112998;112984/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113279,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2023-10-22T03:52:58+00:00","raw_file":"raw/codex_api_v1/05c310a2e43a25cef557efc8abb78d08e3282613971fb1f949f4d401e11807fa_1790824041474830100_0.json","raw_sha256":"06275f053755243837bd950c2a032e528759a141759c26078d708e55d401af9b","revision_guid":"2A50B353-4221-4415-9CF9-F570A015D99B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2A50B353-4221-4415-9CF9-F570A015D99B/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Freezing Soul","author_url":"https://biology.stackexchange.com/users/71062/freezing-soul","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Freezing Soul","profile_url":"https://biology.stackexchange.com/users/71062/freezing-soul","user_type":"registered"},"created_at":"2023-10-20T20:00:34+00:00","raw_file":"raw/codex_api_v1/05c310a2e43a25cef557efc8abb78d08e3282613971fb1f949f4d401e11807fa_1790824041474830100_0.json","raw_sha256":"06275f053755243837bd950c2a032e528759a141759c26078d708e55d401af9b","revision_guid":"D6FA7212-DDC6-4B74-A3D6-2FAC696AAEE9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D6FA7212-DDC6-4B74-A3D6-2FAC696AAEE9/view-source"}],"url":"https://biology.stackexchange.com/questions/113279/how-do-i-create-sustainable-readily-available-stock-cultures-to-act-as-gram-stai"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"113289","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2023-10-22T03:52:58+00:00","raw_file":"raw/codex_api_v1/05c310a2e43a25cef557efc8abb78d08e3282613971fb1f949f4d401e11807fa_1790824041474830100_0.json","raw_sha256":"06275f053755243837bd950c2a032e528759a141759c26078d708e55d401af9b","revision_guid":"2A50B353-4221-4415-9CF9-F570A015D99B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2A50B353-4221-4415-9CF9-F570A015D99B/view-source"}],"url":"https://biology.stackexchange.com/a/113289"}],"contexts":[{"context_id":"question","html":"<h2>My investigation on the matter</h2>\n<p><strong>Ref #1</strong></p>\n<blockquote>\n<p>Staining known Gram-positive and Gram-negative organisms on either\nside of your unknown organism act as positive controls for your\ntechnique.</p>\n<p><em>(Microbiology Laboratory Theory and Application (Michael J. Leboffe, Burton E. Pierce)</em></p>\n</blockquote>\n<p><strong>Ref #2</strong></p>\n<blockquote>\n<p>Similarly, cultures should undergo evaluation while they are still\nfresh. Old cultures tend\nto lose the peptidoglycan cell walls, which predisposes gram-positive\ncells to be gram-negative or gram variable.</p>\n<p><em>(Tripathi N, Sapra A. Gram\nStaining. 2023 Aug 14. In: StatPearls [Internet]. Treasure Island\n(FL): StatPearls Publishing; 2023 Jan–. PMID: 32965827.)</em></p>\n</blockquote>\n<p><strong>Ref #3</strong></p>\n<blockquote>\n<p>Refrigeration impedes further growth of the bacteria, so you will have\n&quot;fresh&quot; cultures to work with during the next laboratory session.</p>\n<p><em>(Laboratory Exercises in Microbiology By Robert A. Pollack, Lorraine Findlay, Walter Mondschein, R. Ronald Modesto)</em></p>\n</blockquote>\n<p><strong>Ref #4</strong></p>\n<blockquote>\n<p>Remember the following points concerning your [refrigerated or frozen] slant or agar stab stock\ncultures:\n-Do not use stored stock culture for making slides or routine inoculations.</p>\n<p><em>(Laboratory Practices in Microbiology By Osman Erkmen)</em></p>\n</blockquote>\n<h2><strong>Question</strong></h2>\n<p>How do I create a sustainable readily available pair of stock cultures to act as Gram stain controls (as Ref #1), in the least time-consuming and tedious way?</p>\n<p>From Ref #2 and #3, I can prepare two slant cultures, one is of a Gram-positive bacteria and the other is of a Gram-negative bacteria, then store them in the refrigerator or freezer. Then I can retrieve them daily and use them. After that, they are returned to storage.</p>\n<p>However, Ref #4 argues against using refrigerated/frozen cultures for making slides.</p>\n","text":"My investigation on the matter\n\n\n\n\nRef #1\n\n\n\n\n\n\n\nStaining known Gram-positive and Gram-negative organisms on either\nside of your unknown organism act as positive controls for your\ntechnique.\n\n\n\n\n(Microbiology Laboratory Theory and Application (Michael J. Leboffe, Burton E. Pierce)\n\n\n\n\n\n\n\nRef #2\n\n\n\n\n\n\n\nSimilarly, cultures should undergo evaluation while they are still\nfresh. Old cultures tend\nto lose the peptidoglycan cell walls, which predisposes gram-positive\ncells to be gram-negative or gram variable.\n\n\n\n\n(Tripathi N, Sapra A. Gram\nStaining. 2023 Aug 14. In: StatPearls [Internet]. Treasure Island\n(FL): StatPearls Publishing; 2023 Jan–. PMID: 32965827.)\n\n\n\n\n\n\n\nRef #3\n\n\n\n\n\n\n\nRefrigeration impedes further growth of the bacteria, so you will have\n\"fresh\" cultures to work with during the next laboratory session.\n\n\n\n\n(Laboratory Exercises in Microbiology By Robert A. Pollack, Lorraine Findlay, Walter Mondschein, R. Ronald Modesto)\n\n\n\n\n\n\n\nRef #4\n\n\n\n\n\n\n\nRemember the following points concerning your [refrigerated or frozen] slant or agar stab stock\ncultures:\n-Do not use stored stock culture for making slides or routine inoculations.\n\n\n\n\n(Laboratory Practices in Microbiology By Osman Erkmen)\n\n\n\n\n\n\n\nQuestion\n\n\n\n\nHow do I create a sustainable readily available pair of stock cultures to act as Gram stain controls (as Ref #1), in the least time-consuming and tedious way?\n\n\n\n\nFrom Ref #2 and #3, I can prepare two slant cultures, one is of a Gram-positive bacteria and the other is of a Gram-negative bacteria, then store them in the refrigerator or freezer. Then I can retrieve them daily and use them. After that, they are returned to storage.\n\n\n\n\nHowever, Ref #4 argues against using refrigerated/frozen cultures for making slides."},{"context_id":"113289","html":"<p>Aside from MikeyC's commented suggestion, which I think is a good idea and they should write it up as an answer.</p>\n<p>In my experience, most species of bacteria you might use as controls for Gram staining will easily last 2-4 weeks in the fridge on a plate and still be usable as controls.  These will be genera like <em>Staphylococcus</em> and <em>Escherichia</em>, well known, readily available and well characterized.</p>\n<p>For fairly minimal effort, one can simply take a plate of the organism wanted and re-streak/sub-culture once a week or once every two weeks. The streaking itself should only take you a minute or two, adding in time for labelling of plates and general fluffing around in the lab (opening incubator, placing plate in incubator etc.), maybe a maximum of 5-10 min per plate. I know that with pre-labelled plates and disposable loops, I can sub ~100 plates in about an hour.</p>\n<p>For longer term storage of species, it is best to keep a <a href=\"https://www.addgene.org/protocols/create-glycerol-stock/\" rel=\"nofollow noreferrer\">glycerol stock</a>. These are stored at -80 C (ultracold freezer) and can be used indefinitely. If you wanted to work from glycerol stock (to be sure of getting the right species), add maybe another 5 min to look up location in the freezer and get them out for streaking. There is no need to thaw a glycerol stock (in fact it is detrimental to thaw them) - just use a cooled flamed loop, or a clean disposable loop to scrape a tiny amount of the stock from the top of the tube and streak this out.</p>\n","text":"Aside from MikeyC's commented suggestion, which I think is a good idea and they should write it up as an answer.\n\n\n\n\nIn my experience, most species of bacteria you might use as controls for Gram staining will easily last 2-4 weeks in the fridge on a plate and still be usable as controls.  These will be genera like Staphylococcus and Escherichia, well known, readily available and well characterized.\n\n\n\n\nFor fairly minimal effort, one can simply take a plate of the organism wanted and re-streak/sub-culture once a week or once every two weeks. The streaking itself should only take you a minute or two, adding in time for labelling of plates and general fluffing around in the lab (opening incubator, placing plate in incubator etc.), maybe a maximum of 5-10 min per plate. I know that with pre-labelled plates and disposable loops, I can sub ~100 plates in about an hour.\n\n\n\n\nFor longer term storage of species, it is best to keep a glycerol stock (https://www.addgene.org/protocols/create-glycerol-stock/). These are stored at -80 C (ultracold freezer) and can be used indefinitely. If you wanted to work from glycerol stock (to be sure of getting the right species), add maybe another 5 min to look up location in the freezer and get them out for streaking. There is no need to thaw a glycerol stock (in fact it is detrimental to thaw them) - just use a cooled flamed loop, or a clean disposable loop to scrape a tiny amount of the stock from the top of the tube and streak this out."}],"domain":"biology","external_citations":["https://www.addgene.org/protocols/create-glycerol-stock/"],"ground_truth_type":"metadata_grounded","group_id":"02fa3f7deae1a5552e5f6c631af743eb64af476fb129675a7011ed13a53177b3","hard_case_family":["no_accepted_answer"],"id":"RHM-b6677254897fda69f60b3785","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:11.333206+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/3e71d6afdfe444c721dbb1321f43c14066813d2fd740fb255123cf87e737d071_0.json","raw_sha256":"84992ad678a40907dca3af99f849ee653142b680281a54e02542dc7f47d30773","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=9&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Freezing Soul","profile_url":"https://biology.stackexchange.com/users/71062/freezing-soul","user_type":"registered"},"created_at":"2023-10-20T20:00:34+00:00","raw_file":"raw/codex_api_v1/05c310a2e43a25cef557efc8abb78d08e3282613971fb1f949f4d401e11807fa_1790824041474830100_0.json","raw_sha256":"06275f053755243837bd950c2a032e528759a141759c26078d708e55d401af9b","revision_guid":"D6FA7212-DDC6-4B74-A3D6-2FAC696AAEE9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D6FA7212-DDC6-4B74-A3D6-2FAC696AAEE9/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113279","source_record_sha256":"10e3ca66d3b18e3f14b9e2fe17a650bf70aec18ea270f48a4c8b1f3d086de971","source_url":"https://biology.stackexchange.com/questions/113279/how-do-i-create-sustainable-readily-available-stock-cultures-to-act-as-gram-stai","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How do i create sustainable readily available stock cultures to act as Gram stain controls?\nMy investigation on the matter\n\n\n\n\nRef #1\n\n\n\n\n\n\n\nStaining known Gram-positive and Gram-negative organisms on either\nside of your unknown organism act as positive controls for your\ntechnique.\n\n\n\n\n(Microbiology Laboratory Theory and Application (Michael J. Leboffe, Burton E. Pierce)\n\n\n\n\n\n\n\nRef #2\n\n\n\n\n\n\n\nSimilarly, cultures should undergo evaluation while they are still\nfresh. Old cultures tend\nto lose the peptidoglycan cell walls, which predisposes gram-positive\ncells to be gram-negative or gram variable.\n\n\n\n\n(Tripathi N, Sapra A. Gram\nStaining. 2023 Aug 14. In: StatPearls [Internet]. Treasure Island\n(FL): StatPearls Publishing; 2023 Jan–. PMID: 32965827.)\n\n\n\n\n\n\n\nRef #3\n\n\n\n\n\n\n\nRefrigeration impedes further growth of the bacteria, so you will have\n\"fresh\" cultures to work with during the next laboratory session.\n\n\n\n\n(Laboratory Exercises in Microbiology By Robert A. Pollack, Lorraine Findlay, Walter Mondschein, R. Ronald Modesto)\n\n\n\n\n\n\n\nRef #4\n\n\n\n\n\n\n\nRemember the following points concerning your [refrigerated or frozen] slant or agar stab stock\ncultures:\n-Do not use stored stock culture for making slides or routine inoculations.\n\n\n\n\n(Laboratory Practices in Microbiology By Osman Erkmen)\n\n\n\n\n\n\n\nQuestion\n\n\n\n\nHow do I create a sustainable readily available pair of stock cultures to act as Gram stain controls (as Ref #1), in the least time-consuming and tedious way?\n\n\n\n\nFrom Ref #2 and #3, I can prepare two slant cultures, one is of a Gram-positive bacteria and the other is of a Gram-negative bacteria, then store them in the refrigerator or freezer. Then I can retrieve them daily and use them. After that, they are returned to storage.\n\n\n\n\nHowever, Ref #4 argues against using refrigerated/frozen cultures for making slides.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113289,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<blockquote>\n<p>Can we say that the DNA is coded binary with two options: AT and GC?</p>\n</blockquote>\n<p>Sort of, but really in one aspect. DNA is double stranded. It is replicated by splitting the strands apart and generating two new molecules using the existing strands as a template. The binary pairing you point out guarantees that the two new DNA molecules will be faithful copies of the original molecule.</p>\n<p>However, replication is only one aspect of DNA. <a href=\"https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/#:%7E:text=The%20process%20of%20translation%20can,transcription%20as%20well%20as%20tRNA.&amp;text=The%20genes%20in%20DNA%20encode,the%20functions%20necessary%20for%20life.\" rel=\"nofollow noreferrer\">Translation</a> is the conversion of DNA -&gt; mRNA -&gt; protein. Generation of the mRNA from DNA is also governed by the binary pairing, (except that mRNA uses Uracil, so an A in the DNA will be paired with a U in the corresponding mRNA). However, when it comes to generating a protein from the mRNA, each possible triplet of mRNA bases (which corresponds to a triplet of DNA bases) codes to one particular amino acid in the protein. It's this correspondence between triplets of mRNA bases (and the underlying DNA bases) and amino acids that's referred to as the <a href=\"https://www.nature.com/scitable/definition/genetic-code-13/#:%7E:text=The%20genetic%20code%20is%20a%20set%20of%20three%2Dletter%20combinations,amino%20acid%20or%20stop%20signal.\" rel=\"nofollow noreferrer\">genetic code</a>.</p>\n","answer_id":113401,"answer_text":"Can we say that the DNA is coded binary with two options: AT and GC?\n\n\n\n\n\n\n\nSort of, but really in one aspect. DNA is double stranded. It is replicated by splitting the strands apart and generating two new molecules using the existing strands as a template. The binary pairing you point out guarantees that the two new DNA molecules will be faithful copies of the original molecule.\n\n\n\n\nHowever, replication is only one aspect of DNA. Translation (https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/#:%7E:text=The%20process%20of%20translation%20can,transcription%20as%20well%20as%20tRNA.&text=The%20genes%20in%20DNA%20encode,the%20functions%20necessary%20for%20life.) is the conversion of DNA -> mRNA -> protein. Generation of the mRNA from DNA is also governed by the binary pairing, (except that mRNA uses Uracil, so an A in the DNA will be paired with a U in the corresponding mRNA). However, when it comes to generating a protein from the mRNA, each possible triplet of mRNA bases (which corresponds to a triplet of DNA bases) codes to one particular amino acid in the protein. It's this correspondence between triplets of mRNA bases (and the underlying DNA bases) and amino acids that's referred to as the genetic code (https://www.nature.com/scitable/definition/genetic-code-13/#:%7E:text=The%20genetic%20code%20is%20a%20set%20of%20three%2Dletter%20combinations,amino%20acid%20or%20stop%20signal.).","answer_url":"https://biology.stackexchange.com/a/113401","author":"user21857","author_url":null,"content_license":"CC BY-SA 4.0","created_at":"2023-11-04T18:23:25+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:36.208962+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/ce9de3cf6525f1e283f75a76c7c279c0bd53024cf8e6597abc34f072e18cfbf7_0.json","raw_sha256":"c65c49a81e92972be3758d3b220c036300d85c38ce4d9079a6203d2eeac0d96d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113468;113465;113459;113453;113451;113449;113442;113437;113425;113421;113416;113415;113413;113406;113400;113398;113386;113378;113364;113363;113347;113340;113333;113324;113317;113315;113310;113303;113307;113299;113293;113291;113284;113282;113279;113277;113275;113274;113263;113253;113252;113243;113239;113235;113231;113229;113223;113221;113218;113216;113210;113198;113191;113183;113180;113175;113164;113158;113153;113146;113141;113118;113116;113115;113113;113110;113109;113106;113104;113101;113095;113089;113086;113081;113080;113077;113076;113075;113070;113067;113064;113053;113046;113043;113039;113031;113030;113028;113027;113024;113017;113016;113015;113014;113009;113008;113007;113005;112998;112984/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113400,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user21857","profile_url":null,"user_type":"does_not_exist"},"created_at":"2023-11-04T18:23:25+00:00","raw_file":"raw/codex_api_v1/90c6546608151c55782a98b278e0bff1131c56a003319717b96f8124b5cd81ad_1790824039302420800_0.json","raw_sha256":"9f60f0aa014afb8146c20434cb45e9daca2b9f5585a871678859e9e68314a991","revision_guid":"47252C52-4C09-4FC4-BB39-7A883A92001C","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/47252C52-4C09-4FC4-BB39-7A883A92001C/view-source"}],"score":1},{"answer_html":"<p>This does not appear to be a question about biology but a semantic question in the realm of information technology. However, the answer is NO.</p>\n<p>First, linguistically I would <strong>never</strong> use the word “coded” to describe or specify the sequence of DNA — which is what the poster appears to wish to do — any more than I would use the word to do likewise for proteins (I would <strong>not</strong> say that “a protein is coded by 20 amino acids”). The use of the word is poor — you can say “RNA is coded by DNA”. (I prefer to say “DNA encodes RNA”, as it is a single word that only exists as a verb.) But “DNA <strong>is composed of</strong> four different bases”. Keep the two ideas (template and composition) separate.</p>\n<p>From a computational standpoint one can say that a DNA sequence can be described or specified using <strong>four</strong> characters and hence represented most compactly as a number to the base 4 — a <strong>quaternary</strong> number. NOT a binary number.</p>\n<p>The fact that the poster’s logic is incorrect is simply demonstrated: the single strand of a DNA with the sequence ATGC is not the same as AAGC, TAGC, TTGC, ATGG, ATCG, ATCG etc.</p>\n<p>The logical flaw is in an implicit assumption that because the sequence of the second strand is specified unambiguously by that of the first strand this somehow influences the numerical complexity of the first strand. It does not.</p>\n","answer_id":113402,"answer_text":"This does not appear to be a question about biology but a semantic question in the realm of information technology. However, the answer is NO.\n\n\n\n\nFirst, linguistically I would never use the word “coded” to describe or specify the sequence of DNA — which is what the poster appears to wish to do — any more than I would use the word to do likewise for proteins (I would not say that “a protein is coded by 20 amino acids”). The use of the word is poor — you can say “RNA is coded by DNA”. (I prefer to say “DNA encodes RNA”, as it is a single word that only exists as a verb.) But “DNA is composed of four different bases”. Keep the two ideas (template and composition) separate.\n\n\n\n\nFrom a computational standpoint one can say that a DNA sequence can be described or specified using four characters and hence represented most compactly as a number to the base 4 — a quaternary number. NOT a binary number.\n\n\n\n\nThe fact that the poster’s logic is incorrect is simply demonstrated: the single strand of a DNA with the sequence ATGC is not the same as AAGC, TAGC, TTGC, ATGG, ATCG, ATCG etc.\n\n\n\n\nThe logical flaw is in an implicit assumption that because the sequence of the second strand is specified unambiguously by that of the first strand this somehow influences the numerical complexity of the first strand. It does not.","answer_url":"https://biology.stackexchange.com/a/113402","author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","created_at":"2023-11-04T19:02:46+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:36.208962+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/ce9de3cf6525f1e283f75a76c7c279c0bd53024cf8e6597abc34f072e18cfbf7_0.json","raw_sha256":"c65c49a81e92972be3758d3b220c036300d85c38ce4d9079a6203d2eeac0d96d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113468;113465;113459;113453;113451;113449;113442;113437;113425;113421;113416;113415;113413;113406;113400;113398;113386;113378;113364;113363;113347;113340;113333;113324;113317;113315;113310;113303;113307;113299;113293;113291;113284;113282;113279;113277;113275;113274;113263;113253;113252;113243;113239;113235;113231;113229;113223;113221;113218;113216;113210;113198;113191;113183;113180;113175;113164;113158;113153;113146;113141;113118;113116;113115;113113;113110;113109;113106;113104;113101;113095;113089;113086;113081;113080;113077;113076;113075;113070;113067;113064;113053;113046;113043;113039;113031;113030;113028;113027;113024;113017;113016;113015;113014;113009;113008;113007;113005;112998;112984/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113400,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2023-11-04T19:02:46+00:00","raw_file":"raw/codex_api_v1/90c6546608151c55782a98b278e0bff1131c56a003319717b96f8124b5cd81ad_1790824039302420800_0.json","raw_sha256":"9f60f0aa014afb8146c20434cb45e9daca2b9f5585a871678859e9e68314a991","revision_guid":"3E594DC5-07E0-46AD-8861-46A4993FE919","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3E594DC5-07E0-46AD-8861-46A4993FE919/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"abbassix","author_url":"https://biology.stackexchange.com/users/65368/abbassix","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"abbassix","profile_url":"https://biology.stackexchange.com/users/65368/abbassix","user_type":"registered"},"created_at":"2023-11-04T17:16:43+00:00","raw_file":"raw/codex_api_v1/90c6546608151c55782a98b278e0bff1131c56a003319717b96f8124b5cd81ad_1790824039302420800_0.json","raw_sha256":"9f60f0aa014afb8146c20434cb45e9daca2b9f5585a871678859e9e68314a991","revision_guid":"61104239-C4A0-494E-A225-A24375336024","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/61104239-C4A0-494E-A225-A24375336024/view-source"},{"content_license":null,"contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2023-11-04T19:04:29+00:00","raw_file":"raw/codex_api_v1/90c6546608151c55782a98b278e0bff1131c56a003319717b96f8124b5cd81ad_1790824039302420800_0.json","raw_sha256":"9f60f0aa014afb8146c20434cb45e9daca2b9f5585a871678859e9e68314a991","revision_guid":"DADB7DF5-7D85-46B1-A5E3-4B6FC9C228D4","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DADB7DF5-7D85-46B1-A5E3-4B6FC9C228D4/view-source"}],"url":"https://biology.stackexchange.com/questions/113400/how-many-base-codes-are-in-dna-two-or-four"},{"author":"user21857","author_url":null,"content_license":"CC BY-SA 4.0","context_id":"113401","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user21857","profile_url":null,"user_type":"does_not_exist"},"created_at":"2023-11-04T18:23:25+00:00","raw_file":"raw/codex_api_v1/90c6546608151c55782a98b278e0bff1131c56a003319717b96f8124b5cd81ad_1790824039302420800_0.json","raw_sha256":"9f60f0aa014afb8146c20434cb45e9daca2b9f5585a871678859e9e68314a991","revision_guid":"47252C52-4C09-4FC4-BB39-7A883A92001C","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/47252C52-4C09-4FC4-BB39-7A883A92001C/view-source"}],"url":"https://biology.stackexchange.com/a/113401"},{"author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","context_id":"113402","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2023-11-04T19:02:46+00:00","raw_file":"raw/codex_api_v1/90c6546608151c55782a98b278e0bff1131c56a003319717b96f8124b5cd81ad_1790824039302420800_0.json","raw_sha256":"9f60f0aa014afb8146c20434cb45e9daca2b9f5585a871678859e9e68314a991","revision_guid":"3E594DC5-07E0-46AD-8861-46A4993FE919","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3E594DC5-07E0-46AD-8861-46A4993FE919/view-source"}],"url":"https://biology.stackexchange.com/a/113402"}],"contexts":[{"context_id":"question","html":"<p>We know there are four bases found in a DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). We also know that A always pairs with T and G always pairs with C. Can we say that the DNA is coded binary with two options: AT and GC?</p>\n","text":"We know there are four bases found in a DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). We also know that A always pairs with T and G always pairs with C. Can we say that the DNA is coded binary with two options: AT and GC?"},{"context_id":"113401","html":"<blockquote>\n<p>Can we say that the DNA is coded binary with two options: AT and GC?</p>\n</blockquote>\n<p>Sort of, but really in one aspect. DNA is double stranded. It is replicated by splitting the strands apart and generating two new molecules using the existing strands as a template. The binary pairing you point out guarantees that the two new DNA molecules will be faithful copies of the original molecule.</p>\n<p>However, replication is only one aspect of DNA. <a href=\"https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/#:%7E:text=The%20process%20of%20translation%20can,transcription%20as%20well%20as%20tRNA.&amp;text=The%20genes%20in%20DNA%20encode,the%20functions%20necessary%20for%20life.\" rel=\"nofollow noreferrer\">Translation</a> is the conversion of DNA -&gt; mRNA -&gt; protein. Generation of the mRNA from DNA is also governed by the binary pairing, (except that mRNA uses Uracil, so an A in the DNA will be paired with a U in the corresponding mRNA). However, when it comes to generating a protein from the mRNA, each possible triplet of mRNA bases (which corresponds to a triplet of DNA bases) codes to one particular amino acid in the protein. It's this correspondence between triplets of mRNA bases (and the underlying DNA bases) and amino acids that's referred to as the <a href=\"https://www.nature.com/scitable/definition/genetic-code-13/#:%7E:text=The%20genetic%20code%20is%20a%20set%20of%20three%2Dletter%20combinations,amino%20acid%20or%20stop%20signal.\" rel=\"nofollow noreferrer\">genetic code</a>.</p>\n","text":"Can we say that the DNA is coded binary with two options: AT and GC?\n\n\n\n\n\n\n\nSort of, but really in one aspect. DNA is double stranded. It is replicated by splitting the strands apart and generating two new molecules using the existing strands as a template. The binary pairing you point out guarantees that the two new DNA molecules will be faithful copies of the original molecule.\n\n\n\n\nHowever, replication is only one aspect of DNA. Translation (https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/#:%7E:text=The%20process%20of%20translation%20can,transcription%20as%20well%20as%20tRNA.&text=The%20genes%20in%20DNA%20encode,the%20functions%20necessary%20for%20life.) is the conversion of DNA -> mRNA -> protein. Generation of the mRNA from DNA is also governed by the binary pairing, (except that mRNA uses Uracil, so an A in the DNA will be paired with a U in the corresponding mRNA). However, when it comes to generating a protein from the mRNA, each possible triplet of mRNA bases (which corresponds to a triplet of DNA bases) codes to one particular amino acid in the protein. It's this correspondence between triplets of mRNA bases (and the underlying DNA bases) and amino acids that's referred to as the genetic code (https://www.nature.com/scitable/definition/genetic-code-13/#:%7E:text=The%20genetic%20code%20is%20a%20set%20of%20three%2Dletter%20combinations,amino%20acid%20or%20stop%20signal.)."},{"context_id":"113402","html":"<p>This does not appear to be a question about biology but a semantic question in the realm of information technology. However, the answer is NO.</p>\n<p>First, linguistically I would <strong>never</strong> use the word “coded” to describe or specify the sequence of DNA — which is what the poster appears to wish to do — any more than I would use the word to do likewise for proteins (I would <strong>not</strong> say that “a protein is coded by 20 amino acids”). The use of the word is poor — you can say “RNA is coded by DNA”. (I prefer to say “DNA encodes RNA”, as it is a single word that only exists as a verb.) But “DNA <strong>is composed of</strong> four different bases”. Keep the two ideas (template and composition) separate.</p>\n<p>From a computational standpoint one can say that a DNA sequence can be described or specified using <strong>four</strong> characters and hence represented most compactly as a number to the base 4 — a <strong>quaternary</strong> number. NOT a binary number.</p>\n<p>The fact that the poster’s logic is incorrect is simply demonstrated: the single strand of a DNA with the sequence ATGC is not the same as AAGC, TAGC, TTGC, ATGG, ATCG, ATCG etc.</p>\n<p>The logical flaw is in an implicit assumption that because the sequence of the second strand is specified unambiguously by that of the first strand this somehow influences the numerical complexity of the first strand. It does not.</p>\n","text":"This does not appear to be a question about biology but a semantic question in the realm of information technology. However, the answer is NO.\n\n\n\n\nFirst, linguistically I would never use the word “coded” to describe or specify the sequence of DNA — which is what the poster appears to wish to do — any more than I would use the word to do likewise for proteins (I would not say that “a protein is coded by 20 amino acids”). The use of the word is poor — you can say “RNA is coded by DNA”. (I prefer to say “DNA encodes RNA”, as it is a single word that only exists as a verb.) But “DNA is composed of four different bases”. Keep the two ideas (template and composition) separate.\n\n\n\n\nFrom a computational standpoint one can say that a DNA sequence can be described or specified using four characters and hence represented most compactly as a number to the base 4 — a quaternary number. NOT a binary number.\n\n\n\n\nThe fact that the poster’s logic is incorrect is simply demonstrated: the single strand of a DNA with the sequence ATGC is not the same as AAGC, TAGC, TTGC, ATGG, ATCG, ATCG etc.\n\n\n\n\nThe logical flaw is in an implicit assumption that because the sequence of the second strand is specified unambiguously by that of the first strand this somehow influences the numerical complexity of the first strand. It does not."}],"domain":"biology","external_citations":["https://www.nature.com/scitable/definition/genetic-code-13/#:%7E:text=The%20genetic%20code%20is%20a%20set%20of%20three%2Dletter%20combinations,amino%20acid%20or%20stop%20signal.","https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/#:%7E:text=The%20process%20of%20translation%20can,transcription%20as%20well%20as%20tRNA.&text=The%20genes%20in%20DNA%20encode,the%20functions%20necessary%20for%20life."],"ground_truth_type":"metadata_grounded","group_id":"e714682a5cca9ab0bc3a9425ce62c0c4f6a3daa2dfe0cd653943dfd29fea3dbe","hard_case_family":["no_accepted_answer","multiple_sources","multiple_answer_candidates"],"id":"RHM-6a0555e5a25f2529482077ae","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:11.333206+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/3e71d6afdfe444c721dbb1321f43c14066813d2fd740fb255123cf87e737d071_0.json","raw_sha256":"84992ad678a40907dca3af99f849ee653142b680281a54e02542dc7f47d30773","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=9&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"abbassix","profile_url":"https://biology.stackexchange.com/users/65368/abbassix","user_type":"registered"},"created_at":"2023-11-04T17:16:43+00:00","raw_file":"raw/codex_api_v1/90c6546608151c55782a98b278e0bff1131c56a003319717b96f8124b5cd81ad_1790824039302420800_0.json","raw_sha256":"9f60f0aa014afb8146c20434cb45e9daca2b9f5585a871678859e9e68314a991","revision_guid":"61104239-C4A0-494E-A225-A24375336024","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/61104239-C4A0-494E-A225-A24375336024/view-source"},{"content_license":null,"contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2023-11-04T19:04:29+00:00","raw_file":"raw/codex_api_v1/90c6546608151c55782a98b278e0bff1131c56a003319717b96f8124b5cd81ad_1790824039302420800_0.json","raw_sha256":"9f60f0aa014afb8146c20434cb45e9daca2b9f5585a871678859e9e68314a991","revision_guid":"DADB7DF5-7D85-46B1-A5E3-4B6FC9C228D4","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DADB7DF5-7D85-46B1-A5E3-4B6FC9C228D4/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113400","source_record_sha256":"b8c647404a7bab2fa978387a15029d2895a59b5cdda877b5b7d357d622838832","source_url":"https://biology.stackexchange.com/questions/113400/how-many-base-codes-are-in-dna-two-or-four","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How many base codes are in DNA? Two or four?\nWe know there are four bases found in a DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). We also know that A always pairs with T and G always pairs with C. Can we say that the DNA is coded binary with two options: AT and GC?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113401,"score":1},{"answer_id":113402,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>First and foremost, congratulations!</p>\n<p>Yes, it is extremely rare for dizygotic twins (two eggs/zygotes, fraternal) to share a single placenta. This is referred to as monochorionic (one placenta) dizigotic twins (MCDT). This is the rarest of all twins.</p>\n<p>It was a well known occurrence in cattle, but until recently not recognized in humans. For this reason, articles you find online will often still state that twins with shared placentas are monozygotic (identical) twins. The rate is influenced by assisted reproductive technology (ART) e.g. IVF, which itself increases the rate of twin births. The exact rate is not known, but it is probably more common than estimated, as more testing is now being done on monochorionic twins.*</p>\n<p>This happens because the two placentas happen to implant too closely to each other in the uterus, and sharing a relatively small space grow together to form one whole. The degree to which they grow together is variable.</p>\n<p>Without IVF, twin birth (in the US) occurs in about 2% of births, so 1 in 50. Including IVF, twin births increase the total to about 3 in 50 births (numbers vary from country to country). In one study of 31 MCDTs, 87% followed assisted reproductive technology; only about 18% were conceived naturally. So, 18% of (2/100) is about 1 in 250 naturally conceived twin births. If ASR twins are included, it increases, but it's still uncommon.</p>\n<p>*<sub>In one case, a pair of monochorionic twins were found to be dizigotic <em>at 14 months of age</em> after testing because the parents believed they were not identical.</sub></p>\n<p><sub><a href=\"https://www.cambridge.org/core/journals/twin-research-and-human-genetics/article/unusual-twinning-resulting-in-chimerism-a-systematic-review-on-monochorionic-dizygotic-twins/22C37BE56B706ED27D34C1DF3AC30D8D\" rel=\"nofollow noreferrer\">Unusual Twinning Resulting in Chimerism: A Systematic Review on Monochorionic Dizygotic Twins</a></sub><br />\n<sub><a href=\"https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.35957\" rel=\"nofollow noreferrer\">Chimerism in monochorionic dizygotic twins: Case study and review</a></sub></p>\n","answer_id":113409,"answer_text":"First and foremost, congratulations!\n\n\n\n\nYes, it is extremely rare for dizygotic twins (two eggs/zygotes, fraternal) to share a single placenta. This is referred to as monochorionic (one placenta) dizigotic twins (MCDT). This is the rarest of all twins.\n\n\n\n\nIt was a well known occurrence in cattle, but until recently not recognized in humans. For this reason, articles you find online will often still state that twins with shared placentas are monozygotic (identical) twins. The rate is influenced by assisted reproductive technology (ART) e.g. IVF, which itself increases the rate of twin births. The exact rate is not known, but it is probably more common than estimated, as more testing is now being done on monochorionic twins.*\n\n\n\n\nThis happens because the two placentas happen to implant too closely to each other in the uterus, and sharing a relatively small space grow together to form one whole. The degree to which they grow together is variable.\n\n\n\n\nWithout IVF, twin birth (in the US) occurs in about 2% of births, so 1 in 50. Including IVF, twin births increase the total to about 3 in 50 births (numbers vary from country to country). In one study of 31 MCDTs, 87% followed assisted reproductive technology; only about 18% were conceived naturally. So, 18% of (2/100) is about 1 in 250 naturally conceived twin births. If ASR twins are included, it increases, but it's still uncommon.\n\n\n\n\n*In one case, a pair of monochorionic twins were found to be dizigotic at 14 months of age after testing because the parents believed they were not identical.\n\n\n\n\nUnusual Twinning Resulting in Chimerism: A Systematic Review on Monochorionic Dizygotic Twins (https://www.cambridge.org/core/journals/twin-research-and-human-genetics/article/unusual-twinning-resulting-in-chimerism-a-systematic-review-on-monochorionic-dizygotic-twins/22C37BE56B706ED27D34C1DF3AC30D8D)\n\nChimerism in monochorionic dizygotic twins: Case study and review (https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.35957)","answer_url":"https://biology.stackexchange.com/a/113409","author":"anongoodnurse","author_url":"https://biology.stackexchange.com/users/5198/anongoodnurse","content_license":"CC BY-SA 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Mollick","profile_url":"https://biology.stackexchange.com/users/77597/saruque-ahamed-mollick","user_type":"registered"},"created_at":"2023-11-05T02:03:02+00:00","raw_file":"raw/codex_api_v1/90c6546608151c55782a98b278e0bff1131c56a003319717b96f8124b5cd81ad_1790824039302420800_0.json","raw_sha256":"9f60f0aa014afb8146c20434cb45e9daca2b9f5585a871678859e9e68314a991","revision_guid":"04A5A4A3-8178-47C9-B1E3-050CC550133F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/04A5A4A3-8178-47C9-B1E3-050CC550133F/view-source"}],"url":"https://biology.stackexchange.com/questions/113406/twin-with-one-boy-and-one-girl-with-single-placenta"},{"author":"anongoodnurse","author_url":"https://biology.stackexchange.com/users/5198/anongoodnurse","content_license":"CC BY-SA 4.0","context_id":"113409","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"anongoodnurse","profile_url":"https://biology.stackexchange.com/users/5198/anongoodnurse","user_type":"registered"},"created_at":"2023-11-05T14:48:34+00:00","raw_file":"raw/codex_api_v1/90c6546608151c55782a98b278e0bff1131c56a003319717b96f8124b5cd81ad_1790824039302420800_0.json","raw_sha256":"9f60f0aa014afb8146c20434cb45e9daca2b9f5585a871678859e9e68314a991","revision_guid":"03DF2280-0437-460F-A6E6-C492D30B0656","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/03DF2280-0437-460F-A6E6-C492D30B0656/view-source"},{"content_license":"CC BY-SA 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is it a rare case that I got a baby boy and a baby girl who were sharing a single placenta?\nJust curious to know. If yes then what was the probability of this case?</p>\n","text":"I am 27,male and just become father of twins.\nOne baby boy and one baby girl.\nAccording to my wife’s medical report both of the babies were sharing a single placenta.\nI am not an expert in medical science but through internet I have read that the twins will be either boy or girl.\nSo is it a rare case that I got a baby boy and a baby girl who were sharing a single placenta?\nJust curious to know. If yes then what was the probability of this case?"},{"context_id":"113409","html":"<p>First and foremost, congratulations!</p>\n<p>Yes, it is extremely rare for dizygotic twins (two eggs/zygotes, fraternal) to share a single placenta. This is referred to as monochorionic (one placenta) dizigotic twins (MCDT). This is the rarest of all twins.</p>\n<p>It was a well known occurrence in cattle, but until recently not recognized in humans. For this reason, articles you find online will often still state that twins with shared placentas are monozygotic (identical) twins. The rate is influenced by assisted reproductive technology (ART) e.g. IVF, which itself increases the rate of twin births. The exact rate is not known, but it is probably more common than estimated, as more testing is now being done on monochorionic twins.*</p>\n<p>This happens because the two placentas happen to implant too closely to each other in the uterus, and sharing a relatively small space grow together to form one whole. The degree to which they grow together is variable.</p>\n<p>Without IVF, twin birth (in the US) occurs in about 2% of births, so 1 in 50. Including IVF, twin births increase the total to about 3 in 50 births (numbers vary from country to country). In one study of 31 MCDTs, 87% followed assisted reproductive technology; only about 18% were conceived naturally. So, 18% of (2/100) is about 1 in 250 naturally conceived twin births. If ASR twins are included, it increases, but it's still uncommon.</p>\n<p>*<sub>In one case, a pair of monochorionic twins were found to be dizigotic <em>at 14 months of age</em> after testing because the parents believed they were not identical.</sub></p>\n<p><sub><a href=\"https://www.cambridge.org/core/journals/twin-research-and-human-genetics/article/unusual-twinning-resulting-in-chimerism-a-systematic-review-on-monochorionic-dizygotic-twins/22C37BE56B706ED27D34C1DF3AC30D8D\" rel=\"nofollow noreferrer\">Unusual Twinning Resulting in Chimerism: A Systematic Review on Monochorionic Dizygotic Twins</a></sub><br />\n<sub><a href=\"https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.35957\" rel=\"nofollow noreferrer\">Chimerism in monochorionic dizygotic twins: Case study and review</a></sub></p>\n","text":"First and foremost, congratulations!\n\n\n\n\nYes, it is extremely rare for dizygotic twins (two eggs/zygotes, fraternal) to share a single placenta. This is referred to as monochorionic (one placenta) dizigotic twins (MCDT). This is the rarest of all twins.\n\n\n\n\nIt was a well known occurrence in cattle, but until recently not recognized in humans. For this reason, articles you find online will often still state that twins with shared placentas are monozygotic (identical) twins. The rate is influenced by assisted reproductive technology (ART) e.g. IVF, which itself increases the rate of twin births. The exact rate is not known, but it is probably more common than estimated, as more testing is now being done on monochorionic twins.*\n\n\n\n\nThis happens because the two placentas happen to implant too closely to each other in the uterus, and sharing a relatively small space grow together to form one whole. The degree to which they grow together is variable.\n\n\n\n\nWithout IVF, twin birth (in the US) occurs in about 2% of births, so 1 in 50. Including IVF, twin births increase the total to about 3 in 50 births (numbers vary from country to country). In one study of 31 MCDTs, 87% followed assisted reproductive technology; only about 18% were conceived naturally. So, 18% of (2/100) is about 1 in 250 naturally conceived twin births. If ASR twins are included, it increases, but it's still uncommon.\n\n\n\n\n*In one case, a pair of monochorionic twins were found to be dizigotic at 14 months of age after testing because the parents believed they were not identical.\n\n\n\n\nUnusual Twinning Resulting in Chimerism: A Systematic Review on Monochorionic Dizygotic Twins (https://www.cambridge.org/core/journals/twin-research-and-human-genetics/article/unusual-twinning-resulting-in-chimerism-a-systematic-review-on-monochorionic-dizygotic-twins/22C37BE56B706ED27D34C1DF3AC30D8D)\n\nChimerism in monochorionic dizygotic twins: Case study and review (https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.35957)"}],"domain":"biology","external_citations":["https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.35957","https://www.cambridge.org/core/journals/twin-research-and-human-genetics/article/unusual-twinning-resulting-in-chimerism-a-systematic-review-on-monochorionic-dizygotic-twins/22C37BE56B706ED27D34C1DF3AC30D8D"],"ground_truth_type":"metadata_grounded","group_id":"de555ffcb329e629bea75aec8814c1ec3a9973a676f226311a09fbdafd002048","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-1033026bbeae0d2c664be488","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:11.333206+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/3e71d6afdfe444c721dbb1321f43c14066813d2fd740fb255123cf87e737d071_0.json","raw_sha256":"84992ad678a40907dca3af99f849ee653142b680281a54e02542dc7f47d30773","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=9&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Saruque Ahamed Mollick","profile_url":"https://biology.stackexchange.com/users/77597/saruque-ahamed-mollick","user_type":"registered"},"created_at":"2023-11-05T02:03:02+00:00","raw_file":"raw/codex_api_v1/90c6546608151c55782a98b278e0bff1131c56a003319717b96f8124b5cd81ad_1790824039302420800_0.json","raw_sha256":"9f60f0aa014afb8146c20434cb45e9daca2b9f5585a871678859e9e68314a991","revision_guid":"04A5A4A3-8178-47C9-B1E3-050CC550133F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/04A5A4A3-8178-47C9-B1E3-050CC550133F/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113406","source_record_sha256":"e7a0e71e9dd8d923d61dbefa18fbeca108e331f9becedd89e431019c9c492ee0","source_url":"https://biology.stackexchange.com/questions/113406/twin-with-one-boy-and-one-girl-with-single-placenta","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Twin with one boy and one girl with single placenta\nI am 27,male and just become father of twins.\nOne baby boy and one baby girl.\nAccording to my wife’s medical report both of the babies were sharing a single placenta.\nI am not an expert in medical science but through internet I have read that the twins will be either boy or girl.\nSo is it a rare case that I got a baby boy and a baby girl who were sharing a single placenta?\nJust curious to know. If yes then what was the probability of this case?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113409,"score":5}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Short of someone from either one of those committees being on here and seeing the question the answer is &quot;<em>Because we said so</em>&quot;.</p>\n<p>The respective committees are the authorities on the subject and get to make their own rules, even if they aren't consistent with committees covering similar aspects in other areas of biology.</p>\n<p>For those interested, the committees have their rules available online and the ones relevant to the question are <a href=\"https://www.iapt-taxon.org/nomen/pages/main/art_32.html#Art32.1\" rel=\"nofollow noreferrer\">32.1c</a> and <a href=\"https://www.iapt-taxon.org/nomen/pages/main/art_23.html\" rel=\"nofollow noreferrer\">23.4</a> from the <a href=\"https://www.iapt-taxon.org/nomen/main.php\" rel=\"nofollow noreferrer\">International Code of Nomenclature for Algae, Fungi, and Plants</a> and <a href=\"https://www.iczn.org/the-code/the-code-online/\" rel=\"nofollow noreferrer\">23.3.7</a> (under Chapter 6, Article 23, section 23.3; no direct link possible) for the <a href=\"https://www.iczn.org/\" rel=\"nofollow noreferrer\">International Commission on Zoological Nomenclature</a>.</p>\n","answer_id":113456,"answer_text":"Short of someone from either one of those committees being on here and seeing the question the answer is \"Because we said so\".\n\n\n\n\nThe respective committees are the authorities on the subject and get to make their own rules, even if they aren't consistent with committees covering similar aspects in other areas of biology.\n\n\n\n\nFor those interested, the committees have their rules available online and the ones relevant to the question are 32.1c (https://www.iapt-taxon.org/nomen/pages/main/art_32.html#Art32.1) and 23.4 (https://www.iapt-taxon.org/nomen/pages/main/art_23.html) from the International Code of Nomenclature for Algae, Fungi, and Plants (https://www.iapt-taxon.org/nomen/main.php) and 23.3.7 (https://www.iczn.org/the-code/the-code-online/) (under Chapter 6, Article 23, section 23.3; no direct link possible) for the International Commission on Zoological Nomenclature (https://www.iczn.org/).","answer_url":"https://biology.stackexchange.com/a/113456","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2023-11-10T00:02:12+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:37.585395+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/d8f0ba725c7d7cdce167507177cd9e8c354e0409a9f0824b4ba8dffcb28b6eed_0.json","raw_sha256":"7275599cd4dfa07c5d9ad8953eeb29f56ff2d11403ea7cd58a0dd6a1c9b3b64c","source_api":"Stack Exchange API 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4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2023-11-10T00:02:12+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"4F469246-28C0-4DFA-8BE0-7D248ECE3754","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4F469246-28C0-4DFA-8BE0-7D248ECE3754/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"imrobert","author_url":"https://biology.stackexchange.com/users/75153/imrobert","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"imrobert","profile_url":"https://biology.stackexchange.com/users/75153/imrobert","user_type":"registered"},"created_at":"2023-11-09T16:34:02+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"38EBE114-4721-49FA-A50D-8A2792FF6D30","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/38EBE114-4721-49FA-A50D-8A2792FF6D30/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2023-11-09T17:37:12+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"8F632A9D-071F-482E-B22C-F69A3989D4D7","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8F632A9D-071F-482E-B22C-F69A3989D4D7/view-source"}],"url":"https://biology.stackexchange.com/questions/113451/why-is-tautonymy-forbidden-in-botany"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"113456","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2023-11-10T00:02:12+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"4F469246-28C0-4DFA-8BE0-7D248ECE3754","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4F469246-28C0-4DFA-8BE0-7D248ECE3754/view-source"}],"url":"https://biology.stackexchange.com/a/113456"}],"contexts":[{"context_id":"question","html":"<p>From <a href=\"https://www.merriam-webster.com/dictionary/tautonym#:%7E:text=noun,tautonymy\" rel=\"nofollow noreferrer\">Merriam Webster</a>:</p>\n<blockquote>\n<p>tautonym: a taxonomic binomial in which the generic name and specific epithet are alike and <strong>which is common in zoology</strong> especially to designate a typical form <strong>but is forbidden to botany under the International Code of Botanical Nomenclature</strong></p>\n</blockquote>\n<p>(My emphasis)</p>\n<p>From basic research on Google I couldn't find a reason as to why this is.</p>\n<p><strong>Q: Why is tautonymy permitted in zoological nomenclature but forbidden in botanical nomenclature?</strong></p>\n","text":"From Merriam Webster (https://www.merriam-webster.com/dictionary/tautonym#:%7E:text=noun,tautonymy):\n\n\n\n\n\n\n\ntautonym: a taxonomic binomial in which the generic name and specific epithet are alike and which is common in zoology especially to designate a typical form but is forbidden to botany under the International Code of Botanical Nomenclature\n\n\n\n\n\n\n\n(My emphasis)\n\n\n\n\nFrom basic research on Google I couldn't find a reason as to why this is.\n\n\n\n\nQ: Why is tautonymy permitted in zoological nomenclature but forbidden in botanical nomenclature?"},{"context_id":"113456","html":"<p>Short of someone from either one of those committees being on here and seeing the question the answer is &quot;<em>Because we said so</em>&quot;.</p>\n<p>The respective committees are the authorities on the subject and get to make their own rules, even if they aren't consistent with committees covering similar aspects in other areas of biology.</p>\n<p>For those interested, the committees have their rules available online and the ones relevant to the question are <a href=\"https://www.iapt-taxon.org/nomen/pages/main/art_32.html#Art32.1\" rel=\"nofollow noreferrer\">32.1c</a> and <a href=\"https://www.iapt-taxon.org/nomen/pages/main/art_23.html\" rel=\"nofollow noreferrer\">23.4</a> from the <a href=\"https://www.iapt-taxon.org/nomen/main.php\" rel=\"nofollow noreferrer\">International Code of Nomenclature for Algae, Fungi, and Plants</a> and <a href=\"https://www.iczn.org/the-code/the-code-online/\" rel=\"nofollow noreferrer\">23.3.7</a> (under Chapter 6, Article 23, section 23.3; no direct link possible) for the <a href=\"https://www.iczn.org/\" rel=\"nofollow noreferrer\">International Commission on Zoological Nomenclature</a>.</p>\n","text":"Short of someone from either one of those committees being on here and seeing the question the answer is \"Because we said so\".\n\n\n\n\nThe respective committees are the authorities on the subject and get to make their own rules, even if they aren't consistent with committees covering similar aspects in other areas of biology.\n\n\n\n\nFor those interested, the committees have their rules available online and the ones relevant to the question are 32.1c (https://www.iapt-taxon.org/nomen/pages/main/art_32.html#Art32.1) and 23.4 (https://www.iapt-taxon.org/nomen/pages/main/art_23.html) from the International Code of Nomenclature for Algae, Fungi, and Plants (https://www.iapt-taxon.org/nomen/main.php) and 23.3.7 (https://www.iczn.org/the-code/the-code-online/) (under Chapter 6, Article 23, section 23.3; no direct link possible) for the International Commission on Zoological Nomenclature (https://www.iczn.org/)."}],"domain":"biology","external_citations":["https://www.iapt-taxon.org/nomen/main.php","https://www.iapt-taxon.org/nomen/pages/main/art_23.html","https://www.iapt-taxon.org/nomen/pages/main/art_32.html#Art32.1","https://www.iczn.org/","https://www.iczn.org/the-code/the-code-online/","https://www.merriam-webster.com/dictionary/tautonym#:%7E:text=noun,tautonymy"],"ground_truth_type":"metadata_grounded","group_id":"aca94a0172cb7c4f625b5bf796041df63dab0b33a80567a87af3d60e2bba7fba","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-898f53a3ce3fdea460b41fef","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:11.333206+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/3e71d6afdfe444c721dbb1321f43c14066813d2fd740fb255123cf87e737d071_0.json","raw_sha256":"84992ad678a40907dca3af99f849ee653142b680281a54e02542dc7f47d30773","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=9&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"imrobert","profile_url":"https://biology.stackexchange.com/users/75153/imrobert","user_type":"registered"},"created_at":"2023-11-09T16:34:02+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"38EBE114-4721-49FA-A50D-8A2792FF6D30","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/38EBE114-4721-49FA-A50D-8A2792FF6D30/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2023-11-09T17:37:12+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"8F632A9D-071F-482E-B22C-F69A3989D4D7","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8F632A9D-071F-482E-B22C-F69A3989D4D7/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113451","source_record_sha256":"ee113305d1c714f29d5614fec2c098d8423b2270ae7201db7db726c74ad74f3f","source_url":"https://biology.stackexchange.com/questions/113451/why-is-tautonymy-forbidden-in-botany","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Why is tautonymy forbidden in botany?\nFrom Merriam Webster (https://www.merriam-webster.com/dictionary/tautonym#:%7E:text=noun,tautonymy):\n\n\n\n\n\n\n\ntautonym: a taxonomic binomial in which the generic name and specific epithet are alike and which is common in zoology especially to designate a typical form but is forbidden to botany under the International Code of Botanical Nomenclature\n\n\n\n\n\n\n\n(My emphasis)\n\n\n\n\nFrom basic research on Google I couldn't find a reason as to why this is.\n\n\n\n\nQ: Why is tautonymy permitted in zoological nomenclature but forbidden in botanical nomenclature?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113456,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Every organism(sexually reproducing) <a href=\"https://www.ncbi.nlm.nih.gov/books/NBK554562/\" rel=\"nofollow noreferrer\">starts</a> life from a single cell zygote formed by union of sperm and ovum.</p>\n<p>Since all cells are formed by mitotic divisions and differentiation of the zygote, the number and type of chromosomes remain same in every cell of the body.</p>\n<p>In <a href=\"https://www.sciencedirect.com/science/article/pii/S0925443912001470\" rel=\"nofollow noreferrer\">rare cases</a> however there maybe chances of aneuoploidy of the chromosomes during cleavage or later mitotic divisions. As given in the article, post-implantation mitotic aneuploidy is rare and is checked. Should it escape:</p>\n<blockquote>\n<p>Mitotic aneuploidies have been suggested to affect the developmental potential of human preimplantation embryos, possibly leading to developmental arrest or embryo loss at later stages of development. Mitotic aneuploidies may contribute to implantation failure or when compatible with implantation, may result in fetal or confined placental mosaicism. It might also cause serious fetal complications like intrauterine growth delay, congenital malformations, mental retardation, and uniparental disomy.</p>\n</blockquote>\n<p>If chromosomal abnormalities occur after immune system has started working, it can be taken care of.</p>\n<p>It's rare to have mitotic aneuploidy in a  person. To have it in two chromosomes(the allosomes) is even rarer</p>\n<p><strong>In conclusion it will be extremely rare for a living cell to have different sex than that of the person</strong></p>\n<p>For plants though it is much more common.</p>\n<p>Edit: As @BryanKrause has pointed out. <a href=\"https://en.m.wikipedia.org/wiki/Chimera_(genetics)\" rel=\"nofollow noreferrer\">Chimera</a> are another cause. If chimera  due to organ transplant is also considered makes it not so rare as I mentioned</p>\n","answer_id":113556,"answer_text":"Every organism(sexually reproducing) starts (https://www.ncbi.nlm.nih.gov/books/NBK554562/) life from a single cell zygote formed by union of sperm and ovum.\n\n\n\n\nSince all cells are formed by mitotic divisions and differentiation of the zygote, the number and type of chromosomes remain same in every cell of the body.\n\n\n\n\nIn rare cases (https://www.sciencedirect.com/science/article/pii/S0925443912001470) however there maybe chances of aneuoploidy of the chromosomes during cleavage or later mitotic divisions. As given in the article, post-implantation mitotic aneuploidy is rare and is checked. Should it escape:\n\n\n\n\n\n\n\nMitotic aneuploidies have been suggested to affect the developmental potential of human preimplantation embryos, possibly leading to developmental arrest or embryo loss at later stages of development. Mitotic aneuploidies may contribute to implantation failure or when compatible with implantation, may result in fetal or confined placental mosaicism. It might also cause serious fetal complications like intrauterine growth delay, congenital malformations, mental retardation, and uniparental disomy.\n\n\n\n\n\n\n\nIf chromosomal abnormalities occur after immune system has started working, it can be taken care of.\n\n\n\n\nIt's rare to have mitotic aneuploidy in a  person. To have it in two chromosomes(the allosomes) is even rarer\n\n\n\n\nIn conclusion it will be extremely rare for a living cell to have different sex than that of the person\n\n\n\n\nFor plants though it is much more common.\n\n\n\n\nEdit: As @BryanKrause has pointed out. Chimera (https://en.m.wikipedia.org/wiki/Chimera_(genetics)) are another cause. If chimera  due to organ transplant is also considered makes it not so rare as I mentioned","answer_url":"https://biology.stackexchange.com/a/113556","author":"Aurelius","author_url":"https://biology.stackexchange.com/users/68545/aurelius","content_license":"CC BY-SA 4.0","created_at":"2023-11-25T20:35:15+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:33.526680+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/d1acc50471f82e02a014a291913995889f5ddcd7076433532102b9b97a4a3a3d_0.json","raw_sha256":"e6b5a7d5e11f0ac54d756d69e21baee1de119b759ec7e8caa7f174d67cf80eff","source_api":"Stack Exchange API 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And vice versa.....</p>\n","text":"I mean like every cell has a sex chromosome.So does a male with XY chromosomes has all the cells in all the organs inside his body of XY chromosomes only? And vice versa....."},{"context_id":"113556","html":"<p>Every organism(sexually reproducing) <a href=\"https://www.ncbi.nlm.nih.gov/books/NBK554562/\" rel=\"nofollow noreferrer\">starts</a> life from a single cell zygote formed by union of sperm and ovum.</p>\n<p>Since all cells are formed by mitotic divisions and differentiation of the zygote, the number and type of chromosomes remain same in every cell of the body.</p>\n<p>In <a href=\"https://www.sciencedirect.com/science/article/pii/S0925443912001470\" rel=\"nofollow noreferrer\">rare cases</a> however there maybe chances of aneuoploidy of the chromosomes during cleavage or later mitotic divisions. As given in the article, post-implantation mitotic aneuploidy is rare and is checked. Should it escape:</p>\n<blockquote>\n<p>Mitotic aneuploidies have been suggested to affect the developmental potential of human preimplantation embryos, possibly leading to developmental arrest or embryo loss at later stages of development. Mitotic aneuploidies may contribute to implantation failure or when compatible with implantation, may result in fetal or confined placental mosaicism. It might also cause serious fetal complications like intrauterine growth delay, congenital malformations, mental retardation, and uniparental disomy.</p>\n</blockquote>\n<p>If chromosomal abnormalities occur after immune system has started working, it can be taken care of.</p>\n<p>It's rare to have mitotic aneuploidy in a  person. To have it in two chromosomes(the allosomes) is even rarer</p>\n<p><strong>In conclusion it will be extremely rare for a living cell to have different sex than that of the person</strong></p>\n<p>For plants though it is much more common.</p>\n<p>Edit: As @BryanKrause has pointed out. <a href=\"https://en.m.wikipedia.org/wiki/Chimera_(genetics)\" rel=\"nofollow noreferrer\">Chimera</a> are another cause. If chimera  due to organ transplant is also considered makes it not so rare as I mentioned</p>\n","text":"Every organism(sexually reproducing) starts (https://www.ncbi.nlm.nih.gov/books/NBK554562/) life from a single cell zygote formed by union of sperm and ovum.\n\n\n\n\nSince all cells are formed by mitotic divisions and differentiation of the zygote, the number and type of chromosomes remain same in every cell of the body.\n\n\n\n\nIn rare cases (https://www.sciencedirect.com/science/article/pii/S0925443912001470) however there maybe chances of aneuoploidy of the chromosomes during cleavage or later mitotic divisions. As given in the article, post-implantation mitotic aneuploidy is rare and is checked. Should it escape:\n\n\n\n\n\n\n\nMitotic aneuploidies have been suggested to affect the developmental potential of human preimplantation embryos, possibly leading to developmental arrest or embryo loss at later stages of development. Mitotic aneuploidies may contribute to implantation failure or when compatible with implantation, may result in fetal or confined placental mosaicism. It might also cause serious fetal complications like intrauterine growth delay, congenital malformations, mental retardation, and uniparental disomy.\n\n\n\n\n\n\n\nIf chromosomal abnormalities occur after immune system has started working, it can be taken care of.\n\n\n\n\nIt's rare to have mitotic aneuploidy in a  person. To have it in two chromosomes(the allosomes) is even rarer\n\n\n\n\nIn conclusion it will be extremely rare for a living cell to have different sex than that of the person\n\n\n\n\nFor plants though it is much more common.\n\n\n\n\nEdit: As @BryanKrause has pointed out. Chimera (https://en.m.wikipedia.org/wiki/Chimera_(genetics)) are another cause. If chimera  due to organ transplant is also considered makes it not so rare as I mentioned"}],"domain":"biology","external_citations":["https://en.m.wikipedia.org/wiki/Chimera_(genetics)","https://www.ncbi.nlm.nih.gov/books/NBK554562/","https://www.sciencedirect.com/science/article/pii/S0925443912001470"],"ground_truth_type":"metadata_grounded","group_id":"1ea321ba76839cdcae485a30cfd8cb8bc4d72680d528cccda11d380ae6919d86","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-d3658097b30d5fd5e9e56cda","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:09.960411+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f3d8f52a1a12ba8e3a85266c887134296fd3686fb5ffec1a38526e2b8ccdcc24_0.json","raw_sha256":"b1b59ebb5f220f357ffaa8464594a3d8f391df66ad06b024355499ef7eff18cb","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=8&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"PAWAN","profile_url":"https://biology.stackexchange.com/users/77891/pawan","user_type":"registered"},"created_at":"2023-11-25T17:31:40+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"94342197-6ECC-4DD4-9D73-CC21FFEE1395","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/94342197-6ECC-4DD4-9D73-CC21FFEE1395/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113554","source_record_sha256":"2191b68af9f68c9d5d48d7498c1d31d36bc5f56e31eb9da5a55bd131eb1d1d6f","source_url":"https://biology.stackexchange.com/questions/113554/can-a-person-have-different-sex-at-cellular-level","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Can a person have different sex at cellular level?\nI mean like every cell has a sex chromosome.So does a male with XY chromosomes has all the cells in all the organs inside his body of XY chromosomes only? And vice versa.....","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113556,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":113563,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I would start with the <a href=\"https://en.m.wikipedia.org/wiki/Goldman_equation\" rel=\"nofollow noreferrer\">Goldman equation</a>, plug in some reasonable values and experiment with the results. Your reasoning I think comes from a common misconception that involves counting positive charges and forgetting that any solution with sodium or potassium cations comes with an equal balanced number of anions. You're never adding just sodium or potassium; if you did, you'd have enough energy in a small solution to create lightning and the charges would rebalance themselves. Membrane potentials are based on really tiny charge imbalances.</p>\n<p>Potassium is high inside cells and low outside; if a cell is only permeable to potassium, that would mean a bit of potassium leaks out, following that concentration gradient. The result is a cell that's a bit negatively charged inside. If you increase the potassium concentration outside to equal the inside, there's no concentration gradient for those ions to travel down, so no membrane potential. If the potassium concentration outside is greater than inside, potassium ions flowing down their concentration gradient results in a positive charge inside the cell.</p>\n<p>If there is little sodium conductance, changes in sodium don't affect the membrane potential. If you add a bunch more sodium outside, it will depolarize the cell a little bit if there's some sodium conductance, but as long as most of the conductance is for potassium it's mainly the potassium concentration gradient that matters.</p>\n<p>Also, this experiment is just adding 20 mM additional sodium or potassium extracellularly; for potassium that may be doubling the concentration or more. For sodium it's more likely a 10-20% increase.</p>\n","answer_id":113563,"answer_text":"I would start with the Goldman equation (https://en.m.wikipedia.org/wiki/Goldman_equation), plug in some reasonable values and experiment with the results. Your reasoning I think comes from a common misconception that involves counting positive charges and forgetting that any solution with sodium or potassium cations comes with an equal balanced number of anions. You're never adding just sodium or potassium; if you did, you'd have enough energy in a small solution to create lightning and the charges would rebalance themselves. Membrane potentials are based on really tiny charge imbalances.\n\n\n\n\nPotassium is high inside cells and low outside; if a cell is only permeable to potassium, that would mean a bit of potassium leaks out, following that concentration gradient. The result is a cell that's a bit negatively charged inside. If you increase the potassium concentration outside to equal the inside, there's no concentration gradient for those ions to travel down, so no membrane potential. If the potassium concentration outside is greater than inside, potassium ions flowing down their concentration gradient results in a positive charge inside the cell.\n\n\n\n\nIf there is little sodium conductance, changes in sodium don't affect the membrane potential. If you add a bunch more sodium outside, it will depolarize the cell a little bit if there's some sodium conductance, but as long as most of the conductance is for potassium it's mainly the potassium concentration gradient that matters.\n\n\n\n\nAlso, this experiment is just adding 20 mM additional sodium or potassium extracellularly; for potassium that may be doubling the concentration or more. For sodium it's more likely a 10-20% increase.","answer_url":"https://biology.stackexchange.com/a/113563","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2023-11-26T04:00:19+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:33.526680+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/d1acc50471f82e02a014a291913995889f5ddcd7076433532102b9b97a4a3a3d_0.json","raw_sha256":"e6b5a7d5e11f0ac54d756d69e21baee1de119b759ec7e8caa7f174d67cf80eff","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113978;113977;113976;113967;113965;113959;113955;113947;113946;113937;113936;113924;113918;113912;113907;113904;113902;113898;113897;113887;113884;113873;113869;113863;113858;113855;113849;113846;113836;113833;113828;113827;113822;113811;113810;113806;113795;113788;113781;113780;113777;113775;113773;113763;113761;113748;113747;113739;113738;113734;113722;113715;113712;113694;113688;113681;113678;113677;113655;113654;113648;113647;113643;113642;113638;113634;113633;113631;113614;113611;113599;113598;113596;113595;113593;113590;113581;113576;113575;113570;113569;113566;113561;113557;113554;113551;113545;113537;113534;113531;113515;113508;113507;113505;113498;113491;113484;113483;113471;113469/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113561,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2023-11-26T04:00:19+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"1B6C6C20-36B3-407A-94FA-F84E9E1CE1A8","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/1B6C6C20-36B3-407A-94FA-F84E9E1CE1A8/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2023-11-26T04:34:47+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"8DC2E8D9-7B48-4C0B-90A7-9A6D0C50D217","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8DC2E8D9-7B48-4C0B-90A7-9A6D0C50D217/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"ceno980","author_url":"https://biology.stackexchange.com/users/62032/ceno980","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"ceno980","profile_url":"https://biology.stackexchange.com/users/62032/ceno980","user_type":"registered"},"created_at":"2023-11-26T03:01:28+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"9303BEAB-A6F6-446A-81D0-7CFE38888885","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9303BEAB-A6F6-446A-81D0-7CFE38888885/view-source"}],"url":"https://biology.stackexchange.com/questions/113561/why-doesnt-treating-neurons-with-a-high-sodium-solution-depolarize-their-membra"},{"author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","context_id":"113563","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2023-11-26T04:00:19+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"1B6C6C20-36B3-407A-94FA-F84E9E1CE1A8","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/1B6C6C20-36B3-407A-94FA-F84E9E1CE1A8/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2023-11-26T04:34:47+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"8DC2E8D9-7B48-4C0B-90A7-9A6D0C50D217","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8DC2E8D9-7B48-4C0B-90A7-9A6D0C50D217/view-source"}],"url":"https://biology.stackexchange.com/a/113563"}],"contexts":[{"context_id":"question","html":"<p>I am reading a <a href=\"https://www.science.org/doi/full/10.1126/sciadv.adg0666\" rel=\"nofollow noreferrer\">journal paper</a>, and in one of their experiments they treated organotypic hippocampal slice cultures with a high potassium solution to depolarize the neuronal membranes:</p>\n<blockquote>\n<p>We found that the medium from control slices, transduced with\nAAV-CMV-LacZ, incubated in high potassium solution (+20 mM) over 24\nhours contained statistically significantly higher IGF1 than that in\nhigh sodium solution (+20 mM), consistent with our hypothesis that\nIGF1 is released from pyramidal neurons in an activity-dependent\nmanner.</p>\n</blockquote>\n<p>I know that increasing extracellular KCl concentrations is commonly used to depolarize neurons in experiments. I have read that the resting neuronal membrane is highly permeable to K+, and that the membrane potential is sensitive to changes in extracellular K+ concentration. Increasing extracellular K+ depolarizes membranes.</p>\n<p>This is due to the influx of K+ ions through potassium leak channels (though neurons also have voltage-gated K+ channels, I'm assuming that they have more potassium leak channels).</p>\n<p>Under resting conditions, there is a higher concentration of Na+ ions in the extracellular fluid compared to the cytosol of the neuron.</p>\n<p>At rest, both the electrical and diffusion forces are driving Na+ towards the inside of the neuron (since the inside of the neuron is more negatively charged compared to the extracellular space).</p>\n<p>In the paper, they incubated neurons for 24 hours in serum-free medium plus 20 mM NaCl.</p>\n<p>However, increasing extracellular Na+ levels did not depolarize the neuronal membrane (unlike increasing extracellular K+ levels).</p>\n<p>Why is this the case? I know that the neuronal membrane contains voltage-gated sodium channels and sodium leak channels. Is it because neurons have a higher number of voltage-gated sodium channels in their membranes compared to sodium leak channels?</p>\n<p>I.e. to depolarize the membrane, the Na+ leak channels are not enough, you also need the opening of the voltage-gated Na+ channels.</p>\n<p>Any advice is appreciated.</p>\n","text":"I am reading a journal paper (https://www.science.org/doi/full/10.1126/sciadv.adg0666), and in one of their experiments they treated organotypic hippocampal slice cultures with a high potassium solution to depolarize the neuronal membranes:\n\n\n\n\n\n\n\nWe found that the medium from control slices, transduced with\nAAV-CMV-LacZ, incubated in high potassium solution (+20 mM) over 24\nhours contained statistically significantly higher IGF1 than that in\nhigh sodium solution (+20 mM), consistent with our hypothesis that\nIGF1 is released from pyramidal neurons in an activity-dependent\nmanner.\n\n\n\n\n\n\n\nI know that increasing extracellular KCl concentrations is commonly used to depolarize neurons in experiments. I have read that the resting neuronal membrane is highly permeable to K+, and that the membrane potential is sensitive to changes in extracellular K+ concentration. Increasing extracellular K+ depolarizes membranes.\n\n\n\n\nThis is due to the influx of K+ ions through potassium leak channels (though neurons also have voltage-gated K+ channels, I'm assuming that they have more potassium leak channels).\n\n\n\n\nUnder resting conditions, there is a higher concentration of Na+ ions in the extracellular fluid compared to the cytosol of the neuron.\n\n\n\n\nAt rest, both the electrical and diffusion forces are driving Na+ towards the inside of the neuron (since the inside of the neuron is more negatively charged compared to the extracellular space).\n\n\n\n\nIn the paper, they incubated neurons for 24 hours in serum-free medium plus 20 mM NaCl.\n\n\n\n\nHowever, increasing extracellular Na+ levels did not depolarize the neuronal membrane (unlike increasing extracellular K+ levels).\n\n\n\n\nWhy is this the case? I know that the neuronal membrane contains voltage-gated sodium channels and sodium leak channels. Is it because neurons have a higher number of voltage-gated sodium channels in their membranes compared to sodium leak channels?\n\n\n\n\nI.e. to depolarize the membrane, the Na+ leak channels are not enough, you also need the opening of the voltage-gated Na+ channels.\n\n\n\n\nAny advice is appreciated."},{"context_id":"113563","html":"<p>I would start with the <a href=\"https://en.m.wikipedia.org/wiki/Goldman_equation\" rel=\"nofollow noreferrer\">Goldman equation</a>, plug in some reasonable values and experiment with the results. Your reasoning I think comes from a common misconception that involves counting positive charges and forgetting that any solution with sodium or potassium cations comes with an equal balanced number of anions. You're never adding just sodium or potassium; if you did, you'd have enough energy in a small solution to create lightning and the charges would rebalance themselves. Membrane potentials are based on really tiny charge imbalances.</p>\n<p>Potassium is high inside cells and low outside; if a cell is only permeable to potassium, that would mean a bit of potassium leaks out, following that concentration gradient. The result is a cell that's a bit negatively charged inside. If you increase the potassium concentration outside to equal the inside, there's no concentration gradient for those ions to travel down, so no membrane potential. If the potassium concentration outside is greater than inside, potassium ions flowing down their concentration gradient results in a positive charge inside the cell.</p>\n<p>If there is little sodium conductance, changes in sodium don't affect the membrane potential. If you add a bunch more sodium outside, it will depolarize the cell a little bit if there's some sodium conductance, but as long as most of the conductance is for potassium it's mainly the potassium concentration gradient that matters.</p>\n<p>Also, this experiment is just adding 20 mM additional sodium or potassium extracellularly; for potassium that may be doubling the concentration or more. For sodium it's more likely a 10-20% increase.</p>\n","text":"I would start with the Goldman equation (https://en.m.wikipedia.org/wiki/Goldman_equation), plug in some reasonable values and experiment with the results. Your reasoning I think comes from a common misconception that involves counting positive charges and forgetting that any solution with sodium or potassium cations comes with an equal balanced number of anions. You're never adding just sodium or potassium; if you did, you'd have enough energy in a small solution to create lightning and the charges would rebalance themselves. Membrane potentials are based on really tiny charge imbalances.\n\n\n\n\nPotassium is high inside cells and low outside; if a cell is only permeable to potassium, that would mean a bit of potassium leaks out, following that concentration gradient. The result is a cell that's a bit negatively charged inside. If you increase the potassium concentration outside to equal the inside, there's no concentration gradient for those ions to travel down, so no membrane potential. If the potassium concentration outside is greater than inside, potassium ions flowing down their concentration gradient results in a positive charge inside the cell.\n\n\n\n\nIf there is little sodium conductance, changes in sodium don't affect the membrane potential. If you add a bunch more sodium outside, it will depolarize the cell a little bit if there's some sodium conductance, but as long as most of the conductance is for potassium it's mainly the potassium concentration gradient that matters.\n\n\n\n\nAlso, this experiment is just adding 20 mM additional sodium or potassium extracellularly; for potassium that may be doubling the concentration or more. For sodium it's more likely a 10-20% increase."}],"domain":"biology","external_citations":["https://en.m.wikipedia.org/wiki/Goldman_equation","https://www.science.org/doi/full/10.1126/sciadv.adg0666"],"ground_truth_type":"metadata_grounded","group_id":"6f8cbb5e1827a6411a78ef15c4902faf0325356a1828e29f28660efdacb74eab","hard_case_family":["multiple_sources"],"id":"RHM-fb2032f79d351d3203db867d","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:09.960411+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f3d8f52a1a12ba8e3a85266c887134296fd3686fb5ffec1a38526e2b8ccdcc24_0.json","raw_sha256":"b1b59ebb5f220f357ffaa8464594a3d8f391df66ad06b024355499ef7eff18cb","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=8&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"ceno980","profile_url":"https://biology.stackexchange.com/users/62032/ceno980","user_type":"registered"},"created_at":"2023-11-26T03:01:28+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"9303BEAB-A6F6-446A-81D0-7CFE38888885","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9303BEAB-A6F6-446A-81D0-7CFE38888885/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113561","source_record_sha256":"c989391f685d216c3cecdb924000ab7eba2e14fb8c1e6a391d3abfbc32cd4dfb","source_url":"https://biology.stackexchange.com/questions/113561/why-doesnt-treating-neurons-with-a-high-sodium-solution-depolarize-their-membra","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Why doesn't treating neurons with a high sodium solution depolarize their membranes?\nI am reading a journal paper (https://www.science.org/doi/full/10.1126/sciadv.adg0666), and in one of their experiments they treated organotypic hippocampal slice cultures with a high potassium solution to depolarize the neuronal membranes:\n\n\n\n\n\n\n\nWe found that the medium from control slices, transduced with\nAAV-CMV-LacZ, incubated in high potassium solution (+20 mM) over 24\nhours contained statistically significantly higher IGF1 than that in\nhigh sodium solution (+20 mM), consistent with our hypothesis that\nIGF1 is released from pyramidal neurons in an activity-dependent\nmanner.\n\n\n\n\n\n\n\nI know that increasing extracellular KCl concentrations is commonly used to depolarize neurons in experiments. I have read that the resting neuronal membrane is highly permeable to K+, and that the membrane potential is sensitive to changes in extracellular K+ concentration. Increasing extracellular K+ depolarizes membranes.\n\n\n\n\nThis is due to the influx of K+ ions through potassium leak channels (though neurons also have voltage-gated K+ channels, I'm assuming that they have more potassium leak channels).\n\n\n\n\nUnder resting conditions, there is a higher concentration of Na+ ions in the extracellular fluid compared to the cytosol of the neuron.\n\n\n\n\nAt rest, both the electrical and diffusion forces are driving Na+ towards the inside of the neuron (since the inside of the neuron is more negatively charged compared to the extracellular space).\n\n\n\n\nIn the paper, they incubated neurons for 24 hours in serum-free medium plus 20 mM NaCl.\n\n\n\n\nHowever, increasing extracellular Na+ levels did not depolarize the neuronal membrane (unlike increasing extracellular K+ levels).\n\n\n\n\nWhy is this the case? I know that the neuronal membrane contains voltage-gated sodium channels and sodium leak channels. Is it because neurons have a higher number of voltage-gated sodium channels in their membranes compared to sodium leak channels?\n\n\n\n\nI.e. to depolarize the membrane, the Na+ leak channels are not enough, you also need the opening of the voltage-gated Na+ channels.\n\n\n\n\nAny advice is appreciated.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113563,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>A [drupe][1] is defined as a fleshy fruit, that does not open at maturity, with a single seed enclosed in a hard shell. Against all evidence, a coconut is a fleshy fruit - that corky brown husk around the seed is botanically the same as the flesh of a mango or a grape. Coconut fruits <em>never</em> contain more than one seed, and that seed is contained within a hard, woody shell. So, coconuts meet all of the technical criteria to be drupes.</p>\n<p>EDIT:The fleshy part of a pomegranate seed is a sarcotesta, a fleshy outer seed coat, not an aril, which is a growth separate from the seed coat attached to the seed's hilum.\n[1]: <a href=\"https://en.wikipedia.org/wiki/Drupe\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/Drupe</a></p>\n","answer_id":114485,"answer_text":"A [drupe][1] is defined as a fleshy fruit, that does not open at maturity, with a single seed enclosed in a hard shell. Against all evidence, a coconut is a fleshy fruit - that corky brown husk around the seed is botanically the same as the flesh of a mango or a grape. Coconut fruits never contain more than one seed, and that seed is contained within a hard, woody shell. So, coconuts meet all of the technical criteria to be drupes.\n\n\n\n\nEDIT:The fleshy part of a pomegranate seed is a sarcotesta, a fleshy outer seed coat, not an aril, which is a growth separate from the seed coat attached to the seed's hilum.\n[1]: https://en.wikipedia.org/wiki/Drupe (https://en.wikipedia.org/wiki/Drupe)","answer_url":"https://biology.stackexchange.com/a/114485","author":"Sir Thinksalot","author_url":"https://biology.stackexchange.com/users/77161/sir-thinksalot","content_license":"CC BY-SA 4.0","created_at":"2024-04-12T16:40:17+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:34.916452+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/c30b2ee4524dfb46e5f33f4b25903a084dac408b994a072a95a23d5316da77d4_0.json","raw_sha256":"d256e999531c4e9fa8d45412ad1eaf748ed7e9e1e333fecd19223242a3776160","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113978;113977;113976;113967;113965;113959;113955;113947;113946;113937;113936;113924;113918;113912;113907;113904;113902;113898;113897;113887;113884;113873;113869;113863;113858;113855;113849;113846;113836;113833;113828;113827;113822;113811;113810;113806;113795;113788;113781;113780;113777;113775;113773;113763;113761;113748;113747;113739;113738;113734;113722;113715;113712;113694;113688;113681;113678;113677;113655;113654;113648;113647;113643;113642;113638;113634;113633;113631;113614;113611;113599;113598;113596;113595;113593;113590;113581;113576;113575;113570;113569;113566;113561;113557;113554;113551;113545;113537;113534;113531;113515;113508;113507;113505;113498;113491;113484;113483;113471;113469/answers?filter=withbody&order=asc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113569,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Sir Thinksalot","profile_url":"https://biology.stackexchange.com/users/77161/sir-thinksalot","user_type":"registered"},"created_at":"2024-04-12T16:40:17+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"98CC8FC9-2929-47E7-A421-21279507F760","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/98CC8FC9-2929-47E7-A421-21279507F760/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Sir Thinksalot","profile_url":"https://biology.stackexchange.com/users/77161/sir-thinksalot","user_type":"registered"},"created_at":"2024-04-13T05:53:46+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"CFBBBCDA-025F-4C4C-B295-4B42593D36F3","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CFBBBCDA-025F-4C4C-B295-4B42593D36F3/view-source"},{"content_license":null,"contributor":{"display_name":"theforestecologist","profile_url":"https://biology.stackexchange.com/users/16866/theforestecologist","user_type":"registered"},"created_at":"2024-05-14T03:34:26+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"D29FA2DD-F9B2-4733-9F5C-578ED5B929C6","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/D29FA2DD-F9B2-4733-9F5C-578ED5B929C6/view-source"}],"score":0},{"answer_html":"<p>The <a href=\"https://en.wikipedia.org/wiki/Drupe\" rel=\"nofollow noreferrer\">drupe</a> definition from other answers is correct: it is a fruit with a fleshy outer part (exocarp and mesocarp), and a single hard endocarp. A drupe does not split open on its own (it is indehiscent).</p>\n<p>A coconut fruit matches this description. The exocarp and mesocarp are fibrous (which botanically counts as fleshy), and the endocarp is hardened.</p>\n<p><img src=\"https://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Cocos_nucifera_%28coconut%29_5_%2838507429165%29.jpg/310px-Cocos_nucifera_%28coconut%29_5_%2838507429165%29.jpg\" alt=\"A niu kafa coconut split longitudinally showing the fibrous mesocarp, white endosperm, and solid endocarp between the two. The seed coat is too thin to be visible.\" title=\"The fibrous part of this coconut is the mesocarp.\" /></p>\n<p><img src=\"https://upload.wikimedia.org/wikipedia/commons/thumb/f/f1/Coconuts_-_single_and_cracked_open.jpg/320px-Coconuts_-_single_and_cracked_open.jpg\" alt=\"Two shucked coconuts, one intact and one split open. The hard shell of a shucked coconut is the endocarp. The seed coat is barely visible in the split coconut between the white endosperm and the dark brown endocarp.\" title=\"The hard brown shell of a shucked coconut is the endocarp. The seed coat is just visible between the white endosperm and the endocarp.\" /></p>\n<p>The hard shell of the shucked coconut is the endocarp, and is derived from the ovary wall. The white flesh is part of the seed, called endosperm, and the outermost layer of the seed is the seed coat. The seed coat is a very thin layer between the hard, dark brown endoderm and the endosperm.</p>\n<p>A coconut also only contains one locule, or chamber of the ovary.</p>\n<p>A durian, on the other hand, is a very different fruit architecture. A durian fruit contains multiple locules, and these will eventually split apart once the fruit is ripe enough (it is dehiscent). This makes it a type of fruit called a capsule. Capsules are normally described as &quot;dry fruits&quot; by botanists, but that descriptor is a little stretched here since the exo- meso- and endocarp that make up the walls and structure of the ovary chambers are, if not soft and pulpy, not exactly hard or papery.</p>\n<p>The soft fleshy part of the durian that people eat is a part of the seed called an aril. Not all seeds have an aril—it's an extra fleshy bit on the outside of the seed that usually enhances seed distribution. (The red juicy bit of a pomegranate seed is also an aril.)</p>\n<p>Finally, often the layers of a fruit can be hard to distinguish because they are compressed or of a similar structure. Botanists can identify fruit layers by tracking the development of the fruit and what the young tissues become.</p>\n","answer_id":114487,"answer_text":"The drupe (https://en.wikipedia.org/wiki/Drupe) definition from other answers is correct: it is a fruit with a fleshy outer part (exocarp and mesocarp), and a single hard endocarp. A drupe does not split open on its own (it is indehiscent).\n\n\n\n\nA coconut fruit matches this description. The exocarp and mesocarp are fibrous (which botanically counts as fleshy), and the endocarp is hardened.\n\n\n\n\n[image: A niu kafa coconut split longitudinally showing the fibrous mesocarp, white endosperm, and solid endocarp between the two. The seed coat is too thin to be visible.; source: https://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Cocos_nucifera_%28coconut%29_5_%2838507429165%29.jpg/310px-Cocos_nucifera_%28coconut%29_5_%2838507429165%29.jpg]\n\n\n\n\n[image: Two shucked coconuts, one intact and one split open. The hard shell of a shucked coconut is the endocarp. The seed coat is barely visible in the split coconut between the white endosperm and the dark brown endocarp.; source: https://upload.wikimedia.org/wikipedia/commons/thumb/f/f1/Coconuts_-_single_and_cracked_open.jpg/320px-Coconuts_-_single_and_cracked_open.jpg]\n\n\n\n\nThe hard shell of the shucked coconut is the endocarp, and is derived from the ovary wall. The white flesh is part of the seed, called endosperm, and the outermost layer of the seed is the seed coat. The seed coat is a very thin layer between the hard, dark brown endoderm and the endosperm.\n\n\n\n\nA coconut also only contains one locule, or chamber of the ovary.\n\n\n\n\nA durian, on the other hand, is a very different fruit architecture. A durian fruit contains multiple locules, and these will eventually split apart once the fruit is ripe enough (it is dehiscent). This makes it a type of fruit called a capsule. Capsules are normally described as \"dry fruits\" by botanists, but that descriptor is a little stretched here since the exo- meso- and endocarp that make up the walls and structure of the ovary chambers are, if not soft and pulpy, not exactly hard or papery.\n\n\n\n\nThe soft fleshy part of the durian that people eat is a part of the seed called an aril. Not all seeds have an aril—it's an extra fleshy bit on the outside of the seed that usually enhances seed distribution. (The red juicy bit of a pomegranate seed is also an aril.)\n\n\n\n\nFinally, often the layers of a fruit can be hard to distinguish because they are compressed or of a similar structure. Botanists can identify fruit layers by tracking the development of the fruit and what the young tissues become.","answer_url":"https://biology.stackexchange.com/a/114487","author":"Darlingtonia","author_url":"https://biology.stackexchange.com/users/1197/darlingtonia","content_license":"CC BY-SA 4.0","created_at":"2024-04-12T22:34:00+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:34.916452+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/c30b2ee4524dfb46e5f33f4b25903a084dac408b994a072a95a23d5316da77d4_0.json","raw_sha256":"d256e999531c4e9fa8d45412ad1eaf748ed7e9e1e333fecd19223242a3776160","source_api":"Stack Exchange API 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4.0","contributor":{"display_name":"Darlingtonia","profile_url":"https://biology.stackexchange.com/users/1197/darlingtonia","user_type":"registered"},"created_at":"2024-04-12T22:34:00+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"C32F768B-B53F-48BE-8DB0-58C1D4BEFBD6","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C32F768B-B53F-48BE-8DB0-58C1D4BEFBD6/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Jj Luntayan","author_url":"https://biology.stackexchange.com/users/76757/jj-luntayan","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Jj Luntayan","profile_url":"https://biology.stackexchange.com/users/76757/jj-luntayan","user_type":"registered"},"created_at":"2023-11-27T01:23:08+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"958D2C50-379C-44F7-ABDB-9788D0FB80B2","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/958D2C50-379C-44F7-ABDB-9788D0FB80B2/view-source"},{"content_license":null,"contributor":{"display_name":"Darlingtonia","profile_url":"https://biology.stackexchange.com/users/1197/darlingtonia","user_type":"registered"},"created_at":"2024-04-12T22:38:26+00:00","raw_file":"raw/codex_api_v1/4b31ece29d49640766904acfb09f413caa800382e2048749dca713fe1c36c614_1790824046659275600_0.json","raw_sha256":"d34fed5816d7a26a5c9619cd4bcaa8f6e5ab3886f8bed7f16f08fb06ee93b82d","revision_guid":"90E11F99-92CC-424A-9C61-922EF9ABBB1C","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/90E11F99-92CC-424A-9C61-922EF9ABBB1C/view-source"}],"url":"https://biology.stackexchange.com/questions/113569/why-is-coconut-a-fleshy-fruit"},{"author":"Sir Thinksalot","author_url":"https://biology.stackexchange.com/users/77161/sir-thinksalot","content_license":"CC BY-SA 4.0","context_id":"114485","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Sir Thinksalot","profile_url":"https://biology.stackexchange.com/users/77161/sir-thinksalot","user_type":"registered"},"created_at":"2024-04-12T16:40:17+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"98CC8FC9-2929-47E7-A421-21279507F760","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/98CC8FC9-2929-47E7-A421-21279507F760/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Sir Thinksalot","profile_url":"https://biology.stackexchange.com/users/77161/sir-thinksalot","user_type":"registered"},"created_at":"2024-04-13T05:53:46+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"CFBBBCDA-025F-4C4C-B295-4B42593D36F3","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CFBBBCDA-025F-4C4C-B295-4B42593D36F3/view-source"},{"content_license":null,"contributor":{"display_name":"theforestecologist","profile_url":"https://biology.stackexchange.com/users/16866/theforestecologist","user_type":"registered"},"created_at":"2024-05-14T03:34:26+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"D29FA2DD-F9B2-4733-9F5C-578ED5B929C6","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/D29FA2DD-F9B2-4733-9F5C-578ED5B929C6/view-source"}],"url":"https://biology.stackexchange.com/a/114485"},{"author":"Darlingtonia","author_url":"https://biology.stackexchange.com/users/1197/darlingtonia","content_license":"CC BY-SA 4.0","context_id":"114487","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Darlingtonia","profile_url":"https://biology.stackexchange.com/users/1197/darlingtonia","user_type":"registered"},"created_at":"2024-04-12T22:34:00+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"C32F768B-B53F-48BE-8DB0-58C1D4BEFBD6","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C32F768B-B53F-48BE-8DB0-58C1D4BEFBD6/view-source"}],"url":"https://biology.stackexchange.com/a/114487"}],"contexts":[{"context_id":"question","html":"<p>Firstly, I understand that it is classified as a drupe and its mesocarp is fibrous hence its hardness. However, how did botanists conclude such? Putting both mango and coconut side by side, we can at least see that the mango has fleshy mesocarp and soft exocarp. I would argue that the coconut's structure bears more similarity to the durian yet the latter is a capsule (or dry).</p>\n<p>With that in mind, I cannot comprehend how the pericarp is distinguishable in 3 layers in coconut but not in durian yet they seem to be same? If coconut is like a deviant under drupes due to its fibrous mesocarp, (1) how'd they even distinguish that it was a mesocarp and (2) what is the clincher that made them conclude that coconut is indeed a fleshy and drupe despite seemingly deviant from common examples such as mango?</p>\n<p>Apologies for not being articulate enough to explain.</p>\n","text":"Firstly, I understand that it is classified as a drupe and its mesocarp is fibrous hence its hardness. However, how did botanists conclude such? Putting both mango and coconut side by side, we can at least see that the mango has fleshy mesocarp and soft exocarp. I would argue that the coconut's structure bears more similarity to the durian yet the latter is a capsule (or dry).\n\n\n\n\nWith that in mind, I cannot comprehend how the pericarp is distinguishable in 3 layers in coconut but not in durian yet they seem to be same? If coconut is like a deviant under drupes due to its fibrous mesocarp, (1) how'd they even distinguish that it was a mesocarp and (2) what is the clincher that made them conclude that coconut is indeed a fleshy and drupe despite seemingly deviant from common examples such as mango?\n\n\n\n\nApologies for not being articulate enough to explain."},{"context_id":"114485","html":"<p>A [drupe][1] is defined as a fleshy fruit, that does not open at maturity, with a single seed enclosed in a hard shell. Against all evidence, a coconut is a fleshy fruit - that corky brown husk around the seed is botanically the same as the flesh of a mango or a grape. Coconut fruits <em>never</em> contain more than one seed, and that seed is contained within a hard, woody shell. So, coconuts meet all of the technical criteria to be drupes.</p>\n<p>EDIT:The fleshy part of a pomegranate seed is a sarcotesta, a fleshy outer seed coat, not an aril, which is a growth separate from the seed coat attached to the seed's hilum.\n[1]: <a href=\"https://en.wikipedia.org/wiki/Drupe\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/Drupe</a></p>\n","text":"A [drupe][1] is defined as a fleshy fruit, that does not open at maturity, with a single seed enclosed in a hard shell. Against all evidence, a coconut is a fleshy fruit - that corky brown husk around the seed is botanically the same as the flesh of a mango or a grape. Coconut fruits never contain more than one seed, and that seed is contained within a hard, woody shell. So, coconuts meet all of the technical criteria to be drupes.\n\n\n\n\nEDIT:The fleshy part of a pomegranate seed is a sarcotesta, a fleshy outer seed coat, not an aril, which is a growth separate from the seed coat attached to the seed's hilum.\n[1]: https://en.wikipedia.org/wiki/Drupe (https://en.wikipedia.org/wiki/Drupe)"},{"context_id":"114487","html":"<p>The <a href=\"https://en.wikipedia.org/wiki/Drupe\" rel=\"nofollow noreferrer\">drupe</a> definition from other answers is correct: it is a fruit with a fleshy outer part (exocarp and mesocarp), and a single hard endocarp. A drupe does not split open on its own (it is indehiscent).</p>\n<p>A coconut fruit matches this description. The exocarp and mesocarp are fibrous (which botanically counts as fleshy), and the endocarp is hardened.</p>\n<p><img src=\"https://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Cocos_nucifera_%28coconut%29_5_%2838507429165%29.jpg/310px-Cocos_nucifera_%28coconut%29_5_%2838507429165%29.jpg\" alt=\"A niu kafa coconut split longitudinally showing the fibrous mesocarp, white endosperm, and solid endocarp between the two. The seed coat is too thin to be visible.\" title=\"The fibrous part of this coconut is the mesocarp.\" /></p>\n<p><img src=\"https://upload.wikimedia.org/wikipedia/commons/thumb/f/f1/Coconuts_-_single_and_cracked_open.jpg/320px-Coconuts_-_single_and_cracked_open.jpg\" alt=\"Two shucked coconuts, one intact and one split open. The hard shell of a shucked coconut is the endocarp. The seed coat is barely visible in the split coconut between the white endosperm and the dark brown endocarp.\" title=\"The hard brown shell of a shucked coconut is the endocarp. The seed coat is just visible between the white endosperm and the endocarp.\" /></p>\n<p>The hard shell of the shucked coconut is the endocarp, and is derived from the ovary wall. The white flesh is part of the seed, called endosperm, and the outermost layer of the seed is the seed coat. The seed coat is a very thin layer between the hard, dark brown endoderm and the endosperm.</p>\n<p>A coconut also only contains one locule, or chamber of the ovary.</p>\n<p>A durian, on the other hand, is a very different fruit architecture. A durian fruit contains multiple locules, and these will eventually split apart once the fruit is ripe enough (it is dehiscent). This makes it a type of fruit called a capsule. Capsules are normally described as &quot;dry fruits&quot; by botanists, but that descriptor is a little stretched here since the exo- meso- and endocarp that make up the walls and structure of the ovary chambers are, if not soft and pulpy, not exactly hard or papery.</p>\n<p>The soft fleshy part of the durian that people eat is a part of the seed called an aril. Not all seeds have an aril—it's an extra fleshy bit on the outside of the seed that usually enhances seed distribution. (The red juicy bit of a pomegranate seed is also an aril.)</p>\n<p>Finally, often the layers of a fruit can be hard to distinguish because they are compressed or of a similar structure. Botanists can identify fruit layers by tracking the development of the fruit and what the young tissues become.</p>\n","text":"The drupe (https://en.wikipedia.org/wiki/Drupe) definition from other answers is correct: it is a fruit with a fleshy outer part (exocarp and mesocarp), and a single hard endocarp. A drupe does not split open on its own (it is indehiscent).\n\n\n\n\nA coconut fruit matches this description. The exocarp and mesocarp are fibrous (which botanically counts as fleshy), and the endocarp is hardened.\n\n\n\n\n[image: A niu kafa coconut split longitudinally showing the fibrous mesocarp, white endosperm, and solid endocarp between the two. The seed coat is too thin to be visible.; source: https://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Cocos_nucifera_%28coconut%29_5_%2838507429165%29.jpg/310px-Cocos_nucifera_%28coconut%29_5_%2838507429165%29.jpg]\n\n\n\n\n[image: Two shucked coconuts, one intact and one split open. The hard shell of a shucked coconut is the endocarp. The seed coat is barely visible in the split coconut between the white endosperm and the dark brown endocarp.; source: https://upload.wikimedia.org/wikipedia/commons/thumb/f/f1/Coconuts_-_single_and_cracked_open.jpg/320px-Coconuts_-_single_and_cracked_open.jpg]\n\n\n\n\nThe hard shell of the shucked coconut is the endocarp, and is derived from the ovary wall. The white flesh is part of the seed, called endosperm, and the outermost layer of the seed is the seed coat. The seed coat is a very thin layer between the hard, dark brown endoderm and the endosperm.\n\n\n\n\nA coconut also only contains one locule, or chamber of the ovary.\n\n\n\n\nA durian, on the other hand, is a very different fruit architecture. A durian fruit contains multiple locules, and these will eventually split apart once the fruit is ripe enough (it is dehiscent). This makes it a type of fruit called a capsule. Capsules are normally described as \"dry fruits\" by botanists, but that descriptor is a little stretched here since the exo- meso- and endocarp that make up the walls and structure of the ovary chambers are, if not soft and pulpy, not exactly hard or papery.\n\n\n\n\nThe soft fleshy part of the durian that people eat is a part of the seed called an aril. Not all seeds have an aril—it's an extra fleshy bit on the outside of the seed that usually enhances seed distribution. (The red juicy bit of a pomegranate seed is also an aril.)\n\n\n\n\nFinally, often the layers of a fruit can be hard to distinguish because they are compressed or of a similar structure. Botanists can identify fruit layers by tracking the development of the fruit and what the young tissues become."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Drupe"],"ground_truth_type":"metadata_grounded","group_id":"6e66b2582666c546dc9d3f4bd45d76713ad05e8222bc0a338cc5767aedec6edf","hard_case_family":["no_accepted_answer","multiple_answer_candidates"],"id":"RHM-f5d5ae77c8e9de96e49db6b2","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:09.960411+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f3d8f52a1a12ba8e3a85266c887134296fd3686fb5ffec1a38526e2b8ccdcc24_0.json","raw_sha256":"b1b59ebb5f220f357ffaa8464594a3d8f391df66ad06b024355499ef7eff18cb","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=8&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Jj Luntayan","profile_url":"https://biology.stackexchange.com/users/76757/jj-luntayan","user_type":"registered"},"created_at":"2023-11-27T01:23:08+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"958D2C50-379C-44F7-ABDB-9788D0FB80B2","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/958D2C50-379C-44F7-ABDB-9788D0FB80B2/view-source"},{"content_license":null,"contributor":{"display_name":"Darlingtonia","profile_url":"https://biology.stackexchange.com/users/1197/darlingtonia","user_type":"registered"},"created_at":"2024-04-12T22:38:26+00:00","raw_file":"raw/codex_api_v1/4b31ece29d49640766904acfb09f413caa800382e2048749dca713fe1c36c614_1790824046659275600_0.json","raw_sha256":"d34fed5816d7a26a5c9619cd4bcaa8f6e5ab3886f8bed7f16f08fb06ee93b82d","revision_guid":"90E11F99-92CC-424A-9C61-922EF9ABBB1C","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/90E11F99-92CC-424A-9C61-922EF9ABBB1C/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113569","source_record_sha256":"b3cedf777190f26507f500dec6a896b89f01dfc887ea4e1f69f0616afe9baf99","source_url":"https://biology.stackexchange.com/questions/113569/why-is-coconut-a-fleshy-fruit","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Why is coconut a fleshy fruit?\nFirstly, I understand that it is classified as a drupe and its mesocarp is fibrous hence its hardness. However, how did botanists conclude such? Putting both mango and coconut side by side, we can at least see that the mango has fleshy mesocarp and soft exocarp. I would argue that the coconut's structure bears more similarity to the durian yet the latter is a capsule (or dry).\n\n\n\n\nWith that in mind, I cannot comprehend how the pericarp is distinguishable in 3 layers in coconut but not in durian yet they seem to be same? If coconut is like a deviant under drupes due to its fibrous mesocarp, (1) how'd they even distinguish that it was a mesocarp and (2) what is the clincher that made them conclude that coconut is indeed a fleshy and drupe despite seemingly deviant from common examples such as mango?\n\n\n\n\nApologies for not being articulate enough to explain.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114485,"score":0},{"answer_id":114487,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>When <a href=\"https://en.wikipedia.org/wiki/Chromosomal_crossover\" rel=\"nofollow noreferrer\">crossover</a> happens, it's a whole swap from that point on, not just a little chunk. So if there's only one crossover event, then the lengths are &quot;p&quot; and &quot;100% - p&quot;, where p is the position along the chromosome. The only way to get a small piece of one chromosome amidst a mostly intact copy of the other would be for there to be two crossovers close to each other.</p>\n<p>This existing Q&amp;A talks about the rate of crossovers in human chromosomes:</p>\n<p><a href=\"https://biology.stackexchange.com/questions/19005/how-many-recombination-events-are-there-per-generation-in-humans\">How many recombination events are there per generation in humans?</a></p>\n<p>It varies by which chromosome you're talking about and other factors, but something along the order of 1 to 4 events per chromosome would be a reasonable ballpark. 0 is possible, too.</p>\n","answer_id":113577,"answer_text":"When crossover (https://en.wikipedia.org/wiki/Chromosomal_crossover) happens, it's a whole swap from that point on, not just a little chunk. So if there's only one crossover event, then the lengths are \"p\" and \"100% - p\", where p is the position along the chromosome. The only way to get a small piece of one chromosome amidst a mostly intact copy of the other would be for there to be two crossovers close to each other.\n\n\n\n\nThis existing Q&A talks about the rate of crossovers in human chromosomes:\n\n\n\n\nHow many recombination events are there per generation in humans? (https://biology.stackexchange.com/questions/19005/how-many-recombination-events-are-there-per-generation-in-humans)\n\n\n\n\nIt varies by which chromosome you're talking about and other factors, but something along the order of 1 to 4 events per chromosome would be a reasonable ballpark. 0 is possible, too.","answer_url":"https://biology.stackexchange.com/a/113577","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2023-11-28T14:28:49+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:33.526680+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/d1acc50471f82e02a014a291913995889f5ddcd7076433532102b9b97a4a3a3d_0.json","raw_sha256":"e6b5a7d5e11f0ac54d756d69e21baee1de119b759ec7e8caa7f174d67cf80eff","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113978;113977;113976;113967;113965;113959;113955;113947;113946;113937;113936;113924;113918;113912;113907;113904;113902;113898;113897;113887;113884;113873;113869;113863;113858;113855;113849;113846;113836;113833;113828;113827;113822;113811;113810;113806;113795;113788;113781;113780;113777;113775;113773;113763;113761;113748;113747;113739;113738;113734;113722;113715;113712;113694;113688;113681;113678;113677;113655;113654;113648;113647;113643;113642;113638;113634;113633;113631;113614;113611;113599;113598;113596;113595;113593;113590;113581;113576;113575;113570;113569;113566;113561;113557;113554;113551;113545;113537;113534;113531;113515;113508;113507;113505;113498;113491;113484;113483;113471;113469/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113576,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2023-11-28T14:28:49+00:00","raw_file":"raw/codex_api_v1/4b31ece29d49640766904acfb09f413caa800382e2048749dca713fe1c36c614_1790824046659275600_0.json","raw_sha256":"d34fed5816d7a26a5c9619cd4bcaa8f6e5ab3886f8bed7f16f08fb06ee93b82d","revision_guid":"48488FDC-9143-4AE1-94BB-1E0CE9067522","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/48488FDC-9143-4AE1-94BB-1E0CE9067522/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"user265902","author_url":"https://biology.stackexchange.com/users/13384/user265902","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user265902","profile_url":"https://biology.stackexchange.com/users/13384/user265902","user_type":"registered"},"created_at":"2023-11-28T07:37:18+00:00","raw_file":"raw/codex_api_v1/4b31ece29d49640766904acfb09f413caa800382e2048749dca713fe1c36c614_1790824046659275600_0.json","raw_sha256":"d34fed5816d7a26a5c9619cd4bcaa8f6e5ab3886f8bed7f16f08fb06ee93b82d","revision_guid":"68106151-C005-402F-86BE-063A21E727F8","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/68106151-C005-402F-86BE-063A21E727F8/view-source"}],"url":"https://biology.stackexchange.com/questions/113576/how-frequently-does-recombination-occur-and-how-long-are-the-recombinated-fragm"},{"author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","context_id":"113577","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2023-11-28T14:28:49+00:00","raw_file":"raw/codex_api_v1/4b31ece29d49640766904acfb09f413caa800382e2048749dca713fe1c36c614_1790824046659275600_0.json","raw_sha256":"d34fed5816d7a26a5c9619cd4bcaa8f6e5ab3886f8bed7f16f08fb06ee93b82d","revision_guid":"48488FDC-9143-4AE1-94BB-1E0CE9067522","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/48488FDC-9143-4AE1-94BB-1E0CE9067522/view-source"}],"url":"https://biology.stackexchange.com/a/113577"}],"contexts":[{"context_id":"question","html":"<p>I understand the mechanics of recombination, but am struggling with the 'scale'.</p>\n<ol>\n<li><p>When two homologous chromosomes pair, roughly how many recombination events occur on average? I understand there will be a distribution, and it will vary between species - but are we talking one, two, or hundreds/thousands?</p>\n</li>\n<li><p>How are long are recombination fragments relative to the entire length of the chromosome? With the same caveat as above, I'm trying to get a sense of scale - 0.001%, 1%, 10%, 25%?</p>\n</li>\n</ol>\n","text":"I understand the mechanics of recombination, but am struggling with the 'scale'.\n\n\n\n\n\n\n\nWhen two homologous chromosomes pair, roughly how many recombination events occur on average? I understand there will be a distribution, and it will vary between species - but are we talking one, two, or hundreds/thousands?\n\n\n\n\n\n\n\n\n\nHow are long are recombination fragments relative to the entire length of the chromosome? With the same caveat as above, I'm trying to get a sense of scale - 0.001%, 1%, 10%, 25%?"},{"context_id":"113577","html":"<p>When <a href=\"https://en.wikipedia.org/wiki/Chromosomal_crossover\" rel=\"nofollow noreferrer\">crossover</a> happens, it's a whole swap from that point on, not just a little chunk. So if there's only one crossover event, then the lengths are &quot;p&quot; and &quot;100% - p&quot;, where p is the position along the chromosome. The only way to get a small piece of one chromosome amidst a mostly intact copy of the other would be for there to be two crossovers close to each other.</p>\n<p>This existing Q&amp;A talks about the rate of crossovers in human chromosomes:</p>\n<p><a href=\"https://biology.stackexchange.com/questions/19005/how-many-recombination-events-are-there-per-generation-in-humans\">How many recombination events are there per generation in humans?</a></p>\n<p>It varies by which chromosome you're talking about and other factors, but something along the order of 1 to 4 events per chromosome would be a reasonable ballpark. 0 is possible, too.</p>\n","text":"When crossover (https://en.wikipedia.org/wiki/Chromosomal_crossover) happens, it's a whole swap from that point on, not just a little chunk. So if there's only one crossover event, then the lengths are \"p\" and \"100% - p\", where p is the position along the chromosome. The only way to get a small piece of one chromosome amidst a mostly intact copy of the other would be for there to be two crossovers close to each other.\n\n\n\n\nThis existing Q&A talks about the rate of crossovers in human chromosomes:\n\n\n\n\nHow many recombination events are there per generation in humans? (https://biology.stackexchange.com/questions/19005/how-many-recombination-events-are-there-per-generation-in-humans)\n\n\n\n\nIt varies by which chromosome you're talking about and other factors, but something along the order of 1 to 4 events per chromosome would be a reasonable ballpark. 0 is possible, too."}],"domain":"biology","external_citations":["https://biology.stackexchange.com/questions/19005/how-many-recombination-events-are-there-per-generation-in-humans","https://en.wikipedia.org/wiki/Chromosomal_crossover"],"ground_truth_type":"metadata_grounded","group_id":"b6567648e6edcae32826b624af2714fef164ea219eb1361913ed1e3ef133615d","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-b32182c1c80919caba0d2bfb","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:09.960411+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f3d8f52a1a12ba8e3a85266c887134296fd3686fb5ffec1a38526e2b8ccdcc24_0.json","raw_sha256":"b1b59ebb5f220f357ffaa8464594a3d8f391df66ad06b024355499ef7eff18cb","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=8&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user265902","profile_url":"https://biology.stackexchange.com/users/13384/user265902","user_type":"registered"},"created_at":"2023-11-28T07:37:18+00:00","raw_file":"raw/codex_api_v1/4b31ece29d49640766904acfb09f413caa800382e2048749dca713fe1c36c614_1790824046659275600_0.json","raw_sha256":"d34fed5816d7a26a5c9619cd4bcaa8f6e5ab3886f8bed7f16f08fb06ee93b82d","revision_guid":"68106151-C005-402F-86BE-063A21E727F8","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/68106151-C005-402F-86BE-063A21E727F8/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113576","source_record_sha256":"f43c76036d7130205076ecda921115af424ed00b0d2d6e7a1e44557821293826","source_url":"https://biology.stackexchange.com/questions/113576/how-frequently-does-recombination-occur-and-how-long-are-the-recombinated-fragm","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How frequently does recombination occur, and how long are the recombinated fragments?\nI understand the mechanics of recombination, but am struggling with the 'scale'.\n\n\n\n\n\n\n\nWhen two homologous chromosomes pair, roughly how many recombination events occur on average? I understand there will be a distribution, and it will vary between species - but are we talking one, two, or hundreds/thousands?\n\n\n\n\n\n\n\n\n\nHow are long are recombination fragments relative to the entire length of the chromosome? With the same caveat as above, I'm trying to get a sense of scale - 0.001%, 1%, 10%, 25%?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113577,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>First, the definition of VHH (and VH) from the article by S Muyldermans\n— “Nanobodies: Natural Single-Domain Antibodies” in <a href=\"https://pubmed.ncbi.nlm.nih.gov/23495938/\" rel=\"nofollow noreferrer\"><em>Annu. Rev. Biochem.</em> 2013. <strong>82</strong>:775–97</a>.</p>\n<blockquote>\n<p><strong>VHH</strong>: antigen-binding variable domain of the H chain of heavy-chain\nantibodies</p>\n</blockquote>\n<blockquote>\n<p><strong>VH</strong>: the variable domain of the heavy chain of\nimmunoglobulins</p>\n</blockquote>\n<p>So the poster’s definition is incorrect — the term VHH refers to a single domain of the antibody, not the (single-domain) antibody itself.</p>\n<p>Why use this acronym, rather than VH, which seems equally applicable? The key point, of which I admit I was not previously aware, is that camels possess <em>both</em> ‘normal’ antibodies composed of heavy and light chains, <em>as well as</em> these special ones with only heavy chains. This is shown in the diagram below, adapted from the original <a href=\"https://www.nature.com/articles/363446a0\" rel=\"nofollow noreferrer\">Nature paper describing these antibodies</a>. It actually uses V<sub>H</sub> in both cases:<br>\n<a href=\"https://i.sstatic.net/1pS1Z.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/1pS1Z.png\" alt=\"Camelid Abs compared\" /></a><br>\nSo one can imagine that  the term VHH  was introduced for convenience when talking about the variable heavy domain of both camelid types. (I haven’t searched for the original myself.) This also emphasizes the point that (presumably) emerged later, that the VH region of the two types of camelid antibody had different genetic origins (IGHV3 and IGHV3H) shown in the diagram below, taken from the Muyldermans review.<br>\n<a href=\"https://i.sstatic.net/JS4Tx.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/JS4Tx.png\" alt=\"camelid VH genes\" /></a></p>\n<p>In conclusion, the poster’s assumption was incorrect: the additional H stands for “(of) <strong>H</strong>eavy-chain antibody”.</p>\n","answer_id":113718,"answer_text":"First, the definition of VHH (and VH) from the article by S Muyldermans\n— “Nanobodies: Natural Single-Domain Antibodies” in Annu. Rev. Biochem. 2013. 82:775–97 (https://pubmed.ncbi.nlm.nih.gov/23495938/).\n\n\n\n\n\n\n\nVHH: antigen-binding variable domain of the H chain of heavy-chain\nantibodies\n\n\n\n\n\n\n\n\n\n\nVH: the variable domain of the heavy chain of\nimmunoglobulins\n\n\n\n\n\n\n\nSo the poster’s definition is incorrect — the term VHH refers to a single domain of the antibody, not the (single-domain) antibody itself.\n\n\n\n\nWhy use this acronym, rather than VH, which seems equally applicable? The key point, of which I admit I was not previously aware, is that camels possess both ‘normal’ antibodies composed of heavy and light chains, as well as these special ones with only heavy chains. This is shown in the diagram below, adapted from the original Nature paper describing these antibodies (https://www.nature.com/articles/363446a0). It actually uses VH in both cases:\n\n[image: Camelid Abs compared; source: https://i.sstatic.net/1pS1Z.png] (https://i.sstatic.net/1pS1Z.png)\n\nSo one can imagine that  the term VHH  was introduced for convenience when talking about the variable heavy domain of both camelid types. (I haven’t searched for the original myself.) This also emphasizes the point that (presumably) emerged later, that the VH region of the two types of camelid antibody had different genetic origins (IGHV3 and IGHV3H) shown in the diagram below, taken from the Muyldermans review.\n\n[image: camelid VH genes; source: https://i.sstatic.net/JS4Tx.png] (https://i.sstatic.net/JS4Tx.png)\n\n\n\n\nIn conclusion, the poster’s assumption was incorrect: the additional H stands for “(of) Heavy-chain antibody”.","answer_url":"https://biology.stackexchange.com/a/113718","author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","created_at":"2023-12-22T13:07:32+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:33.526680+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/d1acc50471f82e02a014a291913995889f5ddcd7076433532102b9b97a4a3a3d_0.json","raw_sha256":"e6b5a7d5e11f0ac54d756d69e21baee1de119b759ec7e8caa7f174d67cf80eff","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113978;113977;113976;113967;113965;113959;113955;113947;113946;113937;113936;113924;113918;113912;113907;113904;113902;113898;113897;113887;113884;113873;113869;113863;113858;113855;113849;113846;113836;113833;113828;113827;113822;113811;113810;113806;113795;113788;113781;113780;113777;113775;113773;113763;113761;113748;113747;113739;113738;113734;113722;113715;113712;113694;113688;113681;113678;113677;113655;113654;113648;113647;113643;113642;113638;113634;113633;113631;113614;113611;113599;113598;113596;113595;113593;113590;113581;113576;113575;113570;113569;113566;113561;113557;113554;113551;113545;113537;113534;113531;113515;113508;113507;113505;113498;113491;113484;113483;113471;113469/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113712,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2023-12-22T13:07:32+00:00","raw_file":"raw/codex_api_v1/4b76a36d403acfa9117b7f3b75e82752ff87ef3625482a25f27c7a9f24c1f834_1790824054076617800_0.json","raw_sha256":"f49ea509a52f9f9993721157653fc6d23e3725c8e5ccf6806a681a879219d452","revision_guid":"25CD1554-D6CA-4E8D-949D-87E16BB24EE6","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/25CD1554-D6CA-4E8D-949D-87E16BB24EE6/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"mgarort","author_url":"https://biology.stackexchange.com/users/78254/mgarort","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"mgarort","profile_url":"https://biology.stackexchange.com/users/78254/mgarort","user_type":"registered"},"created_at":"2023-12-21T13:41:00+00:00","raw_file":"raw/codex_api_v1/4b76a36d403acfa9117b7f3b75e82752ff87ef3625482a25f27c7a9f24c1f834_1790824054076617800_0.json","raw_sha256":"f49ea509a52f9f9993721157653fc6d23e3725c8e5ccf6806a681a879219d452","revision_guid":"E39F7A4D-39B5-46A4-A2D4-B820601E783A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E39F7A4D-39B5-46A4-A2D4-B820601E783A/view-source"}],"url":"https://biology.stackexchange.com/questions/113712/why-are-camelid-derived-nanobodies-called-vhh-variable-heavy-domain-of-heavy-ch"},{"author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","context_id":"113718","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2023-12-22T13:07:32+00:00","raw_file":"raw/codex_api_v1/4b76a36d403acfa9117b7f3b75e82752ff87ef3625482a25f27c7a9f24c1f834_1790824054076617800_0.json","raw_sha256":"f49ea509a52f9f9993721157653fc6d23e3725c8e5ccf6806a681a879219d452","revision_guid":"25CD1554-D6CA-4E8D-949D-87E16BB24EE6","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/25CD1554-D6CA-4E8D-949D-87E16BB24EE6/view-source"}],"url":"https://biology.stackexchange.com/a/113718"}],"contexts":[{"context_id":"question","html":"<p>Single-domain antibodies (or nanobodies) derived from camelid heavy-chain antibodies are called VHH antibodies, where VHH stands for &quot;variable heavy domain of heavy chain&quot;. I assume the reason for this name is that the variable domain in the heavy-chain camelid antibody is heavier than other domains. However, I haven't been able to find the weight of each domain in the camelid antibody in order to verify my assumption.</p>\n<p>Why are single-domain antibodies derived from camelids called &quot;variable heavy domain of heavy chain&quot;?</p>\n","text":"Single-domain antibodies (or nanobodies) derived from camelid heavy-chain antibodies are called VHH antibodies, where VHH stands for \"variable heavy domain of heavy chain\". I assume the reason for this name is that the variable domain in the heavy-chain camelid antibody is heavier than other domains. However, I haven't been able to find the weight of each domain in the camelid antibody in order to verify my assumption.\n\n\n\n\nWhy are single-domain antibodies derived from camelids called \"variable heavy domain of heavy chain\"?"},{"context_id":"113718","html":"<p>First, the definition of VHH (and VH) from the article by S Muyldermans\n— “Nanobodies: Natural Single-Domain Antibodies” in <a href=\"https://pubmed.ncbi.nlm.nih.gov/23495938/\" rel=\"nofollow noreferrer\"><em>Annu. Rev. Biochem.</em> 2013. <strong>82</strong>:775–97</a>.</p>\n<blockquote>\n<p><strong>VHH</strong>: antigen-binding variable domain of the H chain of heavy-chain\nantibodies</p>\n</blockquote>\n<blockquote>\n<p><strong>VH</strong>: the variable domain of the heavy chain of\nimmunoglobulins</p>\n</blockquote>\n<p>So the poster’s definition is incorrect — the term VHH refers to a single domain of the antibody, not the (single-domain) antibody itself.</p>\n<p>Why use this acronym, rather than VH, which seems equally applicable? The key point, of which I admit I was not previously aware, is that camels possess <em>both</em> ‘normal’ antibodies composed of heavy and light chains, <em>as well as</em> these special ones with only heavy chains. This is shown in the diagram below, adapted from the original <a href=\"https://www.nature.com/articles/363446a0\" rel=\"nofollow noreferrer\">Nature paper describing these antibodies</a>. It actually uses V<sub>H</sub> in both cases:<br>\n<a href=\"https://i.sstatic.net/1pS1Z.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/1pS1Z.png\" alt=\"Camelid Abs compared\" /></a><br>\nSo one can imagine that  the term VHH  was introduced for convenience when talking about the variable heavy domain of both camelid types. (I haven’t searched for the original myself.) This also emphasizes the point that (presumably) emerged later, that the VH region of the two types of camelid antibody had different genetic origins (IGHV3 and IGHV3H) shown in the diagram below, taken from the Muyldermans review.<br>\n<a href=\"https://i.sstatic.net/JS4Tx.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/JS4Tx.png\" alt=\"camelid VH genes\" /></a></p>\n<p>In conclusion, the poster’s assumption was incorrect: the additional H stands for “(of) <strong>H</strong>eavy-chain antibody”.</p>\n","text":"First, the definition of VHH (and VH) from the article by S Muyldermans\n— “Nanobodies: Natural Single-Domain Antibodies” in Annu. Rev. Biochem. 2013. 82:775–97 (https://pubmed.ncbi.nlm.nih.gov/23495938/).\n\n\n\n\n\n\n\nVHH: antigen-binding variable domain of the H chain of heavy-chain\nantibodies\n\n\n\n\n\n\n\n\n\n\nVH: the variable domain of the heavy chain of\nimmunoglobulins\n\n\n\n\n\n\n\nSo the poster’s definition is incorrect — the term VHH refers to a single domain of the antibody, not the (single-domain) antibody itself.\n\n\n\n\nWhy use this acronym, rather than VH, which seems equally applicable? The key point, of which I admit I was not previously aware, is that camels possess both ‘normal’ antibodies composed of heavy and light chains, as well as these special ones with only heavy chains. This is shown in the diagram below, adapted from the original Nature paper describing these antibodies (https://www.nature.com/articles/363446a0). It actually uses VH in both cases:\n\n[image: Camelid Abs compared; source: https://i.sstatic.net/1pS1Z.png] (https://i.sstatic.net/1pS1Z.png)\n\nSo one can imagine that  the term VHH  was introduced for convenience when talking about the variable heavy domain of both camelid types. (I haven’t searched for the original myself.) This also emphasizes the point that (presumably) emerged later, that the VH region of the two types of camelid antibody had different genetic origins (IGHV3 and IGHV3H) shown in the diagram below, taken from the Muyldermans review.\n\n[image: camelid VH genes; source: https://i.sstatic.net/JS4Tx.png] (https://i.sstatic.net/JS4Tx.png)\n\n\n\n\nIn conclusion, the poster’s assumption was incorrect: the additional H stands for “(of) Heavy-chain antibody”."}],"domain":"biology","external_citations":["https://i.sstatic.net/1pS1Z.png","https://i.sstatic.net/JS4Tx.png","https://pubmed.ncbi.nlm.nih.gov/23495938/","https://www.nature.com/articles/363446a0"],"ground_truth_type":"metadata_grounded","group_id":"9f42cee8ef3d39db686cc1d286e269be949fa24de3efa92ced607775b3bb95c7","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-005504a84ccf4d5e36db17a9","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:09.960411+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f3d8f52a1a12ba8e3a85266c887134296fd3686fb5ffec1a38526e2b8ccdcc24_0.json","raw_sha256":"b1b59ebb5f220f357ffaa8464594a3d8f391df66ad06b024355499ef7eff18cb","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=8&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"mgarort","profile_url":"https://biology.stackexchange.com/users/78254/mgarort","user_type":"registered"},"created_at":"2023-12-21T13:41:00+00:00","raw_file":"raw/codex_api_v1/4b76a36d403acfa9117b7f3b75e82752ff87ef3625482a25f27c7a9f24c1f834_1790824054076617800_0.json","raw_sha256":"f49ea509a52f9f9993721157653fc6d23e3725c8e5ccf6806a681a879219d452","revision_guid":"E39F7A4D-39B5-46A4-A2D4-B820601E783A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E39F7A4D-39B5-46A4-A2D4-B820601E783A/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113712","source_record_sha256":"1b3c81aa30c6e7f6dbe668cb7cef23ece773ee5f1f0c2f7e187bbc629847c57a","source_url":"https://biology.stackexchange.com/questions/113712/why-are-camelid-derived-nanobodies-called-vhh-variable-heavy-domain-of-heavy-ch","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Why are camelid-derived nanobodies called VHH (variable heavy domain of heavy chain)?\nSingle-domain antibodies (or nanobodies) derived from camelid heavy-chain antibodies are called VHH antibodies, where VHH stands for \"variable heavy domain of heavy chain\". I assume the reason for this name is that the variable domain in the heavy-chain camelid antibody is heavier than other domains. However, I haven't been able to find the weight of each domain in the camelid antibody in order to verify my assumption.\n\n\n\n\nWhy are single-domain antibodies derived from camelids called \"variable heavy domain of heavy chain\"?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113718,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I finally found an answer, probably after getting put on some kind of watch list:\n<a href=\"https://doi.org/10.1038/ncomms1051\" rel=\"nofollow noreferrer\"><strong>water striders.</strong></a>\nIf the female looks like she's going to reject the male, the male will tap on the water surface to attract fish.\nThe female, being closer to the water, is more likely to be eaten.</p>\n","answer_id":114325,"answer_text":"I finally found an answer, probably after getting put on some kind of watch list:\nwater striders. (https://doi.org/10.1038/ncomms1051)\nIf the female looks like she's going to reject the male, the male will tap on the water surface to attract fish.\nThe female, being closer to the water, is more likely to be eaten.","answer_url":"https://biology.stackexchange.com/a/114325","author":"Daniel Shapero","author_url":"https://biology.stackexchange.com/users/78313/daniel-shapero","content_license":"CC BY-SA 4.0","created_at":"2024-03-15T21:22:51+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:34.916452+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/c30b2ee4524dfb46e5f33f4b25903a084dac408b994a072a95a23d5316da77d4_0.json","raw_sha256":"d256e999531c4e9fa8d45412ad1eaf748ed7e9e1e333fecd19223242a3776160","source_api":"Stack Exchange API 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Shapero","author_url":"https://biology.stackexchange.com/users/78313/daniel-shapero","content_license":"CC BY-SA 4.0","context_id":"114325","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Daniel Shapero","profile_url":"https://biology.stackexchange.com/users/78313/daniel-shapero","user_type":"registered"},"created_at":"2024-03-15T21:22:51+00:00","raw_file":"raw/codex_api_v1/356145ed9454fa68b5799624a8ac608fd0a01099c9584be3ddde9028f8d4a699_1790824074064499100_0.json","raw_sha256":"c12e6e91ffeb7f90689cb9c2a2921a638baf9f6d9aa70e58160d45a8011a2090","revision_guid":"CBF3C1C8-A2B1-4360-A2DD-1CA411DA8781","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CBF3C1C8-A2B1-4360-A2DD-1CA411DA8781/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Daniel Shapero","profile_url":"https://biology.stackexchange.com/users/78313/daniel-shapero","user_type":"registered"},"created_at":"2024-03-15T22:25:26+00:00","raw_file":"raw/codex_api_v1/356145ed9454fa68b5799624a8ac608fd0a01099c9584be3ddde9028f8d4a699_1790824074064499100_0.json","raw_sha256":"c12e6e91ffeb7f90689cb9c2a2921a638baf9f6d9aa70e58160d45a8011a2090","revision_guid":"C6185333-95F4-4457-9A59-3A29CFBBED9C","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C6185333-95F4-4457-9A59-3A29CFBBED9C/view-source"}],"url":"https://biology.stackexchange.com/a/114325"}],"contexts":[{"context_id":"question","html":"<p>I read once about a species of animal that engages in, and please forgive me for the terminology but I cannot for the life of me think of any other way to describe it, mutually-assured destructive sexual blackmail.\nIf a male attempts to mate with a female, and the female shows signs that she is going to reject the male's advance, the male will start making a loud call that will attract this species' common predator.\nEssentially, the male is threatening the female that they will both get eaten if she doesn't accept his advance.</p>\n<p>I can't remember what the name of this species was and I really do not like what it's doing to my search history.\n<strong>What species, if any, engage in this type of behavior?\nWhat terminology should one use to describe this behavior?</strong></p>\n<p>I tried asking ChatGPT first (less judgmental) but came up empty.\nThere's a species of orb-weaving spider that will mimic the web vibrations of prey struggling to get free when a female seems likely to reject his advance, in the hopes that the female will accept the male's advances in order to avoid being mistakenly identified as prey.\nThere's the vampire jumping spider, which risks predation during courtship displays.\nNeither of those quite fits the pattern I'm thinking of, where the male exposes both himself and his potential mate to predation.</p>\n<p>If you downvote this question, I... completely understand.</p>\n","text":"I read once about a species of animal that engages in, and please forgive me for the terminology but I cannot for the life of me think of any other way to describe it, mutually-assured destructive sexual blackmail.\nIf a male attempts to mate with a female, and the female shows signs that she is going to reject the male's advance, the male will start making a loud call that will attract this species' common predator.\nEssentially, the male is threatening the female that they will both get eaten if she doesn't accept his advance.\n\n\n\n\nI can't remember what the name of this species was and I really do not like what it's doing to my search history.\nWhat species, if any, engage in this type of behavior?\nWhat terminology should one use to describe this behavior?\n\n\n\n\nI tried asking ChatGPT first (less judgmental) but came up empty.\nThere's a species of orb-weaving spider that will mimic the web vibrations of prey struggling to get free when a female seems likely to reject his advance, in the hopes that the female will accept the male's advances in order to avoid being mistakenly identified as prey.\nThere's the vampire jumping spider, which risks predation during courtship displays.\nNeither of those quite fits the pattern I'm thinking of, where the male exposes both himself and his potential mate to predation.\n\n\n\n\nIf you downvote this question, I... completely understand."},{"context_id":"114325","html":"<p>I finally found an answer, probably after getting put on some kind of watch list:\n<a href=\"https://doi.org/10.1038/ncomms1051\" rel=\"nofollow noreferrer\"><strong>water striders.</strong></a>\nIf the female looks like she's going to reject the male, the male will tap on the water surface to attract fish.\nThe female, being closer to the water, is more likely to be eaten.</p>\n","text":"I finally found an answer, probably after getting put on some kind of watch list:\nwater striders. (https://doi.org/10.1038/ncomms1051)\nIf the female looks like she's going to reject the male, the male will tap on the water surface to attract fish.\nThe female, being closer to the water, is more likely to be eaten."}],"domain":"biology","external_citations":["https://doi.org/10.1038/ncomms1051"],"ground_truth_type":"metadata_grounded","group_id":"60ec4f1e354925c79a09cad6eca72fd93ecefb047970212db38dfb8c416bd028","hard_case_family":["no_accepted_answer"],"id":"RHM-ad6a52875527a433e78d072c","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:09.960411+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f3d8f52a1a12ba8e3a85266c887134296fd3686fb5ffec1a38526e2b8ccdcc24_0.json","raw_sha256":"b1b59ebb5f220f357ffaa8464594a3d8f391df66ad06b024355499ef7eff18cb","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=8&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; 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no LLM truth labels"},"query":"species that alerts predators in order to mate\nI read once about a species of animal that engages in, and please forgive me for the terminology but I cannot for the life of me think of any other way to describe it, mutually-assured destructive sexual blackmail.\nIf a male attempts to mate with a female, and the female shows signs that she is going to reject the male's advance, the male will start making a loud call that will attract this species' common predator.\nEssentially, the male is threatening the female that they will both get eaten if she doesn't accept his advance.\n\n\n\n\nI can't remember what the name of this species was and I really do not like what it's doing to my search history.\nWhat species, if any, engage in this type of behavior?\nWhat terminology should one use to describe this behavior?\n\n\n\n\nI tried asking ChatGPT first (less judgmental) but came up empty.\nThere's a species of orb-weaving spider that will mimic the web vibrations of prey struggling to get free when a female seems likely to reject his advance, in the hopes that the female will accept the male's advances in order to avoid being mistakenly identified as prey.\nThere's the vampire jumping spider, which risks predation during courtship displays.\nNeither of those quite fits the pattern I'm thinking of, where the male exposes both himself and his potential mate to predation.\n\n\n\n\nIf you downvote this question, I... completely understand.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114325,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":113776,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The first is with respect to the transcriptional unit of the <em>IL-1A</em> gene. For example the &quot;-&quot; indicates that it is upstream of transcription start site.</p>\n<p>The second is with respect to the GRCh38 build of the reference human genome, which has a defined orientation.</p>\n<p>I don't have access to the paper that you link, but the <a href=\"https://www.ncbi.nlm.nih.gov/gene/3552\" rel=\"nofollow noreferrer\">NCBI annotation</a> for the gene indicates that it is on the reverse strand of the reference genome sequence.</p>\n<p>That would seem to indicate that the two annotation methods are concordant, if somewhat confusing. One refers to a position's distance from the start of the gene, one refers to a position's distance from the start of the reference chromosome. Those will necessarily diverge in the reference allele for genes transcribed on the reverse strand.</p>\n<p>If you are interested in analyzing the behavior of a specific gene, the transcriptional unit is obviously the relevant level of analysis (for example, predicting translated protein sequence). However, if you are interested in defining global genomic coordinates (for example, mapping sequencing reads), the reference genome become the relevant level of analysis. So each is useful for different purposes.</p>\n<p>So, in brief, the answer to your question is <strong>yes</strong>.</p>\n","answer_id":113776,"answer_text":"The first is with respect to the transcriptional unit of the IL-1A gene. For example the \"-\" indicates that it is upstream of transcription start site.\n\n\n\n\nThe second is with respect to the GRCh38 build of the reference human genome, which has a defined orientation.\n\n\n\n\nI don't have access to the paper that you link, but the NCBI annotation (https://www.ncbi.nlm.nih.gov/gene/3552) for the gene indicates that it is on the reverse strand of the reference genome sequence.\n\n\n\n\nThat would seem to indicate that the two annotation methods are concordant, if somewhat confusing. One refers to a position's distance from the start of the gene, one refers to a position's distance from the start of the reference chromosome. Those will necessarily diverge in the reference allele for genes transcribed on the reverse strand.\n\n\n\n\nIf you are interested in analyzing the behavior of a specific gene, the transcriptional unit is obviously the relevant level of analysis (for example, predicting translated protein sequence). However, if you are interested in defining global genomic coordinates (for example, mapping sequencing reads), the reference genome become the relevant level of analysis. So each is useful for different purposes.\n\n\n\n\nSo, in brief, the answer to your question is yes.","answer_url":"https://biology.stackexchange.com/a/113776","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2024-01-03T05:26:50+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:33.526680+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/d1acc50471f82e02a014a291913995889f5ddcd7076433532102b9b97a4a3a3d_0.json","raw_sha256":"e6b5a7d5e11f0ac54d756d69e21baee1de119b759ec7e8caa7f174d67cf80eff","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113978;113977;113976;113967;113965;113959;113955;113947;113946;113937;113936;113924;113918;113912;113907;113904;113902;113898;113897;113887;113884;113873;113869;113863;113858;113855;113849;113846;113836;113833;113828;113827;113822;113811;113810;113806;113795;113788;113781;113780;113777;113775;113773;113763;113761;113748;113747;113739;113738;113734;113722;113715;113712;113694;113688;113681;113678;113677;113655;113654;113648;113647;113643;113642;113638;113634;113633;113631;113614;113611;113599;113598;113596;113595;113593;113590;113581;113576;113575;113570;113569;113566;113561;113557;113554;113551;113545;113537;113534;113531;113515;113508;113507;113505;113498;113491;113484;113483;113471;113469/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113775,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-01-03T05:26:50+00:00","raw_file":"raw/codex_api_v1/4b76a36d403acfa9117b7f3b75e82752ff87ef3625482a25f27c7a9f24c1f834_1790824054076617800_0.json","raw_sha256":"f49ea509a52f9f9993721157653fc6d23e3725c8e5ccf6806a681a879219d452","revision_guid":"B5914A7D-D318-4504-A29E-F146674A0AF2","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B5914A7D-D318-4504-A29E-F146674A0AF2/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Youcha","author_url":"https://biology.stackexchange.com/users/78376/youcha","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Youcha","profile_url":"https://biology.stackexchange.com/users/78376/youcha","user_type":"registered"},"created_at":"2024-01-02T21:39:41+00:00","raw_file":"raw/codex_api_v1/4b76a36d403acfa9117b7f3b75e82752ff87ef3625482a25f27c7a9f24c1f834_1790824054076617800_0.json","raw_sha256":"f49ea509a52f9f9993721157653fc6d23e3725c8e5ccf6806a681a879219d452","revision_guid":"BFED243E-030C-4CAA-9731-37D925697305","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/BFED243E-030C-4CAA-9731-37D925697305/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2024-01-02T22:49:18+00:00","raw_file":"raw/codex_api_v1/4b76a36d403acfa9117b7f3b75e82752ff87ef3625482a25f27c7a9f24c1f834_1790824054076617800_0.json","raw_sha256":"f49ea509a52f9f9993721157653fc6d23e3725c8e5ccf6806a681a879219d452","revision_guid":"F5C31509-0B5D-4523-AF65-8A99D926FA5E","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F5C31509-0B5D-4523-AF65-8A99D926FA5E/view-source"}],"url":"https://biology.stackexchange.com/questions/113775/is-there-a-convention-regarding-the-use-of-forward-vs-reverse-dna-strand-to-repr"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"113776","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-01-03T05:26:50+00:00","raw_file":"raw/codex_api_v1/4b76a36d403acfa9117b7f3b75e82752ff87ef3625482a25f27c7a9f24c1f834_1790824054076617800_0.json","raw_sha256":"f49ea509a52f9f9993721157653fc6d23e3725c8e5ccf6806a681a879219d452","revision_guid":"B5914A7D-D318-4504-A29E-F146674A0AF2","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B5914A7D-D318-4504-A29E-F146674A0AF2/view-source"}],"url":"https://biology.stackexchange.com/a/113776"}],"contexts":[{"context_id":"question","html":"<p>I see in <a href=\"https://pubmed.ncbi.nlm.nih.gov/18673406/\" rel=\"nofollow noreferrer\">this paper</a> the notation IL-1A C[-889]T which suggests that for this gene, the reference allele is C and the variant is T.</p>\n<p>However, when I look up the <a href=\"https://www.ncbi.nlm.nih.gov/snp/rs1800587\" rel=\"nofollow noreferrer\">same gene</a> on dbSNP, it says the alleles are G&gt;A / G&gt;C / G&gt;T.</p>\n<p>I noticed for a number of other genes I looked up in the same paper, G becomes C and vice-versa, T becomes A and vice-versa. Is it because of different conventions regarding which DNA strand is used to represent DNA sequence (forward vs reverse)?</p>\n","text":"I see in this paper (https://pubmed.ncbi.nlm.nih.gov/18673406/) the notation IL-1A C[-889]T which suggests that for this gene, the reference allele is C and the variant is T.\n\n\n\n\nHowever, when I look up the same gene (https://www.ncbi.nlm.nih.gov/snp/rs1800587) on dbSNP, it says the alleles are G>A / G>C / G>T.\n\n\n\n\nI noticed for a number of other genes I looked up in the same paper, G becomes C and vice-versa, T becomes A and vice-versa. Is it because of different conventions regarding which DNA strand is used to represent DNA sequence (forward vs reverse)?"},{"context_id":"113776","html":"<p>The first is with respect to the transcriptional unit of the <em>IL-1A</em> gene. For example the &quot;-&quot; indicates that it is upstream of transcription start site.</p>\n<p>The second is with respect to the GRCh38 build of the reference human genome, which has a defined orientation.</p>\n<p>I don't have access to the paper that you link, but the <a href=\"https://www.ncbi.nlm.nih.gov/gene/3552\" rel=\"nofollow noreferrer\">NCBI annotation</a> for the gene indicates that it is on the reverse strand of the reference genome sequence.</p>\n<p>That would seem to indicate that the two annotation methods are concordant, if somewhat confusing. One refers to a position's distance from the start of the gene, one refers to a position's distance from the start of the reference chromosome. Those will necessarily diverge in the reference allele for genes transcribed on the reverse strand.</p>\n<p>If you are interested in analyzing the behavior of a specific gene, the transcriptional unit is obviously the relevant level of analysis (for example, predicting translated protein sequence). However, if you are interested in defining global genomic coordinates (for example, mapping sequencing reads), the reference genome become the relevant level of analysis. So each is useful for different purposes.</p>\n<p>So, in brief, the answer to your question is <strong>yes</strong>.</p>\n","text":"The first is with respect to the transcriptional unit of the IL-1A gene. For example the \"-\" indicates that it is upstream of transcription start site.\n\n\n\n\nThe second is with respect to the GRCh38 build of the reference human genome, which has a defined orientation.\n\n\n\n\nI don't have access to the paper that you link, but the NCBI annotation (https://www.ncbi.nlm.nih.gov/gene/3552) for the gene indicates that it is on the reverse strand of the reference genome sequence.\n\n\n\n\nThat would seem to indicate that the two annotation methods are concordant, if somewhat confusing. One refers to a position's distance from the start of the gene, one refers to a position's distance from the start of the reference chromosome. Those will necessarily diverge in the reference allele for genes transcribed on the reverse strand.\n\n\n\n\nIf you are interested in analyzing the behavior of a specific gene, the transcriptional unit is obviously the relevant level of analysis (for example, predicting translated protein sequence). However, if you are interested in defining global genomic coordinates (for example, mapping sequencing reads), the reference genome become the relevant level of analysis. So each is useful for different purposes.\n\n\n\n\nSo, in brief, the answer to your question is yes."}],"domain":"biology","external_citations":["https://pubmed.ncbi.nlm.nih.gov/18673406/","https://www.ncbi.nlm.nih.gov/gene/3552","https://www.ncbi.nlm.nih.gov/snp/rs1800587"],"ground_truth_type":"metadata_grounded","group_id":"612df3ce0c4cc20537cb8ceb745fd7940a1cbf183ae545050075497c289b3575","hard_case_family":["multiple_sources"],"id":"RHM-68c5e58053e76e22097a5255","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:09.960411+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f3d8f52a1a12ba8e3a85266c887134296fd3686fb5ffec1a38526e2b8ccdcc24_0.json","raw_sha256":"b1b59ebb5f220f357ffaa8464594a3d8f391df66ad06b024355499ef7eff18cb","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=8&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Youcha","profile_url":"https://biology.stackexchange.com/users/78376/youcha","user_type":"registered"},"created_at":"2024-01-02T21:39:41+00:00","raw_file":"raw/codex_api_v1/4b76a36d403acfa9117b7f3b75e82752ff87ef3625482a25f27c7a9f24c1f834_1790824054076617800_0.json","raw_sha256":"f49ea509a52f9f9993721157653fc6d23e3725c8e5ccf6806a681a879219d452","revision_guid":"BFED243E-030C-4CAA-9731-37D925697305","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/BFED243E-030C-4CAA-9731-37D925697305/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2024-01-02T22:49:18+00:00","raw_file":"raw/codex_api_v1/4b76a36d403acfa9117b7f3b75e82752ff87ef3625482a25f27c7a9f24c1f834_1790824054076617800_0.json","raw_sha256":"f49ea509a52f9f9993721157653fc6d23e3725c8e5ccf6806a681a879219d452","revision_guid":"F5C31509-0B5D-4523-AF65-8A99D926FA5E","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F5C31509-0B5D-4523-AF65-8A99D926FA5E/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113775","source_record_sha256":"c9fd95207b2a34f3ab1959f8d2b4f037308f1478667e6379ae4c81d8f418300d","source_url":"https://biology.stackexchange.com/questions/113775/is-there-a-convention-regarding-the-use-of-forward-vs-reverse-dna-strand-to-repr","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Is there a convention regarding the use of forward vs reverse DNA strand to represent DNA sequence?\nI see in this paper (https://pubmed.ncbi.nlm.nih.gov/18673406/) the notation IL-1A C[-889]T which suggests that for this gene, the reference allele is C and the variant is T.\n\n\n\n\nHowever, when I look up the same gene (https://www.ncbi.nlm.nih.gov/snp/rs1800587) on dbSNP, it says the alleles are G>A / G>C / G>T.\n\n\n\n\nI noticed for a number of other genes I looked up in the same paper, G becomes C and vice-versa, T becomes A and vice-versa. Is it because of different conventions regarding which DNA strand is used to represent DNA sequence (forward vs reverse)?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113776,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":116065,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The addax lacks the speed or strong defensive weapons of other desert-dwelling ungulates like oryx. Instead, its primary means of survival is avoiding predators by inhabiting the extreme arid regions of the Sahara, where they are rarely exposed to large carnivores. Its specially adapted hooves help it traverse soft sand, but in less harsh environments, it would face both competition from other antelope and greater exposure to predators.</p>\n<p>Here are the relevant excerpts from the book <em><a href=\"https://www.google.com/books/edition/Biotic_Interactions_in_Arid_Lands/W6j7CAAAQBAJ?hl=en&amp;gbpv=1&amp;dq=addax%20defend%20predators&amp;pg=PA173&amp;printsec=frontcover\" rel=\"nofollow noreferrer\">Biotic Interactions in Arid Lands</a></em>\n(By John L. Cloudsley-Thompson):</p>\n<blockquote>\n<p>Larger desert mammals, such as gazelles and antelope, either escape at high speeed or defend themselves with horns and hooves (Sect. 4.8). Addax, which have less formidable defences than oryx (Oryx spp.), inhabit such arid, inhospitable wastes that they are seldom exposed to attack by large predators. Moreover, their hooves are considerably enlarged as an adaptation to walking on soft, sandy soil (Sect. 8.1.4).</p>\n<p><strong>8.1.4 Competitive Advantages</strong></p>\n<p>...</p>\n<p>For example, addax antelope are relatively defenceless in comparison with oryx, yet they are able\nto survive without drinking water in the most arid regions of the Sahara\nwhere even oryx cannot live. Here, they are relatively inaccessible to\ncarnivorous predators against which they would be unable to defend\nthemselves - even though oryx might be able to do so (Sect. 4.8). Addax\nwould probably grow faster and be more healthy, living in a less rigorous\nhabitat, but there they might compete unfavourably with oryx and other\nantelope less well adapted to aridity, in addition to being exposed to\npredation by lions and leopards.</p>\n</blockquote>\n<p>While they are not as well-equipped for defense as oryx, addaxes do have long, twisted horns that they can use if necessary. These horns can be used for self-defense against predators and in competition with other addaxes.</p>\n<blockquote>\n<p>Addax is not naturally aggressive (Delany and\nHappold 1979), although individuals may charge if provoked (Duplaix and Simon 1976).</p>\n<p><sub>Paul R. Krausman, Anne L. Casey, Addax nasomaculatus, Mammalian Species, Issue 807, 2 November 2007, Pages 1–4, <a href=\"https://doi.org/10.1644/807.1\" rel=\"nofollow noreferrer\">https://doi.org/10.1644/807.1</a></sub></p>\n</blockquote>\n<blockquote>\n<p>Similarly, addax mothers rush to defend their offspring from the approach of other animals, even large species. One mother punched a domestic cow with her horn tips and another thrust her horns through a fence at a rutting barasingha stag.</p>\n<p><sub><em><a href=\"https://www.google.com/books/edition/Exotics_on_the_Range/wkfxAAAAMAAJ?hl=en&amp;gbpv=1&amp;bsq=addax%20horn%20defend&amp;dq=addax%20horn%20defend&amp;printsec=frontcover\" rel=\"nofollow noreferrer\">Exotics on the Range: The Texas Example</a> (by Elizabeth C. Mungall and William J. Sheffield)</em></sub></p>\n</blockquote>\n","answer_id":116065,"answer_text":"The addax lacks the speed or strong defensive weapons of other desert-dwelling ungulates like oryx. Instead, its primary means of survival is avoiding predators by inhabiting the extreme arid regions of the Sahara, where they are rarely exposed to large carnivores. Its specially adapted hooves help it traverse soft sand, but in less harsh environments, it would face both competition from other antelope and greater exposure to predators.\n\n\n\n\nHere are the relevant excerpts from the book Biotic Interactions in Arid Lands (https://www.google.com/books/edition/Biotic_Interactions_in_Arid_Lands/W6j7CAAAQBAJ?hl=en&gbpv=1&dq=addax%20defend%20predators&pg=PA173&printsec=frontcover)\n(By John L. Cloudsley-Thompson):\n\n\n\n\n\n\n\nLarger desert mammals, such as gazelles and antelope, either escape at high speeed or defend themselves with horns and hooves (Sect. 4.8). Addax, which have less formidable defences than oryx (Oryx spp.), inhabit such arid, inhospitable wastes that they are seldom exposed to attack by large predators. Moreover, their hooves are considerably enlarged as an adaptation to walking on soft, sandy soil (Sect. 8.1.4).\n\n\n\n\n8.1.4 Competitive Advantages\n\n\n\n\n...\n\n\n\n\nFor example, addax antelope are relatively defenceless in comparison with oryx, yet they are able\nto survive without drinking water in the most arid regions of the Sahara\nwhere even oryx cannot live. Here, they are relatively inaccessible to\ncarnivorous predators against which they would be unable to defend\nthemselves - even though oryx might be able to do so (Sect. 4.8). Addax\nwould probably grow faster and be more healthy, living in a less rigorous\nhabitat, but there they might compete unfavourably with oryx and other\nantelope less well adapted to aridity, in addition to being exposed to\npredation by lions and leopards.\n\n\n\n\n\n\n\nWhile they are not as well-equipped for defense as oryx, addaxes do have long, twisted horns that they can use if necessary. These horns can be used for self-defense against predators and in competition with other addaxes.\n\n\n\n\n\n\n\nAddax is not naturally aggressive (Delany and\nHappold 1979), although individuals may charge if provoked (Duplaix and Simon 1976).\n\n\n\n\nPaul R. Krausman, Anne L. Casey, Addax nasomaculatus, Mammalian Species, Issue 807, 2 November 2007, Pages 1–4, https://doi.org/10.1644/807.1 (https://doi.org/10.1644/807.1)\n\n\n\n\n\n\n\n\n\n\nSimilarly, addax mothers rush to defend their offspring from the approach of other animals, even large species. One mother punched a domestic cow with her horn tips and another thrust her horns through a fence at a rutting barasingha stag.\n\n\n\n\nExotics on the Range: The Texas Example (https://www.google.com/books/edition/Exotics_on_the_Range/wkfxAAAAMAAJ?hl=en&gbpv=1&bsq=addax%20horn%20defend&dq=addax%20horn%20defend&printsec=frontcover) (by Elizabeth C. Mungall and William J. Sheffield)","answer_url":"https://biology.stackexchange.com/a/116065","author":"ermanen","author_url":"https://biology.stackexchange.com/users/6019/ermanen","content_license":"CC BY-SA 4.0","created_at":"2025-02-07T12:54:56+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:34.916452+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/c30b2ee4524dfb46e5f33f4b25903a084dac408b994a072a95a23d5316da77d4_0.json","raw_sha256":"d256e999531c4e9fa8d45412ad1eaf748ed7e9e1e333fecd19223242a3776160","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113978;113977;113976;113967;113965;113959;113955;113947;113946;113937;113936;113924;113918;113912;113907;113904;113902;113898;113897;113887;113884;113873;113869;113863;113858;113855;113849;113846;113836;113833;113828;113827;113822;113811;113810;113806;113795;113788;113781;113780;113777;113775;113773;113763;113761;113748;113747;113739;113738;113734;113722;113715;113712;113694;113688;113681;113678;113677;113655;113654;113648;113647;113643;113642;113638;113634;113633;113631;113614;113611;113599;113598;113596;113595;113593;113590;113581;113576;113575;113570;113569;113566;113561;113557;113554;113551;113545;113537;113534;113531;113515;113508;113507;113505;113498;113491;113484;113483;113471;113469/answers?filter=withbody&order=asc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113780,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"ermanen","profile_url":"https://biology.stackexchange.com/users/6019/ermanen","user_type":"registered"},"created_at":"2025-02-07T12:54:56+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"2BB83B9E-198D-4CC9-B7E9-51A545EA2EAE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2BB83B9E-198D-4CC9-B7E9-51A545EA2EAE/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Triceratops","author_url":"https://biology.stackexchange.com/users/42767/triceratops","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Triceratops","profile_url":"https://biology.stackexchange.com/users/42767/triceratops","user_type":"registered"},"created_at":"2024-01-03T13:15:50+00:00","raw_file":"raw/codex_api_v1/4b76a36d403acfa9117b7f3b75e82752ff87ef3625482a25f27c7a9f24c1f834_1790824054076617800_0.json","raw_sha256":"f49ea509a52f9f9993721157653fc6d23e3725c8e5ccf6806a681a879219d452","revision_guid":"4603B2E5-473A-4C2B-AA1E-3DCCFC24A2F7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4603B2E5-473A-4C2B-AA1E-3DCCFC24A2F7/view-source"}],"url":"https://biology.stackexchange.com/questions/113780/how-do-addax-defend-itself-from-predators"},{"author":"ermanen","author_url":"https://biology.stackexchange.com/users/6019/ermanen","content_license":"CC BY-SA 4.0","context_id":"116065","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"ermanen","profile_url":"https://biology.stackexchange.com/users/6019/ermanen","user_type":"registered"},"created_at":"2025-02-07T12:54:56+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"2BB83B9E-198D-4CC9-B7E9-51A545EA2EAE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2BB83B9E-198D-4CC9-B7E9-51A545EA2EAE/view-source"}],"url":"https://biology.stackexchange.com/a/116065"}],"contexts":[{"context_id":"question","html":"<p>The addax (<em>Addax nasomaculatus</em>) is a critically endangered antelope adapted to live in extreme desert conditions. It has long impressive horns that can potentially serve as a weapon because they are sharp. Does addax use its horn to fend off predators?</p>\n<p>I read somewhere that addax is not a fast animal so trying to escape by running does not seem like a good option for defense.</p>\n<p><a href=\"https://i.sstatic.net/TVWew.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/TVWew.png\" alt=\"Picture of Addax and its horns, taken from Wikipedia, photographer: Zachi Evenor\" /></a></p>\n<p>Picture of Addax and its horns, taken from Wikipedia, photographer: Zachi Evenor\n<a href=\"https://commons.wikimedia.org/wiki/File:Addax-Jerusalem-Biblical-Zoo-IZE-611.jpg\" rel=\"nofollow noreferrer\">https://commons.wikimedia.org/wiki/File:Addax-Jerusalem-Biblical-Zoo-IZE-611.jpg</a></p>\n","text":"The addax (Addax nasomaculatus) is a critically endangered antelope adapted to live in extreme desert conditions. It has long impressive horns that can potentially serve as a weapon because they are sharp. Does addax use its horn to fend off predators?\n\n\n\n\nI read somewhere that addax is not a fast animal so trying to escape by running does not seem like a good option for defense.\n\n\n\n\n[image: Picture of Addax and its horns, taken from Wikipedia, photographer: Zachi Evenor; source: https://i.sstatic.net/TVWew.png] (https://i.sstatic.net/TVWew.png)\n\n\n\n\nPicture of Addax and its horns, taken from Wikipedia, photographer: Zachi Evenor\nhttps://commons.wikimedia.org/wiki/File:Addax-Jerusalem-Biblical-Zoo-IZE-611.jpg (https://commons.wikimedia.org/wiki/File:Addax-Jerusalem-Biblical-Zoo-IZE-611.jpg)"},{"context_id":"116065","html":"<p>The addax lacks the speed or strong defensive weapons of other desert-dwelling ungulates like oryx. Instead, its primary means of survival is avoiding predators by inhabiting the extreme arid regions of the Sahara, where they are rarely exposed to large carnivores. Its specially adapted hooves help it traverse soft sand, but in less harsh environments, it would face both competition from other antelope and greater exposure to predators.</p>\n<p>Here are the relevant excerpts from the book <em><a href=\"https://www.google.com/books/edition/Biotic_Interactions_in_Arid_Lands/W6j7CAAAQBAJ?hl=en&amp;gbpv=1&amp;dq=addax%20defend%20predators&amp;pg=PA173&amp;printsec=frontcover\" rel=\"nofollow noreferrer\">Biotic Interactions in Arid Lands</a></em>\n(By John L. Cloudsley-Thompson):</p>\n<blockquote>\n<p>Larger desert mammals, such as gazelles and antelope, either escape at high speeed or defend themselves with horns and hooves (Sect. 4.8). Addax, which have less formidable defences than oryx (Oryx spp.), inhabit such arid, inhospitable wastes that they are seldom exposed to attack by large predators. Moreover, their hooves are considerably enlarged as an adaptation to walking on soft, sandy soil (Sect. 8.1.4).</p>\n<p><strong>8.1.4 Competitive Advantages</strong></p>\n<p>...</p>\n<p>For example, addax antelope are relatively defenceless in comparison with oryx, yet they are able\nto survive without drinking water in the most arid regions of the Sahara\nwhere even oryx cannot live. Here, they are relatively inaccessible to\ncarnivorous predators against which they would be unable to defend\nthemselves - even though oryx might be able to do so (Sect. 4.8). Addax\nwould probably grow faster and be more healthy, living in a less rigorous\nhabitat, but there they might compete unfavourably with oryx and other\nantelope less well adapted to aridity, in addition to being exposed to\npredation by lions and leopards.</p>\n</blockquote>\n<p>While they are not as well-equipped for defense as oryx, addaxes do have long, twisted horns that they can use if necessary. These horns can be used for self-defense against predators and in competition with other addaxes.</p>\n<blockquote>\n<p>Addax is not naturally aggressive (Delany and\nHappold 1979), although individuals may charge if provoked (Duplaix and Simon 1976).</p>\n<p><sub>Paul R. Krausman, Anne L. Casey, Addax nasomaculatus, Mammalian Species, Issue 807, 2 November 2007, Pages 1–4, <a href=\"https://doi.org/10.1644/807.1\" rel=\"nofollow noreferrer\">https://doi.org/10.1644/807.1</a></sub></p>\n</blockquote>\n<blockquote>\n<p>Similarly, addax mothers rush to defend their offspring from the approach of other animals, even large species. One mother punched a domestic cow with her horn tips and another thrust her horns through a fence at a rutting barasingha stag.</p>\n<p><sub><em><a href=\"https://www.google.com/books/edition/Exotics_on_the_Range/wkfxAAAAMAAJ?hl=en&amp;gbpv=1&amp;bsq=addax%20horn%20defend&amp;dq=addax%20horn%20defend&amp;printsec=frontcover\" rel=\"nofollow noreferrer\">Exotics on the Range: The Texas Example</a> (by Elizabeth C. Mungall and William J. Sheffield)</em></sub></p>\n</blockquote>\n","text":"The addax lacks the speed or strong defensive weapons of other desert-dwelling ungulates like oryx. Instead, its primary means of survival is avoiding predators by inhabiting the extreme arid regions of the Sahara, where they are rarely exposed to large carnivores. Its specially adapted hooves help it traverse soft sand, but in less harsh environments, it would face both competition from other antelope and greater exposure to predators.\n\n\n\n\nHere are the relevant excerpts from the book Biotic Interactions in Arid Lands (https://www.google.com/books/edition/Biotic_Interactions_in_Arid_Lands/W6j7CAAAQBAJ?hl=en&gbpv=1&dq=addax%20defend%20predators&pg=PA173&printsec=frontcover)\n(By John L. Cloudsley-Thompson):\n\n\n\n\n\n\n\nLarger desert mammals, such as gazelles and antelope, either escape at high speeed or defend themselves with horns and hooves (Sect. 4.8). Addax, which have less formidable defences than oryx (Oryx spp.), inhabit such arid, inhospitable wastes that they are seldom exposed to attack by large predators. Moreover, their hooves are considerably enlarged as an adaptation to walking on soft, sandy soil (Sect. 8.1.4).\n\n\n\n\n8.1.4 Competitive Advantages\n\n\n\n\n...\n\n\n\n\nFor example, addax antelope are relatively defenceless in comparison with oryx, yet they are able\nto survive without drinking water in the most arid regions of the Sahara\nwhere even oryx cannot live. Here, they are relatively inaccessible to\ncarnivorous predators against which they would be unable to defend\nthemselves - even though oryx might be able to do so (Sect. 4.8). Addax\nwould probably grow faster and be more healthy, living in a less rigorous\nhabitat, but there they might compete unfavourably with oryx and other\nantelope less well adapted to aridity, in addition to being exposed to\npredation by lions and leopards.\n\n\n\n\n\n\n\nWhile they are not as well-equipped for defense as oryx, addaxes do have long, twisted horns that they can use if necessary. These horns can be used for self-defense against predators and in competition with other addaxes.\n\n\n\n\n\n\n\nAddax is not naturally aggressive (Delany and\nHappold 1979), although individuals may charge if provoked (Duplaix and Simon 1976).\n\n\n\n\nPaul R. Krausman, Anne L. Casey, Addax nasomaculatus, Mammalian Species, Issue 807, 2 November 2007, Pages 1–4, https://doi.org/10.1644/807.1 (https://doi.org/10.1644/807.1)\n\n\n\n\n\n\n\n\n\n\nSimilarly, addax mothers rush to defend their offspring from the approach of other animals, even large species. One mother punched a domestic cow with her horn tips and another thrust her horns through a fence at a rutting barasingha stag.\n\n\n\n\nExotics on the Range: The Texas Example (https://www.google.com/books/edition/Exotics_on_the_Range/wkfxAAAAMAAJ?hl=en&gbpv=1&bsq=addax%20horn%20defend&dq=addax%20horn%20defend&printsec=frontcover) (by Elizabeth C. Mungall and William J. Sheffield)"}],"domain":"biology","external_citations":["https://commons.wikimedia.org/wiki/File:Addax-Jerusalem-Biblical-Zoo-IZE-611.jpg","https://doi.org/10.1644/807.1","https://i.sstatic.net/TVWew.png","https://www.google.com/books/edition/Biotic_Interactions_in_Arid_Lands/W6j7CAAAQBAJ?hl=en&gbpv=1&dq=addax%20defend%20predators&pg=PA173&printsec=frontcover","https://www.google.com/books/edition/Exotics_on_the_Range/wkfxAAAAMAAJ?hl=en&gbpv=1&bsq=addax%20horn%20defend&dq=addax%20horn%20defend&printsec=frontcover"],"ground_truth_type":"metadata_grounded","group_id":"f074f914c5d663fab77daa560bc7cfe99f9d315c4246b6a5565172be7fe1e11f","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-ff9cf7628f1e59bfa8e14da2","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:09.960411+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f3d8f52a1a12ba8e3a85266c887134296fd3686fb5ffec1a38526e2b8ccdcc24_0.json","raw_sha256":"b1b59ebb5f220f357ffaa8464594a3d8f391df66ad06b024355499ef7eff18cb","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=8&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Triceratops","profile_url":"https://biology.stackexchange.com/users/42767/triceratops","user_type":"registered"},"created_at":"2024-01-03T13:15:50+00:00","raw_file":"raw/codex_api_v1/4b76a36d403acfa9117b7f3b75e82752ff87ef3625482a25f27c7a9f24c1f834_1790824054076617800_0.json","raw_sha256":"f49ea509a52f9f9993721157653fc6d23e3725c8e5ccf6806a681a879219d452","revision_guid":"4603B2E5-473A-4C2B-AA1E-3DCCFC24A2F7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4603B2E5-473A-4C2B-AA1E-3DCCFC24A2F7/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113780","source_record_sha256":"72fe9a7efbea5496d633282d137cbbdcedfbc7d6b5deaa856b8a90a1b02d878b","source_url":"https://biology.stackexchange.com/questions/113780/how-do-addax-defend-itself-from-predators","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How do Addax defend itself from predators?\nThe addax (Addax nasomaculatus) is a critically endangered antelope adapted to live in extreme desert conditions. It has long impressive horns that can potentially serve as a weapon because they are sharp. Does addax use its horn to fend off predators?\n\n\n\n\nI read somewhere that addax is not a fast animal so trying to escape by running does not seem like a good option for defense.\n\n\n\n\n[image: Picture of Addax and its horns, taken from Wikipedia, photographer: Zachi Evenor; source: https://i.sstatic.net/TVWew.png] (https://i.sstatic.net/TVWew.png)\n\n\n\n\nPicture of Addax and its horns, taken from Wikipedia, photographer: Zachi Evenor\nhttps://commons.wikimedia.org/wiki/File:Addax-Jerusalem-Biblical-Zoo-IZE-611.jpg (https://commons.wikimedia.org/wiki/File:Addax-Jerusalem-Biblical-Zoo-IZE-611.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116065,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":113785,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Black widows (<em>Latrodectus</em> sp.) are in the Family <em>Theridiidae</em>, or Cobweb Weavers. Your spider's web is an orb web. Cobwebs are messy tangle webs while orb webs are the spiral-like planar polygon figure, sometimes completely vertical and sometimes at an angle, depending on which orb-weaving family made the web. So <strong>this spider is clearly not a Black Widow</strong> from the web alone. Further, your spider's legs are too short to fit the profile of a Latrodectus.</p>\n<p>Searching iNaturalist records for Araneoid spiders (spiders that typically live suspended in webs) in Bolivia, we see the second most-commonly observed spider is one that is black and red.</p>\n<p><a href=\"https://i.sstatic.net/gw9fN.jpg\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/gw9fN.jpg\" alt=\"enter image description here\" /></a></p>\n<p>The second-most observed spider here is from the <em>Alpaida</em> genus, which is in the orb-weaving family <em>Araneidae</em>. And looking at the hundreds of photos available for it, it does indeed build orb webs. However, the ventral markings in the photos of A.versicolor do not match your photos and the legs of A.versicolor are striped/banded while yours are not.</p>\n<p>In many spider families, it is difficult to get an identification to species level through photos. But we can try: browsing those top 15 most-observed Araneoid spiders image in Bolivia, we see a number of species in this genus:</p>\n<ul>\n<li>Alpaida versicolor</li>\n<li>Alpaida veniliae</li>\n<li>Alpaida carminea</li>\n<li>Alpaida bicornuta</li>\n<li>Alpaida rubellula</li>\n</ul>\n<p>Some of these look drastically different from yours. But <strong>A. carminea</strong> matches the general shape, colour and ventral markings.</p>\n<p>I am very confident this is from the genus Alpaida, and I lean towards A. carminea but it could still possibly be A. versicolor or some less-common species. A photo of the dorsal (top-side) markings would help distinguish these species.</p>\n","answer_id":113785,"answer_text":"Black widows (Latrodectus sp.) are in the Family Theridiidae, or Cobweb Weavers. Your spider's web is an orb web. Cobwebs are messy tangle webs while orb webs are the spiral-like planar polygon figure, sometimes completely vertical and sometimes at an angle, depending on which orb-weaving family made the web. So this spider is clearly not a Black Widow from the web alone. Further, your spider's legs are too short to fit the profile of a Latrodectus.\n\n\n\n\nSearching iNaturalist records for Araneoid spiders (spiders that typically live suspended in webs) in Bolivia, we see the second most-commonly observed spider is one that is black and red.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/gw9fN.jpg] (https://i.sstatic.net/gw9fN.jpg)\n\n\n\n\nThe second-most observed spider here is from the Alpaida genus, which is in the orb-weaving family Araneidae. And looking at the hundreds of photos available for it, it does indeed build orb webs. However, the ventral markings in the photos of A.versicolor do not match your photos and the legs of A.versicolor are striped/banded while yours are not.\n\n\n\n\nIn many spider families, it is difficult to get an identification to species level through photos. But we can try: browsing those top 15 most-observed Araneoid spiders image in Bolivia, we see a number of species in this genus:\n\n\n\n\n\nAlpaida versicolor\n\n\n\n\nAlpaida veniliae\n\n\n\n\nAlpaida carminea\n\n\n\n\nAlpaida bicornuta\n\n\n\n\nAlpaida rubellula\n\n\n\n\n\nSome of these look drastically different from yours. But A. carminea matches the general shape, colour and ventral markings.\n\n\n\n\nI am very confident this is from the genus Alpaida, and I lean towards A. carminea but it could still possibly be A. versicolor or some less-common species. A photo of the dorsal (top-side) markings would help distinguish these species.","answer_url":"https://biology.stackexchange.com/a/113785","author":"JimN","author_url":"https://biology.stackexchange.com/users/61490/jimn","content_license":"CC BY-SA 4.0","created_at":"2024-01-04T03:39:24+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:33.526680+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/d1acc50471f82e02a014a291913995889f5ddcd7076433532102b9b97a4a3a3d_0.json","raw_sha256":"e6b5a7d5e11f0ac54d756d69e21baee1de119b759ec7e8caa7f174d67cf80eff","source_api":"Stack Exchange API 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I have been looking all over the internet to try and identify it, but with no luck. Could someone please help me?😁</p>\n<p>Initially I thought that it was a black widow, due to the red marks and the body shape, but what threw me off is the lack of a distinct hourglass and the yellowish stripes in the middle of the abdomen. Also, the top of its abdomen is mostly red, much more than what is typical for black widows as far as I know. Also, the web doesn't look like a typical black widow web…</p>\n<p>The locals told me that they think its a black widow, and that would probably be my best guess, but I'm not 100% convinced… if anyone knows, please let me know!😁</p>\n<p>I have attatched 2 photos below:</p>\n<p><a href=\"https://i.sstatic.net/4BAMU.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/4BAMU.jpg\" alt=\"enter image description here\" /></a>\n<a href=\"https://i.sstatic.net/pwcbe.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/pwcbe.jpg\" alt=\"enter image description here\" /></a></p>\n","text":"I found this spider near La Paz, Bolivia. I have been looking all over the internet to try and identify it, but with no luck. Could someone please help me?😁\n\n\n\n\nInitially I thought that it was a black widow, due to the red marks and the body shape, but what threw me off is the lack of a distinct hourglass and the yellowish stripes in the middle of the abdomen. Also, the top of its abdomen is mostly red, much more than what is typical for black widows as far as I know. Also, the web doesn't look like a typical black widow web…\n\n\n\n\nThe locals told me that they think its a black widow, and that would probably be my best guess, but I'm not 100% convinced… if anyone knows, please let me know!😁\n\n\n\n\nI have attatched 2 photos below:\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/4BAMU.jpg] (https://i.sstatic.net/4BAMU.jpg)\n[image: enter image description here; source: https://i.sstatic.net/pwcbe.jpg] (https://i.sstatic.net/pwcbe.jpg)"},{"context_id":"113785","html":"<p>Black widows (<em>Latrodectus</em> sp.) are in the Family <em>Theridiidae</em>, or Cobweb Weavers. Your spider's web is an orb web. Cobwebs are messy tangle webs while orb webs are the spiral-like planar polygon figure, sometimes completely vertical and sometimes at an angle, depending on which orb-weaving family made the web. So <strong>this spider is clearly not a Black Widow</strong> from the web alone. Further, your spider's legs are too short to fit the profile of a Latrodectus.</p>\n<p>Searching iNaturalist records for Araneoid spiders (spiders that typically live suspended in webs) in Bolivia, we see the second most-commonly observed spider is one that is black and red.</p>\n<p><a href=\"https://i.sstatic.net/gw9fN.jpg\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/gw9fN.jpg\" alt=\"enter image description here\" /></a></p>\n<p>The second-most observed spider here is from the <em>Alpaida</em> genus, which is in the orb-weaving family <em>Araneidae</em>. And looking at the hundreds of photos available for it, it does indeed build orb webs. However, the ventral markings in the photos of A.versicolor do not match your photos and the legs of A.versicolor are striped/banded while yours are not.</p>\n<p>In many spider families, it is difficult to get an identification to species level through photos. But we can try: browsing those top 15 most-observed Araneoid spiders image in Bolivia, we see a number of species in this genus:</p>\n<ul>\n<li>Alpaida versicolor</li>\n<li>Alpaida veniliae</li>\n<li>Alpaida carminea</li>\n<li>Alpaida bicornuta</li>\n<li>Alpaida rubellula</li>\n</ul>\n<p>Some of these look drastically different from yours. But <strong>A. carminea</strong> matches the general shape, colour and ventral markings.</p>\n<p>I am very confident this is from the genus Alpaida, and I lean towards A. carminea but it could still possibly be A. versicolor or some less-common species. A photo of the dorsal (top-side) markings would help distinguish these species.</p>\n","text":"Black widows (Latrodectus sp.) are in the Family Theridiidae, or Cobweb Weavers. Your spider's web is an orb web. Cobwebs are messy tangle webs while orb webs are the spiral-like planar polygon figure, sometimes completely vertical and sometimes at an angle, depending on which orb-weaving family made the web. So this spider is clearly not a Black Widow from the web alone. Further, your spider's legs are too short to fit the profile of a Latrodectus.\n\n\n\n\nSearching iNaturalist records for Araneoid spiders (spiders that typically live suspended in webs) in Bolivia, we see the second most-commonly observed spider is one that is black and red.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/gw9fN.jpg] (https://i.sstatic.net/gw9fN.jpg)\n\n\n\n\nThe second-most observed spider here is from the Alpaida genus, which is in the orb-weaving family Araneidae. And looking at the hundreds of photos available for it, it does indeed build orb webs. However, the ventral markings in the photos of A.versicolor do not match your photos and the legs of A.versicolor are striped/banded while yours are not.\n\n\n\n\nIn many spider families, it is difficult to get an identification to species level through photos. But we can try: browsing those top 15 most-observed Araneoid spiders image in Bolivia, we see a number of species in this genus:\n\n\n\n\n\nAlpaida versicolor\n\n\n\n\nAlpaida veniliae\n\n\n\n\nAlpaida carminea\n\n\n\n\nAlpaida bicornuta\n\n\n\n\nAlpaida rubellula\n\n\n\n\n\nSome of these look drastically different from yours. But A. carminea matches the general shape, colour and ventral markings.\n\n\n\n\nI am very confident this is from the genus Alpaida, and I lean towards A. carminea but it could still possibly be A. versicolor or some less-common species. A photo of the dorsal (top-side) markings would help distinguish these species."}],"domain":"biology","external_citations":["https://i.sstatic.net/4BAMU.jpg","https://i.sstatic.net/gw9fN.jpg","https://i.sstatic.net/pwcbe.jpg"],"ground_truth_type":"metadata_grounded","group_id":"604964decc1e0fe6a06c15125ace59fbc01a8de0433e364801a7e5d124eacd70","hard_case_family":["multiple_sources"],"id":"RHM-45c7942d904bed407037141d","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:09.960411+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f3d8f52a1a12ba8e3a85266c887134296fd3686fb5ffec1a38526e2b8ccdcc24_0.json","raw_sha256":"b1b59ebb5f220f357ffaa8464594a3d8f391df66ad06b024355499ef7eff18cb","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=8&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Henri","profile_url":"https://biology.stackexchange.com/users/78383/henri","user_type":"registered"},"created_at":"2024-01-03T15:38:28+00:00","raw_file":"raw/codex_api_v1/4b76a36d403acfa9117b7f3b75e82752ff87ef3625482a25f27c7a9f24c1f834_1790824054076617800_0.json","raw_sha256":"f49ea509a52f9f9993721157653fc6d23e3725c8e5ccf6806a681a879219d452","revision_guid":"DDBFC2D1-214D-4CE7-9C9D-3694B7597C89","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DDBFC2D1-214D-4CE7-9C9D-3694B7597C89/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113781","source_record_sha256":"705d088f8a82703225c2d50d26d17046c52138ee8f3b7357ad317c79a5f3c618","source_url":"https://biology.stackexchange.com/questions/113781/what-kind-of-bolivian-spider-is-this-is-it-a-black-widow","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What kind of Bolivian spider is this? Is it a black widow?\nI found this spider near La Paz, Bolivia. I have been looking all over the internet to try and identify it, but with no luck. Could someone please help me?😁\n\n\n\n\nInitially I thought that it was a black widow, due to the red marks and the body shape, but what threw me off is the lack of a distinct hourglass and the yellowish stripes in the middle of the abdomen. Also, the top of its abdomen is mostly red, much more than what is typical for black widows as far as I know. Also, the web doesn't look like a typical black widow web…\n\n\n\n\nThe locals told me that they think its a black widow, and that would probably be my best guess, but I'm not 100% convinced… if anyone knows, please let me know!😁\n\n\n\n\nI have attatched 2 photos below:\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/4BAMU.jpg] (https://i.sstatic.net/4BAMU.jpg)\n[image: enter image description here; source: https://i.sstatic.net/pwcbe.jpg] (https://i.sstatic.net/pwcbe.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113785,"score":7}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I have never performed environmental extractions, and I am not familiar with your specific protocol. I would defer to any other commenters with more experience with these methods. However, I would recommend redoing the extractions, if it is feasible. Any time a standard protocol gives results that are significantly unexpected, it's worth thinking hard about. In this case, where it is your initial step, it's even easier to suggest, since there's much less wasted time than if it were later in your protocol. The quality of your data depends on what goes in, so it's not worth risk it.</p>\n<p>Nanodrop quantification is not particularly reliable for low concentrations like this. That makes the ratios even more questionable. I would not try to make too much of these particular metrics beyond &quot;this was a poor extraction.&quot;</p>\n<p>PCR could certainly give you plenty of DNA even from a minuscule sample - that's the whole point of exponential amplification! But if your extractions are poor enough that they are extremely biased, that would carry on through PCR.</p>\n<p>I would worry less about contaminating the sequencing reaction at the end, but it's still worth trying to get pure DNA. What's your cleanup before dilution? Anyway, if you do have an inhibitor, I would expect it to give issues during PCR.  And you'll be diluting them 20? 100?-fold for loading onto the flow cell.</p>\n","answer_id":113830,"answer_text":"I have never performed environmental extractions, and I am not familiar with your specific protocol. I would defer to any other commenters with more experience with these methods. However, I would recommend redoing the extractions, if it is feasible. Any time a standard protocol gives results that are significantly unexpected, it's worth thinking hard about. In this case, where it is your initial step, it's even easier to suggest, since there's much less wasted time than if it were later in your protocol. The quality of your data depends on what goes in, so it's not worth risk it.\n\n\n\n\nNanodrop quantification is not particularly reliable for low concentrations like this. That makes the ratios even more questionable. I would not try to make too much of these particular metrics beyond \"this was a poor extraction.\"\n\n\n\n\nPCR could certainly give you plenty of DNA even from a minuscule sample - that's the whole point of exponential amplification! But if your extractions are poor enough that they are extremely biased, that would carry on through PCR.\n\n\n\n\nI would worry less about contaminating the sequencing reaction at the end, but it's still worth trying to get pure DNA. What's your cleanup before dilution? Anyway, if you do have an inhibitor, I would expect it to give issues during PCR.  And you'll be diluting them 20? 100?-fold for loading onto the flow cell.","answer_url":"https://biology.stackexchange.com/a/113830","author":"ksdjnf","author_url":"https://biology.stackexchange.com/users/53112/ksdjnf","content_license":"CC BY-SA 4.0","created_at":"2024-01-09T03:05:21+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:33.526680+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/d1acc50471f82e02a014a291913995889f5ddcd7076433532102b9b97a4a3a3d_0.json","raw_sha256":"e6b5a7d5e11f0ac54d756d69e21baee1de119b759ec7e8caa7f174d67cf80eff","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/113978;113977;113976;113967;113965;113959;113955;113947;113946;113937;113936;113924;113918;113912;113907;113904;113902;113898;113897;113887;113884;113873;113869;113863;113858;113855;113849;113846;113836;113833;113828;113827;113822;113811;113810;113806;113795;113788;113781;113780;113777;113775;113773;113763;113761;113748;113747;113739;113738;113734;113722;113715;113712;113694;113688;113681;113678;113677;113655;113654;113648;113647;113643;113642;113638;113634;113633;113631;113614;113611;113599;113598;113596;113595;113593;113590;113581;113576;113575;113570;113569;113566;113561;113557;113554;113551;113545;113537;113534;113531;113515;113508;113507;113505;113498;113491;113484;113483;113471;113469/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":113827,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"ksdjnf","profile_url":"https://biology.stackexchange.com/users/53112/ksdjnf","user_type":"registered"},"created_at":"2024-01-09T03:05:21+00:00","raw_file":"raw/codex_api_v1/85b5645347f81712378316d7ce101572df9f33b4b1773526e317a302b1f0b138_1790824051913889100_0.json","raw_sha256":"6c01c074c3b6604e944aeb1c481e22bdf0b7c0a7082c18421dfbb8bc6388be2e","revision_guid":"19E6DFB3-645A-4EF6-B3A2-143B3E9B44A5","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/19E6DFB3-645A-4EF6-B3A2-143B3E9B44A5/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Joel","author_url":"https://biology.stackexchange.com/users/78437/joel","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Joel","profile_url":"https://biology.stackexchange.com/users/78437/joel","user_type":"registered"},"created_at":"2024-01-09T00:34:20+00:00","raw_file":"raw/codex_api_v1/85b5645347f81712378316d7ce101572df9f33b4b1773526e317a302b1f0b138_1790824051913889100_0.json","raw_sha256":"6c01c074c3b6604e944aeb1c481e22bdf0b7c0a7082c18421dfbb8bc6388be2e","revision_guid":"0FB5C92D-DFE4-4660-B878-7A37A0A2CD85","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0FB5C92D-DFE4-4660-B878-7A37A0A2CD85/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2024-02-08T03:06:35+00:00","raw_file":"raw/codex_api_v1/85b5645347f81712378316d7ce101572df9f33b4b1773526e317a302b1f0b138_1790824051913889100_0.json","raw_sha256":"6c01c074c3b6604e944aeb1c481e22bdf0b7c0a7082c18421dfbb8bc6388be2e","revision_guid":"2FD2E58C-EDB4-4742-8681-02A80E3F969C","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/2FD2E58C-EDB4-4742-8681-02A80E3F969C/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2024-06-07T04:02:50+00:00","raw_file":"raw/codex_api_v1/85b5645347f81712378316d7ce101572df9f33b4b1773526e317a302b1f0b138_1790824051913889100_0.json","raw_sha256":"6c01c074c3b6604e944aeb1c481e22bdf0b7c0a7082c18421dfbb8bc6388be2e","revision_guid":"E422987F-911F-4DD2-874D-5968373252C3","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/E422987F-911F-4DD2-874D-5968373252C3/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2024-10-05T04:08:30+00:00","raw_file":"raw/codex_api_v1/85b5645347f81712378316d7ce101572df9f33b4b1773526e317a302b1f0b138_1790824051913889100_0.json","raw_sha256":"6c01c074c3b6604e944aeb1c481e22bdf0b7c0a7082c18421dfbb8bc6388be2e","revision_guid":"18D65182-81CF-4B1A-ABBA-D3919E3E96E3","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/18D65182-81CF-4B1A-ABBA-D3919E3E96E3/view-source"}],"url":"https://biology.stackexchange.com/questions/113827/can-contaminants-in-the-dna-extract-disturb-the-sequencing"},{"author":"ksdjnf","author_url":"https://biology.stackexchange.com/users/53112/ksdjnf","content_license":"CC BY-SA 4.0","context_id":"113830","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"ksdjnf","profile_url":"https://biology.stackexchange.com/users/53112/ksdjnf","user_type":"registered"},"created_at":"2024-01-09T03:05:21+00:00","raw_file":"raw/codex_api_v1/85b5645347f81712378316d7ce101572df9f33b4b1773526e317a302b1f0b138_1790824051913889100_0.json","raw_sha256":"6c01c074c3b6604e944aeb1c481e22bdf0b7c0a7082c18421dfbb8bc6388be2e","revision_guid":"19E6DFB3-645A-4EF6-B3A2-143B3E9B44A5","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/19E6DFB3-645A-4EF6-B3A2-143B3E9B44A5/view-source"}],"url":"https://biology.stackexchange.com/a/113830"}],"contexts":[{"context_id":"question","html":"<p>I'm having troubles with some DNA extractions. The yields are much lower than expected, and the Nanodrop spectrophotometer is showing quite a bit of contamination through the 260/230 ratios (see table below). The samples consist of mixed marine fine-mortarted fauna (environmental samples), of which I want to sequence a couple of marker genes to determine species composition (metabarcoding), using paired-end Illumina MiSeq. I could just go on with the PCR as I'm supposed to and see if that works, but my concerns are still:</p>\n<ol>\n<li>As the DNA extracts contain an order of magnitude less DNA than expected, would you really consider them representations of their whole communities?</li>\n<li>Assuming the PCRs work out and I get nice bands, is there still a risk that the contaminants could disturb the sequencing process? That is, given that I only input 2 out of 25 µl of DNA extract into the first PCR reaction, and just as little PCR product into the second (index/library prep) PCR. Can the Illumina flow cells be sensitive to these contaminants as well?</li>\n</ol>\n<div class=\"s-table-container\">\n<table class=\"s-table\">\n<thead>\n<tr>\n<th>Sample ID</th>\n<th>Nucleic Acid Conc.</th>\n<th>Unit</th>\n<th>A260</th>\n<th>A280</th>\n<th>260/280</th>\n<th>260/230</th>\n<th>Sample Type</th>\n<th>Factor</th>\n</tr>\n</thead>\n<tbody>\n<tr>\n<td>1</td>\n<td>7.6</td>\n<td>ng/µl</td>\n<td>0.152</td>\n<td>0.086</td>\n<td>1.76</td>\n<td>0.71</td>\n<td>DNA</td>\n<td>50</td>\n</tr>\n<tr>\n<td>2</td>\n<td>24</td>\n<td>ng/µl</td>\n<td>0.479</td>\n<td>0.249</td>\n<td>1.93</td>\n<td>1.16</td>\n<td>DNA</td>\n<td>50</td>\n</tr>\n<tr>\n<td>3</td>\n<td>21.9</td>\n<td>ng/µl</td>\n<td>0.439</td>\n<td>0.238</td>\n<td>1.84</td>\n<td>1.15</td>\n<td>DNA</td>\n<td>50</td>\n</tr>\n<tr>\n<td>4</td>\n<td>18.6</td>\n<td>ng/µl</td>\n<td>0.371</td>\n<td>0.190</td>\n<td>1.95</td>\n<td>1.29</td>\n<td>DNA</td>\n<td>50</td>\n</tr>\n<tr>\n<td>5</td>\n<td>18.5</td>\n<td>ng/µl</td>\n<td>0.371</td>\n<td>0.200</td>\n<td>1.85</td>\n<td>1.44</td>\n<td>DNA</td>\n<td>50</td>\n</tr>\n<tr>\n<td>6</td>\n<td>6.9</td>\n<td>ng/µl</td>\n<td>0.138</td>\n<td>0.069</td>\n<td>2.00</td>\n<td>0.70</td>\n<td>DNA</td>\n<td>50</td>\n</tr>\n<tr>\n<td>7</td>\n<td>7.9</td>\n<td>ng/µl</td>\n<td>0.157</td>\n<td>0.092</td>\n<td>1.72</td>\n<td>0.78</td>\n<td>DNA</td>\n<td>50</td>\n</tr>\n<tr>\n<td>8</td>\n<td>35.2</td>\n<td>ng/µl</td>\n<td>0.703</td>\n<td>0.363</td>\n<td>1.94</td>\n<td>1.67</td>\n<td>DNA</td>\n<td>50</td>\n</tr>\n<tr>\n<td>9</td>\n<td>9.6</td>\n<td>ng/µl</td>\n<td>0.192</td>\n<td>0.099</td>\n<td>1.94</td>\n<td>0.85</td>\n<td>DNA</td>\n<td>50</td>\n</tr>\n<tr>\n<td>extraction_blank</td>\n<td>1.6</td>\n<td>ng/µl</td>\n<td>0.031</td>\n<td>0.006</td>\n<td>4.84</td>\n<td>0.19</td>\n<td>DNA</td>\n<td>50</td>\n</tr>\n<tr>\n<td>collection_blank</td>\n<td>3.9</td>\n<td>ng/µl</td>\n<td>0.078</td>\n<td>0.036</td>\n<td>2.19</td>\n<td>0.42</td>\n<td>DNA</td>\n<td>50</td>\n</tr>\n</tbody>\n</table>\n</div>\n<p>According to ThermoFisher &quot;good&quot; values are between 1.8-2.0 for the 260/280 ratio, and 2.0-2.2 for the 260/230 ratio. Less may indicate the presence of salts or EDTA for example. The concentrations are for 100 µl of DNA extract, that is, total DNA yield is given by multiplying the concentrations with 100. For the record, I have heard from people who get 200-300 ng/µl DNA concentrations from marine sediment extractions. My samples should in theory contain even more than that. Although I have earlier only gotten concentrations in the range of 30-100 ng/µl for the same type of samples with the same extraction kit.</p>\n<p>What would you do in this situation? How do you go on with values like this from the spectrophotometer?</p>\n","text":"I'm having troubles with some DNA extractions. The yields are much lower than expected, and the Nanodrop spectrophotometer is showing quite a bit of contamination through the 260/230 ratios (see table below). The samples consist of mixed marine fine-mortarted fauna (environmental samples), of which I want to sequence a couple of marker genes to determine species composition (metabarcoding), using paired-end Illumina MiSeq. I could just go on with the PCR as I'm supposed to and see if that works, but my concerns are still:\n\n\n\n\n\nAs the DNA extracts contain an order of magnitude less DNA than expected, would you really consider them representations of their whole communities?\n\n\n\n\nAssuming the PCRs work out and I get nice bands, is there still a risk that the contaminants could disturb the sequencing process? That is, given that I only input 2 out of 25 µl of DNA extract into the first PCR reaction, and just as little PCR product into the second (index/library prep) PCR. Can the Illumina flow cells be sensitive to these contaminants as well?\n\n\n\n\n\n\n\n\n\n\n\nSample ID\nNucleic Acid Conc.\nUnit\nA260\nA280\n260/280\n260/230\nSample Type\nFactor\n\n\n\n\n\n\n\n\n\t1\n\t7.6\n\tng/µl\n\t0.152\n\t0.086\n\t1.76\n\t0.71\n\tDNA\n\t50\n\n\n\n\n\n\n\t2\n\t24\n\tng/µl\n\t0.479\n\t0.249\n\t1.93\n\t1.16\n\tDNA\n\t50\n\n\n\n\n\n\n\t3\n\t21.9\n\tng/µl\n\t0.439\n\t0.238\n\t1.84\n\t1.15\n\tDNA\n\t50\n\n\n\n\n\n\n\t4\n\t18.6\n\tng/µl\n\t0.371\n\t0.190\n\t1.95\n\t1.29\n\tDNA\n\t50\n\n\n\n\n\n\n\t5\n\t18.5\n\tng/µl\n\t0.371\n\t0.200\n\t1.85\n\t1.44\n\tDNA\n\t50\n\n\n\n\n\n\n\t6\n\t6.9\n\tng/µl\n\t0.138\n\t0.069\n\t2.00\n\t0.70\n\tDNA\n\t50\n\n\n\n\n\n\n\t7\n\t7.9\n\tng/µl\n\t0.157\n\t0.092\n\t1.72\n\t0.78\n\tDNA\n\t50\n\n\n\n\n\n\n\t8\n\t35.2\n\tng/µl\n\t0.703\n\t0.363\n\t1.94\n\t1.67\n\tDNA\n\t50\n\n\n\n\n\n\n\t9\n\t9.6\n\tng/µl\n\t0.192\n\t0.099\n\t1.94\n\t0.85\n\tDNA\n\t50\n\n\n\n\n\n\n\textraction_blank\n\t1.6\n\tng/µl\n\t0.031\n\t0.006\n\t4.84\n\t0.19\n\tDNA\n\t50\n\n\n\n\n\n\n\tcollection_blank\n\t3.9\n\tng/µl\n\t0.078\n\t0.036\n\t2.19\n\t0.42\n\tDNA\n\t50\n\n\n\n\n\n\n\n\n\n\nAccording to ThermoFisher \"good\" values are between 1.8-2.0 for the 260/280 ratio, and 2.0-2.2 for the 260/230 ratio. Less may indicate the presence of salts or EDTA for example. The concentrations are for 100 µl of DNA extract, that is, total DNA yield is given by multiplying the concentrations with 100. For the record, I have heard from people who get 200-300 ng/µl DNA concentrations from marine sediment extractions. My samples should in theory contain even more than that. Although I have earlier only gotten concentrations in the range of 30-100 ng/µl for the same type of samples with the same extraction kit.\n\n\n\n\nWhat would you do in this situation? How do you go on with values like this from the spectrophotometer?"},{"context_id":"113830","html":"<p>I have never performed environmental extractions, and I am not familiar with your specific protocol. I would defer to any other commenters with more experience with these methods. However, I would recommend redoing the extractions, if it is feasible. Any time a standard protocol gives results that are significantly unexpected, it's worth thinking hard about. In this case, where it is your initial step, it's even easier to suggest, since there's much less wasted time than if it were later in your protocol. The quality of your data depends on what goes in, so it's not worth risk it.</p>\n<p>Nanodrop quantification is not particularly reliable for low concentrations like this. That makes the ratios even more questionable. I would not try to make too much of these particular metrics beyond &quot;this was a poor extraction.&quot;</p>\n<p>PCR could certainly give you plenty of DNA even from a minuscule sample - that's the whole point of exponential amplification! But if your extractions are poor enough that they are extremely biased, that would carry on through PCR.</p>\n<p>I would worry less about contaminating the sequencing reaction at the end, but it's still worth trying to get pure DNA. What's your cleanup before dilution? Anyway, if you do have an inhibitor, I would expect it to give issues during PCR.  And you'll be diluting them 20? 100?-fold for loading onto the flow cell.</p>\n","text":"I have never performed environmental extractions, and I am not familiar with your specific protocol. I would defer to any other commenters with more experience with these methods. However, I would recommend redoing the extractions, if it is feasible. Any time a standard protocol gives results that are significantly unexpected, it's worth thinking hard about. In this case, where it is your initial step, it's even easier to suggest, since there's much less wasted time than if it were later in your protocol. The quality of your data depends on what goes in, so it's not worth risk it.\n\n\n\n\nNanodrop quantification is not particularly reliable for low concentrations like this. That makes the ratios even more questionable. I would not try to make too much of these particular metrics beyond \"this was a poor extraction.\"\n\n\n\n\nPCR could certainly give you plenty of DNA even from a minuscule sample - that's the whole point of exponential amplification! But if your extractions are poor enough that they are extremely biased, that would carry on through PCR.\n\n\n\n\nI would worry less about contaminating the sequencing reaction at the end, but it's still worth trying to get pure DNA. What's your cleanup before dilution? Anyway, if you do have an inhibitor, I would expect it to give issues during PCR.  And you'll be diluting them 20? 100?-fold for loading onto the flow cell."}],"domain":"biology","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"ce732160c8bc7677de273dfa1c8eedb712b0491753c58e0e524662cf8b3c7a56","hard_case_family":["no_accepted_answer"],"id":"RHM-6a3002cf87d8a2eb7ffa0d29","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:09.960411+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f3d8f52a1a12ba8e3a85266c887134296fd3686fb5ffec1a38526e2b8ccdcc24_0.json","raw_sha256":"b1b59ebb5f220f357ffaa8464594a3d8f391df66ad06b024355499ef7eff18cb","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=8&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Joel","profile_url":"https://biology.stackexchange.com/users/78437/joel","user_type":"registered"},"created_at":"2024-01-09T00:34:20+00:00","raw_file":"raw/codex_api_v1/85b5645347f81712378316d7ce101572df9f33b4b1773526e317a302b1f0b138_1790824051913889100_0.json","raw_sha256":"6c01c074c3b6604e944aeb1c481e22bdf0b7c0a7082c18421dfbb8bc6388be2e","revision_guid":"0FB5C92D-DFE4-4660-B878-7A37A0A2CD85","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0FB5C92D-DFE4-4660-B878-7A37A0A2CD85/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2024-02-08T03:06:35+00:00","raw_file":"raw/codex_api_v1/85b5645347f81712378316d7ce101572df9f33b4b1773526e317a302b1f0b138_1790824051913889100_0.json","raw_sha256":"6c01c074c3b6604e944aeb1c481e22bdf0b7c0a7082c18421dfbb8bc6388be2e","revision_guid":"2FD2E58C-EDB4-4742-8681-02A80E3F969C","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/2FD2E58C-EDB4-4742-8681-02A80E3F969C/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2024-06-07T04:02:50+00:00","raw_file":"raw/codex_api_v1/85b5645347f81712378316d7ce101572df9f33b4b1773526e317a302b1f0b138_1790824051913889100_0.json","raw_sha256":"6c01c074c3b6604e944aeb1c481e22bdf0b7c0a7082c18421dfbb8bc6388be2e","revision_guid":"E422987F-911F-4DD2-874D-5968373252C3","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/E422987F-911F-4DD2-874D-5968373252C3/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2024-10-05T04:08:30+00:00","raw_file":"raw/codex_api_v1/85b5645347f81712378316d7ce101572df9f33b4b1773526e317a302b1f0b138_1790824051913889100_0.json","raw_sha256":"6c01c074c3b6604e944aeb1c481e22bdf0b7c0a7082c18421dfbb8bc6388be2e","revision_guid":"18D65182-81CF-4B1A-ABBA-D3919E3E96E3","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/18D65182-81CF-4B1A-ABBA-D3919E3E96E3/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113827","source_record_sha256":"8351795abd4cb891aaf4a9a6789721206fd1a9d70f10b72fcd73d16463689217","source_url":"https://biology.stackexchange.com/questions/113827/can-contaminants-in-the-dna-extract-disturb-the-sequencing","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Can contaminants in the DNA extract disturb the sequencing?\nI'm having troubles with some DNA extractions. The yields are much lower than expected, and the Nanodrop spectrophotometer is showing quite a bit of contamination through the 260/230 ratios (see table below). The samples consist of mixed marine fine-mortarted fauna (environmental samples), of which I want to sequence a couple of marker genes to determine species composition (metabarcoding), using paired-end Illumina MiSeq. I could just go on with the PCR as I'm supposed to and see if that works, but my concerns are still:\n\n\n\n\n\nAs the DNA extracts contain an order of magnitude less DNA than expected, would you really consider them representations of their whole communities?\n\n\n\n\nAssuming the PCRs work out and I get nice bands, is there still a risk that the contaminants could disturb the sequencing process? That is, given that I only input 2 out of 25 µl of DNA extract into the first PCR reaction, and just as little PCR product into the second (index/library prep) PCR. Can the Illumina flow cells be sensitive to these contaminants as well?\n\n\n\n\n\n\n\n\n\n\n\nSample ID\nNucleic Acid Conc.\nUnit\nA260\nA280\n260/280\n260/230\nSample Type\nFactor\n\n\n\n\n\n\n\n\n\t1\n\t7.6\n\tng/µl\n\t0.152\n\t0.086\n\t1.76\n\t0.71\n\tDNA\n\t50\n\n\n\n\n\n\n\t2\n\t24\n\tng/µl\n\t0.479\n\t0.249\n\t1.93\n\t1.16\n\tDNA\n\t50\n\n\n\n\n\n\n\t3\n\t21.9\n\tng/µl\n\t0.439\n\t0.238\n\t1.84\n\t1.15\n\tDNA\n\t50\n\n\n\n\n\n\n\t4\n\t18.6\n\tng/µl\n\t0.371\n\t0.190\n\t1.95\n\t1.29\n\tDNA\n\t50\n\n\n\n\n\n\n\t5\n\t18.5\n\tng/µl\n\t0.371\n\t0.200\n\t1.85\n\t1.44\n\tDNA\n\t50\n\n\n\n\n\n\n\t6\n\t6.9\n\tng/µl\n\t0.138\n\t0.069\n\t2.00\n\t0.70\n\tDNA\n\t50\n\n\n\n\n\n\n\t7\n\t7.9\n\tng/µl\n\t0.157\n\t0.092\n\t1.72\n\t0.78\n\tDNA\n\t50\n\n\n\n\n\n\n\t8\n\t35.2\n\tng/µl\n\t0.703\n\t0.363\n\t1.94\n\t1.67\n\tDNA\n\t50\n\n\n\n\n\n\n\t9\n\t9.6\n\tng/µl\n\t0.192\n\t0.099\n\t1.94\n\t0.85\n\tDNA\n\t50\n\n\n\n\n\n\n\textraction_blank\n\t1.6\n\tng/µl\n\t0.031\n\t0.006\n\t4.84\n\t0.19\n\tDNA\n\t50\n\n\n\n\n\n\n\tcollection_blank\n\t3.9\n\tng/µl\n\t0.078\n\t0.036\n\t2.19\n\t0.42\n\tDNA\n\t50\n\n\n\n\n\n\n\n\n\n\nAccording to ThermoFisher \"good\" values are between 1.8-2.0 for the 260/280 ratio, and 2.0-2.2 for the 260/230 ratio. Less may indicate the presence of salts or EDTA for example. The concentrations are for 100 µl of DNA extract, that is, total DNA yield is given by multiplying the concentrations with 100. For the record, I have heard from people who get 200-300 ng/µl DNA concentrations from marine sediment extractions. My samples should in theory contain even more than that. Although I have earlier only gotten concentrations in the range of 30-100 ng/µl for the same type of samples with the same extraction kit.\n\n\n\n\nWhat would you do in this situation? How do you go on with values like this from the spectrophotometer?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113830,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Those are isopods. Springtails are hexapods.</p>\n<p>Some of them are superficially similar, such as <em>Podura aquatica</em>:</p>\n<p><a href=\"https://i.sstatic.net/pe6HE.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/pe6HE.png\" alt=\"enter image description here\" /></a></p>\n","answer_id":114234,"answer_text":"Those are isopods. Springtails are hexapods.\n\n\n\n\nSome of them are superficially similar, such as Podura aquatica:\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/pe6HE.png] (https://i.sstatic.net/pe6HE.png)","answer_url":"https://biology.stackexchange.com/a/114234","author":"solen'ya","author_url":"https://biology.stackexchange.com/users/80107/solenya","content_license":"CC BY-SA 4.0","created_at":"2024-03-03T11:40:37+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:34.916452+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/c30b2ee4524dfb46e5f33f4b25903a084dac408b994a072a95a23d5316da77d4_0.json","raw_sha256":"d256e999531c4e9fa8d45412ad1eaf748ed7e9e1e333fecd19223242a3776160","source_api":"Stack Exchange API 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Is this one or is it something else?</p>\n","text":"[image: enter image description here; source: https://i.sstatic.net/mWAjB.jpg] (https://i.sstatic.net/mWAjB.jpg)\n\n\n\n\nI want to make a terrarium so I was in need for a springtail. Is this one or is it something else?"},{"context_id":"114234","html":"<p>Those are isopods. Springtails are hexapods.</p>\n<p>Some of them are superficially similar, such as <em>Podura aquatica</em>:</p>\n<p><a href=\"https://i.sstatic.net/pe6HE.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/pe6HE.png\" alt=\"enter image description here\" /></a></p>\n","text":"Those are isopods. Springtails are hexapods.\n\n\n\n\nSome of them are superficially similar, such as Podura aquatica:\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/pe6HE.png] (https://i.sstatic.net/pe6HE.png)"}],"domain":"biology","external_citations":["https://i.sstatic.net/mWAjB.jpg","https://i.sstatic.net/pe6HE.png"],"ground_truth_type":"metadata_grounded","group_id":"456d944553735a302d19178a00953edbcf06ba8c7569ee87c789856764319830","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-22a617b36e6ac6620b45768c","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:09.960411+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f3d8f52a1a12ba8e3a85266c887134296fd3686fb5ffec1a38526e2b8ccdcc24_0.json","raw_sha256":"b1b59ebb5f220f357ffaa8464594a3d8f391df66ad06b024355499ef7eff18cb","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=8&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; 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no LLM truth labels"},"query":"An isopod or a springtail?\n[image: enter image description here; source: https://i.sstatic.net/mWAjB.jpg] (https://i.sstatic.net/mWAjB.jpg)\n\n\n\n\nI want to make a terrarium so I was in need for a springtail. Is this one or is it something else?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114234,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>It is the larva of a hemimetabolous insect for sure. Considering it was close to a water body I would say a nymph of some Odonata ?\nThe legs are a bit bulky though, I might be completely wrong.\nThese are not wings yet, they will be there at adult emergence.</p>\n<p>Maybe check these out :\n<a href=\"https://www.pentaxforums.com/gallery/photo-dragonfly-nymph-20082/\" rel=\"noreferrer\">https://www.pentaxforums.com/gallery/photo-dragonfly-nymph-20082/</a></p>\n<p><a href=\"https://www.flyfishbc.com/threads/april-2011-fly-o-the-month-dragonfly-nymph-gomphus.5843/\" rel=\"noreferrer\">https://www.flyfishbc.com/threads/april-2011-fly-o-the-month-dragonfly-nymph-gomphus.5843/</a></p>\n<p>Edit : my colleague Dirk Mikolajewski says it is a Gomphidae larvae. He will probably tell you which species soon.</p>\n","answer_id":113981,"answer_text":"It is the larva of a hemimetabolous insect for sure. Considering it was close to a water body I would say a nymph of some Odonata ?\nThe legs are a bit bulky though, I might be completely wrong.\nThese are not wings yet, they will be there at adult emergence.\n\n\n\n\nMaybe check these out :\nhttps://www.pentaxforums.com/gallery/photo-dragonfly-nymph-20082/ (https://www.pentaxforums.com/gallery/photo-dragonfly-nymph-20082/)\n\n\n\n\nhttps://www.flyfishbc.com/threads/april-2011-fly-o-the-month-dragonfly-nymph-gomphus.5843/ (https://www.flyfishbc.com/threads/april-2011-fly-o-the-month-dragonfly-nymph-gomphus.5843/)\n\n\n\n\nEdit : my colleague Dirk Mikolajewski says it is a Gomphidae larvae. He will probably tell you which species soon.","answer_url":"https://biology.stackexchange.com/a/113981","author":"CaroZ","author_url":"https://biology.stackexchange.com/users/26370/caroz","content_license":"CC BY-SA 4.0","created_at":"2024-01-28T12:43:16+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:34.916452+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/c30b2ee4524dfb46e5f33f4b25903a084dac408b994a072a95a23d5316da77d4_0.json","raw_sha256":"d256e999531c4e9fa8d45412ad1eaf748ed7e9e1e333fecd19223242a3776160","source_api":"Stack Exchange API 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BY-SA 4.0","contributor":{"display_name":"CaroZ","profile_url":"https://biology.stackexchange.com/users/26370/caroz","user_type":"registered"},"created_at":"2024-01-29T13:55:25+00:00","raw_file":"raw/codex_api_v1/7731e95f5b86805dcc210d6fef6f1ae90aedbea29d6d8084621d880fcd44e459_1790824059333573800_0.json","raw_sha256":"75346ea86ff90b8db1427552949ecffb611214a9308b4f99afbdda87d5df239e","revision_guid":"92FD4608-F652-433E-8652-227A9954B3B9","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/92FD4608-F652-433E-8652-227A9954B3B9/view-source"}],"url":"https://biology.stackexchange.com/a/113981"}],"contexts":[{"context_id":"question","html":"<p><a href=\"https://i.sstatic.net/auj8g.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/auj8g.jpg\" alt=\"enter image description here\" /></a><a href=\"https://i.sstatic.net/Orcio.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/Orcio.jpg\" alt=\"enter image description here\" /></a></p>\n<p>It was about 2-3cm long\nIt has two small wings and 6 legs</p>\n","text":"[image: enter image description here; source: https://i.sstatic.net/auj8g.jpg] (https://i.sstatic.net/auj8g.jpg)[image: enter image description here; source: https://i.sstatic.net/Orcio.jpg] (https://i.sstatic.net/Orcio.jpg)\n\n\n\n\nIt was about 2-3cm long\nIt has two small wings and 6 legs"},{"context_id":"113981","html":"<p>It is the larva of a hemimetabolous insect for sure. Considering it was close to a water body I would say a nymph of some Odonata ?\nThe legs are a bit bulky though, I might be completely wrong.\nThese are not wings yet, they will be there at adult emergence.</p>\n<p>Maybe check these out :\n<a href=\"https://www.pentaxforums.com/gallery/photo-dragonfly-nymph-20082/\" rel=\"noreferrer\">https://www.pentaxforums.com/gallery/photo-dragonfly-nymph-20082/</a></p>\n<p><a href=\"https://www.flyfishbc.com/threads/april-2011-fly-o-the-month-dragonfly-nymph-gomphus.5843/\" rel=\"noreferrer\">https://www.flyfishbc.com/threads/april-2011-fly-o-the-month-dragonfly-nymph-gomphus.5843/</a></p>\n<p>Edit : my colleague Dirk Mikolajewski says it is a Gomphidae larvae. He will probably tell you which species soon.</p>\n","text":"It is the larva of a hemimetabolous insect for sure. Considering it was close to a water body I would say a nymph of some Odonata ?\nThe legs are a bit bulky though, I might be completely wrong.\nThese are not wings yet, they will be there at adult emergence.\n\n\n\n\nMaybe check these out :\nhttps://www.pentaxforums.com/gallery/photo-dragonfly-nymph-20082/ (https://www.pentaxforums.com/gallery/photo-dragonfly-nymph-20082/)\n\n\n\n\nhttps://www.flyfishbc.com/threads/april-2011-fly-o-the-month-dragonfly-nymph-gomphus.5843/ (https://www.flyfishbc.com/threads/april-2011-fly-o-the-month-dragonfly-nymph-gomphus.5843/)\n\n\n\n\nEdit : my colleague Dirk Mikolajewski says it is a Gomphidae larvae. He will probably tell you which species soon."}],"domain":"biology","external_citations":["https://i.sstatic.net/Orcio.jpg","https://i.sstatic.net/auj8g.jpg","https://www.flyfishbc.com/threads/april-2011-fly-o-the-month-dragonfly-nymph-gomphus.5843/","https://www.pentaxforums.com/gallery/photo-dragonfly-nymph-20082/"],"ground_truth_type":"metadata_grounded","group_id":"6fa8b19064ef070b34a439196fa4eb727e589641a6fab34a4462b39acca99f2c","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-9acb503cb425ec327527b815","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:09.960411+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f3d8f52a1a12ba8e3a85266c887134296fd3686fb5ffec1a38526e2b8ccdcc24_0.json","raw_sha256":"b1b59ebb5f220f357ffaa8464594a3d8f391df66ad06b024355499ef7eff18cb","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=8&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Robin Schlipper","profile_url":"https://biology.stackexchange.com/users/78715/robin-schlipper","user_type":"registered"},"created_at":"2024-01-27T18:57:57+00:00","raw_file":"raw/codex_api_v1/7731e95f5b86805dcc210d6fef6f1ae90aedbea29d6d8084621d880fcd44e459_1790824059333573800_0.json","raw_sha256":"75346ea86ff90b8db1427552949ecffb611214a9308b4f99afbdda87d5df239e","revision_guid":"53821001-C704-4A35-B84E-801E99FAA91D","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/53821001-C704-4A35-B84E-801E99FAA91D/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Robin Schlipper","profile_url":"https://biology.stackexchange.com/users/78715/robin-schlipper","user_type":"registered"},"created_at":"2024-01-28T23:07:56+00:00","raw_file":"raw/codex_api_v1/7731e95f5b86805dcc210d6fef6f1ae90aedbea29d6d8084621d880fcd44e459_1790824059333573800_0.json","raw_sha256":"75346ea86ff90b8db1427552949ecffb611214a9308b4f99afbdda87d5df239e","revision_guid":"AB6A4F6C-400B-4B82-B30F-61B4EDE44684","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AB6A4F6C-400B-4B82-B30F-61B4EDE44684/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2024-01-29T21:38:19+00:00","raw_file":"raw/codex_api_v1/7731e95f5b86805dcc210d6fef6f1ae90aedbea29d6d8084621d880fcd44e459_1790824059333573800_0.json","raw_sha256":"75346ea86ff90b8db1427552949ecffb611214a9308b4f99afbdda87d5df239e","revision_guid":"DF5C9D7D-FA53-4201-9FB6-847AAFC9F53A","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DF5C9D7D-FA53-4201-9FB6-847AAFC9F53A/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"113978","source_record_sha256":"b26951cc7a833dfa9d47aca81d7ad849244e75e11840d5ce6765363db92a988e","source_url":"https://biology.stackexchange.com/questions/113978/identification-of-an-insect-found-near-the-rhine-germany","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Identification of an insect found near the Rhine, Germany\n[image: enter image description here; source: https://i.sstatic.net/auj8g.jpg] (https://i.sstatic.net/auj8g.jpg)[image: enter image description here; source: https://i.sstatic.net/Orcio.jpg] (https://i.sstatic.net/Orcio.jpg)\n\n\n\n\nIt was about 2-3cm long\nIt has two small wings and 6 legs","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113981,"score":9}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Possibly one of the extremely fast growing aquatic plants such as <a href=\"https://en.wikipedia.org/wiki/Azolla\" rel=\"nofollow noreferrer\">Azolla</a> might be an option. Plants in this genus are sometimes mentioned as carbon dioxide remediation mechanisms due to their extremely fast doubling times.</p>\n<p>Anything else that shows high productivity (rate of carbon fixation/photosynthesis) might be an option. You would obviously need to tailor the environment to suit that high growth rate, as suggested by commenters.</p>\n<p>I was surprised to <a href=\"https://phys.org/news/2013-07-air-hidden-indoor.html\" rel=\"nofollow noreferrer\">read just now</a> that plants apparently are (can be!) actually effective at indoor CO2 remediation. I had not thought that they were terribly effective. Though some of this is due to other associated organisms e.g. bacteria in potting soil.</p>\n","answer_id":114030,"answer_text":"Possibly one of the extremely fast growing aquatic plants such as Azolla (https://en.wikipedia.org/wiki/Azolla) might be an option. Plants in this genus are sometimes mentioned as carbon dioxide remediation mechanisms due to their extremely fast doubling times.\n\n\n\n\nAnything else that shows high productivity (rate of carbon fixation/photosynthesis) might be an option. You would obviously need to tailor the environment to suit that high growth rate, as suggested by commenters.\n\n\n\n\nI was surprised to read just now (https://phys.org/news/2013-07-air-hidden-indoor.html) that plants apparently are (can be!) actually effective at indoor CO2 remediation. I had not thought that they were terribly effective. Though some of this is due to other associated organisms e.g. bacteria in potting soil.","answer_url":"https://biology.stackexchange.com/a/114030","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2024-02-04T21:26:54+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:30.839943+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2139ae0ecb1bf62b149af3f8e91d7ce461ad269d38020aaf05922333eabb51a1_0.json","raw_sha256":"2610bc07f1691b2794681a23d0459bba24822de1f31c7b48d79495b29b0b1285","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/114428;114427;114412;114410;114399;114395;114391;114386;114385;114381;114378;114377;114376;114374;114372;114371;114370;114361;114354;114353;114348;114342;114331;114329;114324;114321;114319;114307;114305;114304;114299;114298;114295;114290;114281;114277;114273;114266;114256;114239;114238;114222;114216;114213;114211;114207;114197;114192;114185;114180;114178;114175;114174;114173;114172;114169;114161;114156;114155;114148;114145;114144;114139;114136;114135;114127;114119;114117;114114;114111;114110;114103;114098;114096;114094;114089;114085;114078;114076;114069;114067;114065;114058;114055;114048;114045;114038;114031;114028;114027;114025;114021;114020;114012;114006;113998;113997;113988;113986;113983/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114025,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-02-04T21:26:54+00:00","raw_file":"raw/codex_api_v1/7731e95f5b86805dcc210d6fef6f1ae90aedbea29d6d8084621d880fcd44e459_1790824059333573800_0.json","raw_sha256":"75346ea86ff90b8db1427552949ecffb611214a9308b4f99afbdda87d5df239e","revision_guid":"0DD08E9C-DE66-4DA1-917D-D7E715DAFA8F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0DD08E9C-DE66-4DA1-917D-D7E715DAFA8F/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"greg messer","author_url":"https://biology.stackexchange.com/users/78782/greg-messer","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"greg messer","profile_url":"https://biology.stackexchange.com/users/78782/greg-messer","user_type":"registered"},"created_at":"2024-02-03T21:42:53+00:00","raw_file":"raw/codex_api_v1/7731e95f5b86805dcc210d6fef6f1ae90aedbea29d6d8084621d880fcd44e459_1790824059333573800_0.json","raw_sha256":"75346ea86ff90b8db1427552949ecffb611214a9308b4f99afbdda87d5df239e","revision_guid":"A86C4E46-EFD9-4603-8ED7-168E3363038E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A86C4E46-EFD9-4603-8ED7-168E3363038E/view-source"}],"url":"https://biology.stackexchange.com/questions/114025/what-indoor-plants-or-groups-of-plants-are-significant-consumers-of-co2"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"114030","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-02-04T21:26:54+00:00","raw_file":"raw/codex_api_v1/7731e95f5b86805dcc210d6fef6f1ae90aedbea29d6d8084621d880fcd44e459_1790824059333573800_0.json","raw_sha256":"75346ea86ff90b8db1427552949ecffb611214a9308b4f99afbdda87d5df239e","revision_guid":"0DD08E9C-DE66-4DA1-917D-D7E715DAFA8F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0DD08E9C-DE66-4DA1-917D-D7E715DAFA8F/view-source"}],"url":"https://biology.stackexchange.com/a/114030"}],"contexts":[{"context_id":"question","html":"<p>I am experimenting with the goal to reduce CO2 ppm in a 4200 sqr ft (12 rooms) dwelling by either distributing more plants through the space, or using a hydroponic garden's air as a source in the dwelling for a CO2 filtering system.\nUsing plants that are high consumers of CO2 will provide ppm data measurements to influence which solution I take.\nWhat plants or groups of plants should I consider?</p>\n<p>Thank You!</p>\n<p>Greg Messer</p>\n","text":"I am experimenting with the goal to reduce CO2 ppm in a 4200 sqr ft (12 rooms) dwelling by either distributing more plants through the space, or using a hydroponic garden's air as a source in the dwelling for a CO2 filtering system.\nUsing plants that are high consumers of CO2 will provide ppm data measurements to influence which solution I take.\nWhat plants or groups of plants should I consider?\n\n\n\n\nThank You!\n\n\n\n\nGreg Messer"},{"context_id":"114030","html":"<p>Possibly one of the extremely fast growing aquatic plants such as <a href=\"https://en.wikipedia.org/wiki/Azolla\" rel=\"nofollow noreferrer\">Azolla</a> might be an option. Plants in this genus are sometimes mentioned as carbon dioxide remediation mechanisms due to their extremely fast doubling times.</p>\n<p>Anything else that shows high productivity (rate of carbon fixation/photosynthesis) might be an option. You would obviously need to tailor the environment to suit that high growth rate, as suggested by commenters.</p>\n<p>I was surprised to <a href=\"https://phys.org/news/2013-07-air-hidden-indoor.html\" rel=\"nofollow noreferrer\">read just now</a> that plants apparently are (can be!) actually effective at indoor CO2 remediation. I had not thought that they were terribly effective. Though some of this is due to other associated organisms e.g. bacteria in potting soil.</p>\n","text":"Possibly one of the extremely fast growing aquatic plants such as Azolla (https://en.wikipedia.org/wiki/Azolla) might be an option. Plants in this genus are sometimes mentioned as carbon dioxide remediation mechanisms due to their extremely fast doubling times.\n\n\n\n\nAnything else that shows high productivity (rate of carbon fixation/photosynthesis) might be an option. You would obviously need to tailor the environment to suit that high growth rate, as suggested by commenters.\n\n\n\n\nI was surprised to read just now (https://phys.org/news/2013-07-air-hidden-indoor.html) that plants apparently are (can be!) actually effective at indoor CO2 remediation. I had not thought that they were terribly effective. Though some of this is due to other associated organisms e.g. bacteria in potting soil."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Azolla","https://phys.org/news/2013-07-air-hidden-indoor.html"],"ground_truth_type":"metadata_grounded","group_id":"fd23d3a48ef0f5fff502e77903752250e36fb6943ef50111f857a623911af899","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-74cccdda3901e5b4a90155ad","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:08.576606+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1051d4f3e38449f1419d1973ac812b2286659e454a76f89a23fdaa941dfadddb_0.json","raw_sha256":"583dcd577e20d33b29e9f8818a7ab6a1fab039c19ab79927e16096cff23fa61d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=7&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"greg messer","profile_url":"https://biology.stackexchange.com/users/78782/greg-messer","user_type":"registered"},"created_at":"2024-02-03T21:42:53+00:00","raw_file":"raw/codex_api_v1/7731e95f5b86805dcc210d6fef6f1ae90aedbea29d6d8084621d880fcd44e459_1790824059333573800_0.json","raw_sha256":"75346ea86ff90b8db1427552949ecffb611214a9308b4f99afbdda87d5df239e","revision_guid":"A86C4E46-EFD9-4603-8ED7-168E3363038E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A86C4E46-EFD9-4603-8ED7-168E3363038E/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114025","source_record_sha256":"30c27145ec443cfa0c77529173f6ac7d97706ac2dde41866f8d128c2fd14bd0a","source_url":"https://biology.stackexchange.com/questions/114025/what-indoor-plants-or-groups-of-plants-are-significant-consumers-of-co2","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What indoor plants or groups of plants are significant consumers of CO2?\nI am experimenting with the goal to reduce CO2 ppm in a 4200 sqr ft (12 rooms) dwelling by either distributing more plants through the space, or using a hydroponic garden's air as a source in the dwelling for a CO2 filtering system.\nUsing plants that are high consumers of CO2 will provide ppm data measurements to influence which solution I take.\nWhat plants or groups of plants should I consider?\n\n\n\n\nThank You!\n\n\n\n\nGreg Messer","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114030,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p><strong>It <em>is</em> theoretically possible</strong><br>\n<a href=\"https://i.sstatic.net/fO67F.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/fO67F.png\" alt=\"ATP and ADP structures compared\" /></a><br>\nThe structures of ATP and ADP are shown above, with the phosphate groups designated α, β and γ. The value of the Gibbs standard free energy of hydrolysis of the α–β phosphoanhydride bond of ADP is <a href=\"https://vrchemistry.chem.ox.ac.uk/chapter22/page29.htm\" rel=\"nofollow noreferrer\">similar</a> to that of the β–γ phosphoanhydride bond of ATP at approx. 30 kJ per mol. Hence it is <em>theoretically</em> possible to couple the hydrolysis of the α–β phosphoanhydride bond of ADP to an energy-requiring process and produce an overall negative ΔG.<br>(The reader may wish to consult an external source — e.g. <a href=\"https://biology.stackexchange.com/questions/44334/what-is-atp-and-why-is-it-said-to-be-a-source-of-energy/44341#44341\">this previous SE Biology answer</a> — if unfamiliar with a chemical account of the popular but imprecise idea of ATP as a “source of energy”.)</p>\n<p><strong>The hydrolysis of the analogous bond of <em>ATP</em> is so used</strong><br>\nMost reactions and processes for which ATP provides the driving free energy change involve the hydrolysis of the β–γ phosphoanhydride bond in the reaction:<br>\n<code>ATP → ADP + Pi</code><br>\nHowever in several synthetic processes the energy is provided from the hydrolysis of the α–β phosphoanhydride bond in the reaction:<br>\n<code>ATP → AMP + PPi</code><br>\nThese include RNA synthesis (to form a phosphodiester bond) and amino-acyl tRNA synthesis (to form the aminoacyl bond, which itself provides the energy to drive peptide bond formation).</p>\n<p><strong>Examples of ADP hydrolysis driving energy-requiring reactions?</strong><br>\nAlthough this may merely reflect my ignorance, <em>I know of no reactions</em> of the sort:<br>\n<code>ADP → AMP + Pi</code><br>\nwhere the energy of hydrolysis is used to form a chemical bond etc. <br>\nSo, although I may be proved wrong, <strong>my</strong> answer is <strong>NO</strong>. But…</p>\n<p>…a <em>possible</em> exception — not producing inorganic phosphate — is the <a href=\"https://en.wikipedia.org/wiki/Adenylate_kinase\" rel=\"nofollow noreferrer\">adenylate kinase</a> reaction, for which the overall standard free energy change is near zero:<br>\n<code>2 ADP ⇔ ATP + AMP</code><br>\nThis could be considered as using the energy of hydrolysis of the α–β phosphoanhydride of one of the molecules of ADP to form the β–γ phosphoanhydride bond of ATP. This is thought to be important in the regulation of glycolysis, the AMP produced serving as a signal for the requirement of energy and acting as an activator of the enzyme phosphofructokinase.</p>\n<p><strong>Why — or why not?</strong><br>\n“Why” questions are dangerous in biology, as there is a tendency to argue that the way things are are the way they must be; and there are generally no tests of hypotheses in support of such a view. Nor did the original poster ask why. But with the strict understanding that what follows is <em>just speculation</em>, I offer these thoughts in support of my generally negative answer:<br></p>\n<ul>\n<li><a href=\"https://biology.stackexchange.com/questions/11286/why-is-atp-the-preferred-choice-for-energy-carriers/50928#50928\">I have argued previously</a> that an NTP (ATP — perhaps by chance)\ndeveloped as the “universal energy currency” because it was already\ninvolved in RNA synthesis in the hypothetical RNA world. Clearly this\nrequires hydrolysis of the α–β phosphoanhydride bond of a nucleoside\nphosphate molecule. The argument for ATP over ADP would be that the\npyrophosphate produced in the former process is further hydrolysed to\ninorganic phosphate by pyrophosphates, and the irreversibility of the\nreaction (heat is produced) is important to prevent RNA synthesis\nreversing. As NTPs had to be synthesized anyway, they could also be\nused for other purposes, but it was energetically more efficient to\nhydrolyse the β–γ phosphoanhydride bond if irreversibility was not\ncrucial (e.g. the product removed).</li>\n<li>Once ATP became fixed as the energy currency, metabolism was tuned\nfor its production and, later regulation. Thus the development of\nsystems for anaerobic and aerobic synthesis of ADP would not have\nconferred any advantage on an organism. When regulatory systems\ndeveloped in involving the relative concentrations of ATP, ADP and\nAMP (as mentioned above), using ADP to drive reactions would have\nbeen disruptive.</li>\n</ul>\n","answer_id":114049,"answer_text":"It is theoretically possible\n\n[image: ATP and ADP structures compared; source: https://i.sstatic.net/fO67F.png] (https://i.sstatic.net/fO67F.png)\n\nThe structures of ATP and ADP are shown above, with the phosphate groups designated α, β and γ. The value of the Gibbs standard free energy of hydrolysis of the α–β phosphoanhydride bond of ADP is similar (https://vrchemistry.chem.ox.ac.uk/chapter22/page29.htm) to that of the β–γ phosphoanhydride bond of ATP at approx. 30 kJ per mol. Hence it is theoretically possible to couple the hydrolysis of the α–β phosphoanhydride bond of ADP to an energy-requiring process and produce an overall negative ΔG.\n(The reader may wish to consult an external source — e.g. this previous SE Biology answer (https://biology.stackexchange.com/questions/44334/what-is-atp-and-why-is-it-said-to-be-a-source-of-energy/44341#44341) — if unfamiliar with a chemical account of the popular but imprecise idea of ATP as a “source of energy”.)\n\n\n\n\nThe hydrolysis of the analogous bond of ATP is so used\n\nMost reactions and processes for which ATP provides the driving free energy change involve the hydrolysis of the β–γ phosphoanhydride bond in the reaction:\n\nATP → ADP + Pi\n\nHowever in several synthetic processes the energy is provided from the hydrolysis of the α–β phosphoanhydride bond in the reaction:\n\nATP → AMP + PPi\n\nThese include RNA synthesis (to form a phosphodiester bond) and amino-acyl tRNA synthesis (to form the aminoacyl bond, which itself provides the energy to drive peptide bond formation).\n\n\n\n\nExamples of ADP hydrolysis driving energy-requiring reactions?\n\nAlthough this may merely reflect my ignorance, I know of no reactions of the sort:\n\nADP → AMP + Pi\n\nwhere the energy of hydrolysis is used to form a chemical bond etc. \n\nSo, although I may be proved wrong, my answer is NO. But…\n\n\n\n\n…a possible exception — not producing inorganic phosphate — is the adenylate kinase (https://en.wikipedia.org/wiki/Adenylate_kinase) reaction, for which the overall standard free energy change is near zero:\n\n2 ADP ⇔ ATP + AMP\n\nThis could be considered as using the energy of hydrolysis of the α–β phosphoanhydride of one of the molecules of ADP to form the β–γ phosphoanhydride bond of ATP. This is thought to be important in the regulation of glycolysis, the AMP produced serving as a signal for the requirement of energy and acting as an activator of the enzyme phosphofructokinase.\n\n\n\n\nWhy — or why not?\n\n“Why” questions are dangerous in biology, as there is a tendency to argue that the way things are are the way they must be; and there are generally no tests of hypotheses in support of such a view. Nor did the original poster ask why. But with the strict understanding that what follows is just speculation, I offer these thoughts in support of my generally negative answer:\n\n\n\n\n\n\nI have argued previously (https://biology.stackexchange.com/questions/11286/why-is-atp-the-preferred-choice-for-energy-carriers/50928#50928) that an NTP (ATP — perhaps by chance)\ndeveloped as the “universal energy currency” because it was already\ninvolved in RNA synthesis in the hypothetical RNA world. Clearly this\nrequires hydrolysis of the α–β phosphoanhydride bond of a nucleoside\nphosphate molecule. The argument for ATP over ADP would be that the\npyrophosphate produced in the former process is further hydrolysed to\ninorganic phosphate by pyrophosphates, and the irreversibility of the\nreaction (heat is produced) is important to prevent RNA synthesis\nreversing. As NTPs had to be synthesized anyway, they could also be\nused for other purposes, but it was energetically more efficient to\nhydrolyse the β–γ phosphoanhydride bond if irreversibility was not\ncrucial (e.g. the product removed).\n\n\n\n\nOnce ATP became fixed as the energy currency, metabolism was tuned\nfor its production and, later regulation. Thus the development of\nsystems for anaerobic and aerobic synthesis of ADP would not have\nconferred any advantage on an organism. When regulatory systems\ndeveloped in involving the relative concentrations of ATP, ADP and\nAMP (as mentioned above), using ADP to drive reactions would have\nbeen disruptive.","answer_url":"https://biology.stackexchange.com/a/114049","author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","created_at":"2024-02-06T17:07:15+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:30.839943+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2139ae0ecb1bf62b149af3f8e91d7ce461ad269d38020aaf05922333eabb51a1_0.json","raw_sha256":"2610bc07f1691b2794681a23d0459bba24822de1f31c7b48d79495b29b0b1285","source_api":"Stack Exchange API 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similar, but I am unaware of instances where its free energy of hydrolysis is used in a similar way. Is this theoretically possible, and are there any actual examples?</p>\n","text":"The free energy of the hydrolysis of the β-γ phosphoanhydride bond of ATP is used to drive energy-requiring biological process such as chemical synthesis, movement, ion transport and production of light.\n\n\n\n\nHowever the chemical structure of the α-β phosphoanhydride bond of ADP appears very similar, but I am unaware of instances where its free energy of hydrolysis is used in a similar way. Is this theoretically possible, and are there any actual examples?"},{"context_id":"114049","html":"<p><strong>It <em>is</em> theoretically possible</strong><br>\n<a href=\"https://i.sstatic.net/fO67F.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/fO67F.png\" alt=\"ATP and ADP structures compared\" /></a><br>\nThe structures of ATP and ADP are shown above, with the phosphate groups designated α, β and γ. The value of the Gibbs standard free energy of hydrolysis of the α–β phosphoanhydride bond of ADP is <a href=\"https://vrchemistry.chem.ox.ac.uk/chapter22/page29.htm\" rel=\"nofollow noreferrer\">similar</a> to that of the β–γ phosphoanhydride bond of ATP at approx. 30 kJ per mol. Hence it is <em>theoretically</em> possible to couple the hydrolysis of the α–β phosphoanhydride bond of ADP to an energy-requiring process and produce an overall negative ΔG.<br>(The reader may wish to consult an external source — e.g. <a href=\"https://biology.stackexchange.com/questions/44334/what-is-atp-and-why-is-it-said-to-be-a-source-of-energy/44341#44341\">this previous SE Biology answer</a> — if unfamiliar with a chemical account of the popular but imprecise idea of ATP as a “source of energy”.)</p>\n<p><strong>The hydrolysis of the analogous bond of <em>ATP</em> is so used</strong><br>\nMost reactions and processes for which ATP provides the driving free energy change involve the hydrolysis of the β–γ phosphoanhydride bond in the reaction:<br>\n<code>ATP → ADP + Pi</code><br>\nHowever in several synthetic processes the energy is provided from the hydrolysis of the α–β phosphoanhydride bond in the reaction:<br>\n<code>ATP → AMP + PPi</code><br>\nThese include RNA synthesis (to form a phosphodiester bond) and amino-acyl tRNA synthesis (to form the aminoacyl bond, which itself provides the energy to drive peptide bond formation).</p>\n<p><strong>Examples of ADP hydrolysis driving energy-requiring reactions?</strong><br>\nAlthough this may merely reflect my ignorance, <em>I know of no reactions</em> of the sort:<br>\n<code>ADP → AMP + Pi</code><br>\nwhere the energy of hydrolysis is used to form a chemical bond etc. <br>\nSo, although I may be proved wrong, <strong>my</strong> answer is <strong>NO</strong>. But…</p>\n<p>…a <em>possible</em> exception — not producing inorganic phosphate — is the <a href=\"https://en.wikipedia.org/wiki/Adenylate_kinase\" rel=\"nofollow noreferrer\">adenylate kinase</a> reaction, for which the overall standard free energy change is near zero:<br>\n<code>2 ADP ⇔ ATP + AMP</code><br>\nThis could be considered as using the energy of hydrolysis of the α–β phosphoanhydride of one of the molecules of ADP to form the β–γ phosphoanhydride bond of ATP. This is thought to be important in the regulation of glycolysis, the AMP produced serving as a signal for the requirement of energy and acting as an activator of the enzyme phosphofructokinase.</p>\n<p><strong>Why — or why not?</strong><br>\n“Why” questions are dangerous in biology, as there is a tendency to argue that the way things are are the way they must be; and there are generally no tests of hypotheses in support of such a view. Nor did the original poster ask why. But with the strict understanding that what follows is <em>just speculation</em>, I offer these thoughts in support of my generally negative answer:<br></p>\n<ul>\n<li><a href=\"https://biology.stackexchange.com/questions/11286/why-is-atp-the-preferred-choice-for-energy-carriers/50928#50928\">I have argued previously</a> that an NTP (ATP — perhaps by chance)\ndeveloped as the “universal energy currency” because it was already\ninvolved in RNA synthesis in the hypothetical RNA world. Clearly this\nrequires hydrolysis of the α–β phosphoanhydride bond of a nucleoside\nphosphate molecule. The argument for ATP over ADP would be that the\npyrophosphate produced in the former process is further hydrolysed to\ninorganic phosphate by pyrophosphates, and the irreversibility of the\nreaction (heat is produced) is important to prevent RNA synthesis\nreversing. As NTPs had to be synthesized anyway, they could also be\nused for other purposes, but it was energetically more efficient to\nhydrolyse the β–γ phosphoanhydride bond if irreversibility was not\ncrucial (e.g. the product removed).</li>\n<li>Once ATP became fixed as the energy currency, metabolism was tuned\nfor its production and, later regulation. Thus the development of\nsystems for anaerobic and aerobic synthesis of ADP would not have\nconferred any advantage on an organism. When regulatory systems\ndeveloped in involving the relative concentrations of ATP, ADP and\nAMP (as mentioned above), using ADP to drive reactions would have\nbeen disruptive.</li>\n</ul>\n","text":"It is theoretically possible\n\n[image: ATP and ADP structures compared; source: https://i.sstatic.net/fO67F.png] (https://i.sstatic.net/fO67F.png)\n\nThe structures of ATP and ADP are shown above, with the phosphate groups designated α, β and γ. The value of the Gibbs standard free energy of hydrolysis of the α–β phosphoanhydride bond of ADP is similar (https://vrchemistry.chem.ox.ac.uk/chapter22/page29.htm) to that of the β–γ phosphoanhydride bond of ATP at approx. 30 kJ per mol. Hence it is theoretically possible to couple the hydrolysis of the α–β phosphoanhydride bond of ADP to an energy-requiring process and produce an overall negative ΔG.\n(The reader may wish to consult an external source — e.g. this previous SE Biology answer (https://biology.stackexchange.com/questions/44334/what-is-atp-and-why-is-it-said-to-be-a-source-of-energy/44341#44341) — if unfamiliar with a chemical account of the popular but imprecise idea of ATP as a “source of energy”.)\n\n\n\n\nThe hydrolysis of the analogous bond of ATP is so used\n\nMost reactions and processes for which ATP provides the driving free energy change involve the hydrolysis of the β–γ phosphoanhydride bond in the reaction:\n\nATP → ADP + Pi\n\nHowever in several synthetic processes the energy is provided from the hydrolysis of the α–β phosphoanhydride bond in the reaction:\n\nATP → AMP + PPi\n\nThese include RNA synthesis (to form a phosphodiester bond) and amino-acyl tRNA synthesis (to form the aminoacyl bond, which itself provides the energy to drive peptide bond formation).\n\n\n\n\nExamples of ADP hydrolysis driving energy-requiring reactions?\n\nAlthough this may merely reflect my ignorance, I know of no reactions of the sort:\n\nADP → AMP + Pi\n\nwhere the energy of hydrolysis is used to form a chemical bond etc. \n\nSo, although I may be proved wrong, my answer is NO. But…\n\n\n\n\n…a possible exception — not producing inorganic phosphate — is the adenylate kinase (https://en.wikipedia.org/wiki/Adenylate_kinase) reaction, for which the overall standard free energy change is near zero:\n\n2 ADP ⇔ ATP + AMP\n\nThis could be considered as using the energy of hydrolysis of the α–β phosphoanhydride of one of the molecules of ADP to form the β–γ phosphoanhydride bond of ATP. This is thought to be important in the regulation of glycolysis, the AMP produced serving as a signal for the requirement of energy and acting as an activator of the enzyme phosphofructokinase.\n\n\n\n\nWhy — or why not?\n\n“Why” questions are dangerous in biology, as there is a tendency to argue that the way things are are the way they must be; and there are generally no tests of hypotheses in support of such a view. Nor did the original poster ask why. But with the strict understanding that what follows is just speculation, I offer these thoughts in support of my generally negative answer:\n\n\n\n\n\n\nI have argued previously (https://biology.stackexchange.com/questions/11286/why-is-atp-the-preferred-choice-for-energy-carriers/50928#50928) that an NTP (ATP — perhaps by chance)\ndeveloped as the “universal energy currency” because it was already\ninvolved in RNA synthesis in the hypothetical RNA world. Clearly this\nrequires hydrolysis of the α–β phosphoanhydride bond of a nucleoside\nphosphate molecule. The argument for ATP over ADP would be that the\npyrophosphate produced in the former process is further hydrolysed to\ninorganic phosphate by pyrophosphates, and the irreversibility of the\nreaction (heat is produced) is important to prevent RNA synthesis\nreversing. As NTPs had to be synthesized anyway, they could also be\nused for other purposes, but it was energetically more efficient to\nhydrolyse the β–γ phosphoanhydride bond if irreversibility was not\ncrucial (e.g. the product removed).\n\n\n\n\nOnce ATP became fixed as the energy currency, metabolism was tuned\nfor its production and, later regulation. Thus the development of\nsystems for anaerobic and aerobic synthesis of ADP would not have\nconferred any advantage on an organism. When regulatory systems\ndeveloped in involving the relative concentrations of ATP, ADP and\nAMP (as mentioned above), using ADP to drive reactions would have\nbeen disruptive."}],"domain":"biology","external_citations":["https://biology.stackexchange.com/questions/11286/why-is-atp-the-preferred-choice-for-energy-carriers/50928#50928","https://biology.stackexchange.com/questions/44334/what-is-atp-and-why-is-it-said-to-be-a-source-of-energy/44341#44341","https://en.wikipedia.org/wiki/Adenylate_kinase","https://i.sstatic.net/fO67F.png","https://vrchemistry.chem.ox.ac.uk/chapter22/page29.htm"],"ground_truth_type":"metadata_grounded","group_id":"3b0e4f0d881c106f3e9f57f5f580b707846bb44c4208cfb6045a7f962cbde6a0","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-7acb481e59a46f8816c7f316","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:08.576606+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1051d4f3e38449f1419d1973ac812b2286659e454a76f89a23fdaa941dfadddb_0.json","raw_sha256":"583dcd577e20d33b29e9f8818a7ab6a1fab039c19ab79927e16096cff23fa61d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=7&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Archonic","profile_url":"https://biology.stackexchange.com/users/78798/archonic","user_type":"registered"},"created_at":"2024-02-05T15:20:43+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"D8171097-037F-41C9-B957-683DE9D7E9F4","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D8171097-037F-41C9-B957-683DE9D7E9F4/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-02-05T23:21:50+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"E20ECB01-A5C9-4913-A04C-5409520218DB","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/E20ECB01-A5C9-4913-A04C-5409520218DB/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2024-02-06T13:21:31+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"9C14198B-6F4E-4A42-AD7E-D6CD2795FB68","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9C14198B-6F4E-4A42-AD7E-D6CD2795FB68/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2024-02-06T15:55:16+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"50BEC3EE-1BDA-4241-A15A-ED122352FC00","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/50BEC3EE-1BDA-4241-A15A-ED122352FC00/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2024-02-06T16:02:38+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"9C57ECE8-B7B9-499B-BE4D-B5C81DE10725","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9C57ECE8-B7B9-499B-BE4D-B5C81DE10725/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114038","source_record_sha256":"a321a7d18213265ee1c9c7f3a7c8bd76f512068533eb9853c4933ab8602e2db1","source_url":"https://biology.stackexchange.com/questions/114038/use-of-adp-hydrolysis-for-driving-energy-requiring-processes","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Use of ADP hydrolysis for driving energy-requiring processes?\nThe free energy of the hydrolysis of the β-γ phosphoanhydride bond of ATP is used to drive energy-requiring biological process such as chemical synthesis, movement, ion transport and production of light.\n\n\n\n\nHowever the chemical structure of the α-β phosphoanhydride bond of ADP appears very similar, but I am unaware of instances where its free energy of hydrolysis is used in a similar way. Is this theoretically possible, and are there any actual examples?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114049,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>this is basically the argument behind maximum likelihood tree inference. <a href=\"https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwif1sTTu6SEAxXOMDQIHUxPCyoQFnoECBoQAQ&amp;url=https%3A%2F%2Facademic.oup.com%2Fsysbio%2Farticle-abstract%2F27%2F4%2F401%2F1734959&amp;usg=AOvVaw1oxVLYPKi5lig3sT5jfAqq&amp;opi=89978449\" rel=\"nofollow noreferrer\">Parsimony can lead to a lot of issues</a>, as argued in the classic Felsenstein paper (linked).</p>\n<p><a href=\"http://abacus.gene.ucl.ac.uk/ziheng/pdf/1993YangMBEv10p1396.pdf\" rel=\"nofollow noreferrer\">Here</a> is a brief paper discussing a particular improvement to the max likelihood method for tree inference in which substitution rates among sites are allowed to vary, which is another critical factor affecting tree topology estimation in a ML framework that can lead to the different mutational paths you show. I think it's a good entry point showing the value of ML over parsimony in incorporating multiple possible mutational paths with different interpretations (topologies).</p>\n<p>If you are talking purely about cases in which the infinite alleles model isn't appropriate, I <a href=\"https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwjlu471u6SEAxWvHTQIHYm3BVcQFnoECBgQAQ&amp;url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC6435258%2F&amp;usg=AOvVaw2j9olDOgQ1_No2bjpqzY72&amp;opi=89978449\" rel=\"nofollow noreferrer\">wrote a review on this topic</a> a few years ago (see box 1 for some mutational paths very similar to the one that you present).</p>\n<p>I am not sure how perturbation analysis fits into this or what the Feynman diagram means.</p>\n","answer_id":114079,"answer_text":"this is basically the argument behind maximum likelihood tree inference. Parsimony can lead to a lot of issues (https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwif1sTTu6SEAxXOMDQIHUxPCyoQFnoECBoQAQ&url=https%3A%2F%2Facademic.oup.com%2Fsysbio%2Farticle-abstract%2F27%2F4%2F401%2F1734959&usg=AOvVaw1oxVLYPKi5lig3sT5jfAqq&opi=89978449), as argued in the classic Felsenstein paper (linked).\n\n\n\n\nHere (http://abacus.gene.ucl.ac.uk/ziheng/pdf/1993YangMBEv10p1396.pdf) is a brief paper discussing a particular improvement to the max likelihood method for tree inference in which substitution rates among sites are allowed to vary, which is another critical factor affecting tree topology estimation in a ML framework that can lead to the different mutational paths you show. I think it's a good entry point showing the value of ML over parsimony in incorporating multiple possible mutational paths with different interpretations (topologies).\n\n\n\n\nIf you are talking purely about cases in which the infinite alleles model isn't appropriate, I wrote a review on this topic (https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjlu471u6SEAxWvHTQIHYm3BVcQFnoECBgQAQ&url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC6435258%2F&usg=AOvVaw2j9olDOgQ1_No2bjpqzY72&opi=89978449) a few years ago (see box 1 for some mutational paths very similar to the one that you present).\n\n\n\n\nI am not sure how perturbation analysis fits into this or what the Feynman diagram means.","answer_url":"https://biology.stackexchange.com/a/114079","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2024-02-11T23:47:32+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:30.839943+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2139ae0ecb1bf62b149af3f8e91d7ce461ad269d38020aaf05922333eabb51a1_0.json","raw_sha256":"2610bc07f1691b2794681a23d0459bba24822de1f31c7b48d79495b29b0b1285","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/114428;114427;114412;114410;114399;114395;114391;114386;114385;114381;114378;114377;114376;114374;114372;114371;114370;114361;114354;114353;114348;114342;114331;114329;114324;114321;114319;114307;114305;114304;114299;114298;114295;114290;114281;114277;114273;114266;114256;114239;114238;114222;114216;114213;114211;114207;114197;114192;114185;114180;114178;114175;114174;114173;114172;114169;114161;114156;114155;114148;114145;114144;114139;114136;114135;114127;114119;114117;114114;114111;114110;114103;114098;114096;114094;114089;114085;114078;114076;114069;114067;114065;114058;114055;114048;114045;114038;114031;114028;114027;114025;114021;114020;114012;114006;113998;113997;113988;113986;113983/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114067,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-02-11T23:47:32+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"F8C83616-81C7-40B7-B2E7-007808E4E1B0","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F8C83616-81C7-40B7-B2E7-007808E4E1B0/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-02-20T21:32:57+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"5FDF3EB2-9774-4FE3-BD6F-2E5EADD94CEF","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5FDF3EB2-9774-4FE3-BD6F-2E5EADD94CEF/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"BigMistake","author_url":"https://biology.stackexchange.com/users/75355/bigmistake","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"BigMistake","profile_url":"https://biology.stackexchange.com/users/75355/bigmistake","user_type":"registered"},"created_at":"2024-02-10T18:10:16+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"45B4C891-3EA1-4586-AC22-4E4D72FD1E10","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/45B4C891-3EA1-4586-AC22-4E4D72FD1E10/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"BigMistake","profile_url":"https://biology.stackexchange.com/users/75355/bigmistake","user_type":"registered"},"created_at":"2024-02-11T17:30:27+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"78EF0BF4-A4F6-479D-9204-E6193948EC19","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/78EF0BF4-A4F6-479D-9204-E6193948EC19/view-source"}],"url":"https://biology.stackexchange.com/questions/114067/has-perturbation-theory-been-applied-to-mutation-process-frameworks"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"114079","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-02-11T23:47:32+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"F8C83616-81C7-40B7-B2E7-007808E4E1B0","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F8C83616-81C7-40B7-B2E7-007808E4E1B0/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-02-20T21:32:57+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"5FDF3EB2-9774-4FE3-BD6F-2E5EADD94CEF","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5FDF3EB2-9774-4FE3-BD6F-2E5EADD94CEF/view-source"}],"url":"https://biology.stackexchange.com/a/114079"}],"contexts":[{"context_id":"question","html":"<p>For example, imagine this Feynman diagram:</p>\n<p><a href=\"https://i.sstatic.net/GpwLi.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/GpwLi.png\" alt=\"Source\" /></a></p>\n<p>This is analogous to mutational homoplasy.</p>\n<p>When comparing haplotypes, there are many possible tree topologies. Under maximum parsimony, we ignore suboptimal tree paths which certainly occur sometimes in reality. For example, imagine the following two haplotypes:</p>\n<p>1: C A T T G</p>\n<p>2: C A T A A</p>\n<p>There are two mutations that make these different.</p>\n<p>Maximum parsimony may infer this intermediate, not directly observed haplotype:</p>\n<p>C A T A G</p>\n<p>If we move from 1 to 2, the tree looks like:</p>\n<p>C A T T G --&gt; C A T A G --&gt; C A T A A</p>\n<p>However, the following is also possible:</p>\n<p>C A T T G --&gt; C A T A G --&gt; C A T T G --&gt; C A T A G</p>\n<p>Or:</p>\n<p>C A T T G --&gt; C A T T C --&gt; C A T A C --&gt; C T T A C --&gt; C A T A C --&gt; C A T A C --&gt; C A T A G</p>\n<p>The not-directly-observed haplotype is analogous to the virtual particle. The directly observed haplotypes are the non-virtual particles. One could construct Feynman diagrams that look similar except have haplotypes instead of particles.</p>\n<p>It is possible to imagine that some less-likely haplotypes actually are more harmonious with the observations. It seems that perturbation theory may help.</p>\n<p>I don't have completely formalized thoughts on this. I am wondering if this has actually been used before to make a mutation process framework (e.g., an improvement to the infinite alleles model).</p>\n","text":"For example, imagine this Feynman diagram:\n\n\n\n\n[image: Source; source: https://i.sstatic.net/GpwLi.png] (https://i.sstatic.net/GpwLi.png)\n\n\n\n\nThis is analogous to mutational homoplasy.\n\n\n\n\nWhen comparing haplotypes, there are many possible tree topologies. Under maximum parsimony, we ignore suboptimal tree paths which certainly occur sometimes in reality. For example, imagine the following two haplotypes:\n\n\n\n\n1: C A T T G\n\n\n\n\n2: C A T A A\n\n\n\n\nThere are two mutations that make these different.\n\n\n\n\nMaximum parsimony may infer this intermediate, not directly observed haplotype:\n\n\n\n\nC A T A G\n\n\n\n\nIf we move from 1 to 2, the tree looks like:\n\n\n\n\nC A T T G --> C A T A G --> C A T A A\n\n\n\n\nHowever, the following is also possible:\n\n\n\n\nC A T T G --> C A T A G --> C A T T G --> C A T A G\n\n\n\n\nOr:\n\n\n\n\nC A T T G --> C A T T C --> C A T A C --> C T T A C --> C A T A C --> C A T A C --> C A T A G\n\n\n\n\nThe not-directly-observed haplotype is analogous to the virtual particle. The directly observed haplotypes are the non-virtual particles. One could construct Feynman diagrams that look similar except have haplotypes instead of particles.\n\n\n\n\nIt is possible to imagine that some less-likely haplotypes actually are more harmonious with the observations. It seems that perturbation theory may help.\n\n\n\n\nI don't have completely formalized thoughts on this. I am wondering if this has actually been used before to make a mutation process framework (e.g., an improvement to the infinite alleles model)."},{"context_id":"114079","html":"<p>this is basically the argument behind maximum likelihood tree inference. <a href=\"https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwif1sTTu6SEAxXOMDQIHUxPCyoQFnoECBoQAQ&amp;url=https%3A%2F%2Facademic.oup.com%2Fsysbio%2Farticle-abstract%2F27%2F4%2F401%2F1734959&amp;usg=AOvVaw1oxVLYPKi5lig3sT5jfAqq&amp;opi=89978449\" rel=\"nofollow noreferrer\">Parsimony can lead to a lot of issues</a>, as argued in the classic Felsenstein paper (linked).</p>\n<p><a href=\"http://abacus.gene.ucl.ac.uk/ziheng/pdf/1993YangMBEv10p1396.pdf\" rel=\"nofollow noreferrer\">Here</a> is a brief paper discussing a particular improvement to the max likelihood method for tree inference in which substitution rates among sites are allowed to vary, which is another critical factor affecting tree topology estimation in a ML framework that can lead to the different mutational paths you show. I think it's a good entry point showing the value of ML over parsimony in incorporating multiple possible mutational paths with different interpretations (topologies).</p>\n<p>If you are talking purely about cases in which the infinite alleles model isn't appropriate, I <a href=\"https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwjlu471u6SEAxWvHTQIHYm3BVcQFnoECBgQAQ&amp;url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC6435258%2F&amp;usg=AOvVaw2j9olDOgQ1_No2bjpqzY72&amp;opi=89978449\" rel=\"nofollow noreferrer\">wrote a review on this topic</a> a few years ago (see box 1 for some mutational paths very similar to the one that you present).</p>\n<p>I am not sure how perturbation analysis fits into this or what the Feynman diagram means.</p>\n","text":"this is basically the argument behind maximum likelihood tree inference. Parsimony can lead to a lot of issues (https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwif1sTTu6SEAxXOMDQIHUxPCyoQFnoECBoQAQ&url=https%3A%2F%2Facademic.oup.com%2Fsysbio%2Farticle-abstract%2F27%2F4%2F401%2F1734959&usg=AOvVaw1oxVLYPKi5lig3sT5jfAqq&opi=89978449), as argued in the classic Felsenstein paper (linked).\n\n\n\n\nHere (http://abacus.gene.ucl.ac.uk/ziheng/pdf/1993YangMBEv10p1396.pdf) is a brief paper discussing a particular improvement to the max likelihood method for tree inference in which substitution rates among sites are allowed to vary, which is another critical factor affecting tree topology estimation in a ML framework that can lead to the different mutational paths you show. I think it's a good entry point showing the value of ML over parsimony in incorporating multiple possible mutational paths with different interpretations (topologies).\n\n\n\n\nIf you are talking purely about cases in which the infinite alleles model isn't appropriate, I wrote a review on this topic (https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjlu471u6SEAxWvHTQIHYm3BVcQFnoECBgQAQ&url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC6435258%2F&usg=AOvVaw2j9olDOgQ1_No2bjpqzY72&opi=89978449) a few years ago (see box 1 for some mutational paths very similar to the one that you present).\n\n\n\n\nI am not sure how perturbation analysis fits into this or what the Feynman diagram means."}],"domain":"biology","external_citations":["http://abacus.gene.ucl.ac.uk/ziheng/pdf/1993YangMBEv10p1396.pdf","https://i.sstatic.net/GpwLi.png","https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwif1sTTu6SEAxXOMDQIHUxPCyoQFnoECBoQAQ&url=https%3A%2F%2Facademic.oup.com%2Fsysbio%2Farticle-abstract%2F27%2F4%2F401%2F1734959&usg=AOvVaw1oxVLYPKi5lig3sT5jfAqq&opi=89978449","https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjlu471u6SEAxWvHTQIHYm3BVcQFnoECBgQAQ&url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC6435258%2F&usg=AOvVaw2j9olDOgQ1_No2bjpqzY72&opi=89978449"],"ground_truth_type":"metadata_grounded","group_id":"3576238525794596442f8d1e6cb748bf286493baf605a67d3ca93ca0f3522dcd","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-7715045a537d3a526da87796","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:08.576606+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1051d4f3e38449f1419d1973ac812b2286659e454a76f89a23fdaa941dfadddb_0.json","raw_sha256":"583dcd577e20d33b29e9f8818a7ab6a1fab039c19ab79927e16096cff23fa61d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=7&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"BigMistake","profile_url":"https://biology.stackexchange.com/users/75355/bigmistake","user_type":"registered"},"created_at":"2024-02-10T18:10:16+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"45B4C891-3EA1-4586-AC22-4E4D72FD1E10","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/45B4C891-3EA1-4586-AC22-4E4D72FD1E10/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"BigMistake","profile_url":"https://biology.stackexchange.com/users/75355/bigmistake","user_type":"registered"},"created_at":"2024-02-11T17:30:27+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"78EF0BF4-A4F6-479D-9204-E6193948EC19","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/78EF0BF4-A4F6-479D-9204-E6193948EC19/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114067","source_record_sha256":"0445b7524055bccad1c44cb53d9266c16c81b8d4c489640e7e8a32e0913034eb","source_url":"https://biology.stackexchange.com/questions/114067/has-perturbation-theory-been-applied-to-mutation-process-frameworks","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Has perturbation theory been applied to mutation process frameworks?\nFor example, imagine this Feynman diagram:\n\n\n\n\n[image: Source; source: https://i.sstatic.net/GpwLi.png] (https://i.sstatic.net/GpwLi.png)\n\n\n\n\nThis is analogous to mutational homoplasy.\n\n\n\n\nWhen comparing haplotypes, there are many possible tree topologies. Under maximum parsimony, we ignore suboptimal tree paths which certainly occur sometimes in reality. For example, imagine the following two haplotypes:\n\n\n\n\n1: C A T T G\n\n\n\n\n2: C A T A A\n\n\n\n\nThere are two mutations that make these different.\n\n\n\n\nMaximum parsimony may infer this intermediate, not directly observed haplotype:\n\n\n\n\nC A T A G\n\n\n\n\nIf we move from 1 to 2, the tree looks like:\n\n\n\n\nC A T T G --> C A T A G --> C A T A A\n\n\n\n\nHowever, the following is also possible:\n\n\n\n\nC A T T G --> C A T A G --> C A T T G --> C A T A G\n\n\n\n\nOr:\n\n\n\n\nC A T T G --> C A T T C --> C A T A C --> C T T A C --> C A T A C --> C A T A C --> C A T A G\n\n\n\n\nThe not-directly-observed haplotype is analogous to the virtual particle. The directly observed haplotypes are the non-virtual particles. One could construct Feynman diagrams that look similar except have haplotypes instead of particles.\n\n\n\n\nIt is possible to imagine that some less-likely haplotypes actually are more harmonious with the observations. It seems that perturbation theory may help.\n\n\n\n\nI don't have completely formalized thoughts on this. I am wondering if this has actually been used before to make a mutation process framework (e.g., an improvement to the infinite alleles model).","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114079,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>There actually is a <a href=\"https://www.nature.com/articles/s41598-020-80891-0\" rel=\"noreferrer\">study</a> in the Nature magazine <strong>identifying the volatile</strong> (in the sense that they easily evaporate, as most aromatic substances do) <strong>organic compounds in cherry flower essential oils</strong> (basically a liquid cherry flower &quot;extract&quot; in which these volatile organic compounds are enriched by a process similar to distillation) the researchers made from cherry flowers from four different cultivators.</p>\n<p>In the study, you find <a href=\"https://www.nature.com/articles/s41598-020-80891-0/tables/6\" rel=\"noreferrer\">a table</a>.\nIt contains a list of the volatile organic compounds found, including\nhow much they found in the essential oil created from the cherry blossoms from each cultivator, respectively.</p>\n<p>I copied (one copy-paste suffices) the table into a spreadsheet program (LibreOffice Calc), and then added a column with the average share (probably wrt. weight, see study for details) of the respective volatile organic compound found (averaged over the four oils the scientists made from the blossoms from the four different cultivators), and sorted the table by that column.</p>\n<p>The compounds with the largest average share are:</p>\n<div class=\"s-table-container\"><table class=\"s-table\">\n<thead>\n<tr>\n<th>compound</th>\n<th style=\"text-align: right;\">average share [%]</th>\n<th>taste</th>\n</tr>\n</thead>\n<tbody>\n<tr>\n<td>Ethanol</td>\n<td style=\"text-align: right;\">15.8600</td>\n<td><a href=\"https://en.wikipedia.org/wiki/Ethanol\" rel=\"noreferrer\">it's alcohol</a></td>\n</tr>\n<tr>\n<td>(E)-2-Hexenal</td>\n<td style=\"text-align: right;\">11.4725</td>\n<td><a href=\"https://de.wikipedia.org/wiki/2-Hexenal\" rel=\"noreferrer\">like green apples</a></td>\n</tr>\n<tr>\n<td>Benzaldehyde</td>\n<td style=\"text-align: right;\">10.4025</td>\n<td><a href=\"https://en.wikipedia.org/wiki/Benzaldehyde\" rel=\"noreferrer\">like cherries</a></td>\n</tr>\n<tr>\n<td>Dimethyl sulfide</td>\n<td style=\"text-align: right;\">5.7000</td>\n<td><a href=\"https://en.wikipedia.org/wiki/Dimethyl_sulfide\" rel=\"noreferrer\">savory</a></td>\n</tr>\n<tr>\n<td>Acetaldehyde</td>\n<td style=\"text-align: right;\">5.4625</td>\n<td><a href=\"https://beerandbrewing.com/off-flavor-of-the-week-acetaldehyde/\" rel=\"noreferrer\">tart flavor, like green apples or dry cider</a></td>\n</tr>\n<tr>\n<td>Linalool</td>\n<td style=\"text-align: right;\">4.0625</td>\n<td><a href=\"https://shop.perfumersapprentice.com/p-6699-linalool-natural.aspx\" rel=\"noreferrer\">flowery and citrus like flavor</a></td>\n</tr>\n</tbody>\n</table></div>\n<p>Followed by compounds with shares of less than 2.8%.</p>\n<p>Now the question remains which of these are most important for the cherry blossom taste you observed.</p>\n<p>Regarding this, I would like to remark the following:</p>\n<ul>\n<li><strong>benzaldehyde and linalool probably play a major role</strong>, as you described the taste as black cherry like, and according to this <a href=\"https://myfoodjobrocks.com/dark-cherry/\" rel=\"noreferrer\">article</a>, <strong>benzaldehyde, linalool and eugenol are the most important constituents of the cherry taste</strong> (eugenol was not found in the essential oil, and methyleugenol only had a very small share, see the original <a href=\"https://www.nature.com/articles/s41598-020-80891-0/tables/6\" rel=\"noreferrer\">table</a>).</li>\n<li><strong>Ethanol probably only has little effect</strong> on the flavor, as it has not that strong of a flavor to begin with, and may even have appeared in the study in such large quantities just because the blossoms were not handled quickly enough and rotted a little, so that possibly, in fresh blossoms, one would find much less ethanol.</li>\n<li><strong>Dimethyl sulfide possibly only has little effect</strong> on the flavor of fresh blossoms, as it's savory taste doesn't fit the taste you described and the quantity found in the study may similarly actually mostly be the result of the blossoms rotting (<a href=\"https://en.wikipedia.org/wiki/Dimethyl_sulfide\" rel=\"noreferrer\">as dimethyl sulfide indicates bacterial contamination when brewing</a>).</li>\n</ul>\n<p><strong>Explaining the time delay:</strong></p>\n<p>Obviously, the compounds are at first contained in the cells of the blossoms (mostly in the vacuoles of the cells). <strong>It takes time for the chewing to destroy those cells and for the compounds to leave the destroyed cells</strong> and enter your saliva by diffusion, possibly explaining the short time delay.</p>\n<p><strong>Safety of eating blossoms:</strong></p>\n<p>As you see, those blossoms contain a variety of organic compounds, some of which are actually poisonous in still quite small amounts.\n<strong>I don't know in what amount, if any, those cherry blossoms you ate are safe to eat, maybe they are totally fine, maybe they are fine in small enough amounts, and maybe those specific cherry blossoms are downright poisonous.</strong> This may even depend on details, maybe some cherry blossoms are safe to eat and others aren't (considering <a href=\"https://www.nature.com/articles/s41598-020-80891-0/tables/6\" rel=\"noreferrer\">that table</a> for example, one of the cherry blossom essential oils tested had 0.54% coumarin, while another had none, and coumarin is poisonous). <strong>Please ask someone qualified whether the cherry blossoms you eat are safe.</strong></p>\n","answer_id":114124,"answer_text":"There actually is a study (https://www.nature.com/articles/s41598-020-80891-0) in the Nature magazine identifying the volatile (in the sense that they easily evaporate, as most aromatic substances do) organic compounds in cherry flower essential oils (basically a liquid cherry flower \"extract\" in which these volatile organic compounds are enriched by a process similar to distillation) the researchers made from cherry flowers from four different cultivators.\n\n\n\n\nIn the study, you find a table (https://www.nature.com/articles/s41598-020-80891-0/tables/6).\nIt contains a list of the volatile organic compounds found, including\nhow much they found in the essential oil created from the cherry blossoms from each cultivator, respectively.\n\n\n\n\nI copied (one copy-paste suffices) the table into a spreadsheet program (LibreOffice Calc), and then added a column with the average share (probably wrt. weight, see study for details) of the respective volatile organic compound found (averaged over the four oils the scientists made from the blossoms from the four different cultivators), and sorted the table by that column.\n\n\n\n\nThe compounds with the largest average share are:\n\n\n\n\n\n\n\n\n\ncompound\naverage share [%]\ntaste\n\n\n\n\n\n\n\n\n\tEthanol\n\t15.8600\n\tit's alcohol (https://en.wikipedia.org/wiki/Ethanol)\n\n\n\n\n\n\n\t(E)-2-Hexenal\n\t11.4725\n\tlike green apples (https://de.wikipedia.org/wiki/2-Hexenal)\n\n\n\n\n\n\n\tBenzaldehyde\n\t10.4025\n\tlike cherries (https://en.wikipedia.org/wiki/Benzaldehyde)\n\n\n\n\n\n\n\tDimethyl sulfide\n\t5.7000\n\tsavory (https://en.wikipedia.org/wiki/Dimethyl_sulfide)\n\n\n\n\n\n\n\tAcetaldehyde\n\t5.4625\n\ttart flavor, like green apples or dry cider (https://beerandbrewing.com/off-flavor-of-the-week-acetaldehyde/)\n\n\n\n\n\n\n\tLinalool\n\t4.0625\n\tflowery and citrus like flavor (https://shop.perfumersapprentice.com/p-6699-linalool-natural.aspx)\n\n\n\n\n\n\n\n\n\nFollowed by compounds with shares of less than 2.8%.\n\n\n\n\nNow the question remains which of these are most important for the cherry blossom taste you observed.\n\n\n\n\nRegarding this, I would like to remark the following:\n\n\n\n\n\nbenzaldehyde and linalool probably play a major role, as you described the taste as black cherry like, and according to this article (https://myfoodjobrocks.com/dark-cherry/), benzaldehyde, linalool and eugenol are the most important constituents of the cherry taste (eugenol was not found in the essential oil, and methyleugenol only had a very small share, see the original table (https://www.nature.com/articles/s41598-020-80891-0/tables/6)).\n\n\n\n\nEthanol probably only has little effect on the flavor, as it has not that strong of a flavor to begin with, and may even have appeared in the study in such large quantities just because the blossoms were not handled quickly enough and rotted a little, so that possibly, in fresh blossoms, one would find much less ethanol.\n\n\n\n\nDimethyl sulfide possibly only has little effect on the flavor of fresh blossoms, as it's savory taste doesn't fit the taste you described and the quantity found in the study may similarly actually mostly be the result of the blossoms rotting (as dimethyl sulfide indicates bacterial contamination when brewing (https://en.wikipedia.org/wiki/Dimethyl_sulfide)).\n\n\n\n\n\nExplaining the time delay:\n\n\n\n\nObviously, the compounds are at first contained in the cells of the blossoms (mostly in the vacuoles of the cells). It takes time for the chewing to destroy those cells and for the compounds to leave the destroyed cells and enter your saliva by diffusion, possibly explaining the short time delay.\n\n\n\n\nSafety of eating blossoms:\n\n\n\n\nAs you see, those blossoms contain a variety of organic compounds, some of which are actually poisonous in still quite small amounts.\nI don't know in what amount, if any, those cherry blossoms you ate are safe to eat, maybe they are totally fine, maybe they are fine in small enough amounts, and maybe those specific cherry blossoms are downright poisonous. This may even depend on details, maybe some cherry blossoms are safe to eat and others aren't (considering that table (https://www.nature.com/articles/s41598-020-80891-0/tables/6) for example, one of the cherry blossom essential oils tested had 0.54% coumarin, while another had none, and coumarin is poisonous). Please ask someone qualified whether the cherry blossoms you eat are safe.","answer_url":"https://biology.stackexchange.com/a/114124","author":"KGM","author_url":"https://biology.stackexchange.com/users/76768/kgm","content_license":"CC BY-SA 4.0","created_at":"2024-02-19T00:43:31+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:30.839943+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2139ae0ecb1bf62b149af3f8e91d7ce461ad269d38020aaf05922333eabb51a1_0.json","raw_sha256":"2610bc07f1691b2794681a23d0459bba24822de1f31c7b48d79495b29b0b1285","source_api":"Stack Exchange API 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BY-SA 4.0","contributor":{"display_name":"uhoh","profile_url":"https://biology.stackexchange.com/users/27918/uhoh","user_type":"registered"},"created_at":"2024-02-23T14:58:02+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"9176DF04-5977-459A-868B-A09DEDBB192A","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9176DF04-5977-459A-868B-A09DEDBB192A/view-source"}],"url":"https://biology.stackexchange.com/questions/114094/what-makes-cherry-blossoms-so-delicious-does-this-delicious-molecule-or-molecu"},{"author":"KGM","author_url":"https://biology.stackexchange.com/users/76768/kgm","content_license":"CC BY-SA 4.0","context_id":"114124","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"KGM","profile_url":"https://biology.stackexchange.com/users/76768/kgm","user_type":"registered"},"created_at":"2024-02-19T00:43:31+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"2FBAF4FC-7CE6-45F4-9FC1-E32E304DD67A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2FBAF4FC-7CE6-45F4-9FC1-E32E304DD67A/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"KGM","profile_url":"https://biology.stackexchange.com/users/76768/kgm","user_type":"registered"},"created_at":"2024-02-19T00:49:52+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"0D6DB8A9-290C-40BD-994C-034AFAB9FE81","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0D6DB8A9-290C-40BD-994C-034AFAB9FE81/view-source"},{"content_license":null,"contributor":{"display_name":"uhoh","profile_url":"https://biology.stackexchange.com/users/27918/uhoh","user_type":"registered"},"created_at":"2024-02-20T01:40:44+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"A9D6260E-5446-4AF1-8A1D-58C5DEB9B27C","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/A9D6260E-5446-4AF1-8A1D-58C5DEB9B27C/view-source"}],"url":"https://biology.stackexchange.com/a/114124"}],"contexts":[{"context_id":"question","html":"<p>My friend showed me a news item about a monkey (or macaque) recently (early February) seen in Taiwan eating cherry blossoms. I assumed it must have been eating caterpillars or other insects that eat the blossoms, but a quick search in google found a related video shot in Japan <a href=\"https://youtu.be/1beZGlaWOvU\" rel=\"nofollow noreferrer\">Monkey Eating Cherry Blossoms in Slow Motion</a>.</p>\n<p>So a few days ago I tried a few. I pulled off the petals (since the monkey also seemed uninterested in them) and when I first started chewing I tasted nothing but inert vegetable matter.</p>\n<p>But then over about 15 to 20 seconds of chewing the little blossom bodies I noticed it first became bitter, then slowly increasing taste of what I describe as &quot;Black Cherry&quot; flavor, but without any sweetness. It continued to get stronger and more delicious, and I did not want to stop!</p>\n<p>That day I'd chewed (and eventually swallowed) about a dozen blossoms and felt absolutely wonderful; like I had been treated to a real delicacy.</p>\n<p><strong>note:</strong> The cherry trees planted and cultiated for their decorative blossoms in the early spring are not the same as the trees that yield commercial cherries. I'm told their fruit is quite sour.</p>\n<p><strong>Question:</strong> What makes cherry blossoms so delicious? Does this delicious molecule (or molecules) have some function in the blossom? Does saliva activate it?</p>\n<p>It's possible that it's stored in structures that take time to break down during chewing, but I got the impression that a chemical reaction was taking place, perhaps a bit like how starch becomes sugar as we continue to chew on bread.</p>\n<hr />\n<p><a href=\"https://i.sstatic.net/RlyKK.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/RlyKK.jpg\" alt=\"decorative cherry blossoms in Taipei in early February\" /></a></p>\n<p><a href=\"https://i.sstatic.net/0L5CU.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/0L5CU.jpg\" alt=\"decorative cherry blossoms in Taipei in early February\" /></a></p>\n","text":"My friend showed me a news item about a monkey (or macaque) recently (early February) seen in Taiwan eating cherry blossoms. I assumed it must have been eating caterpillars or other insects that eat the blossoms, but a quick search in google found a related video shot in Japan Monkey Eating Cherry Blossoms in Slow Motion (https://youtu.be/1beZGlaWOvU).\n\n\n\n\nSo a few days ago I tried a few. I pulled off the petals (since the monkey also seemed uninterested in them) and when I first started chewing I tasted nothing but inert vegetable matter.\n\n\n\n\nBut then over about 15 to 20 seconds of chewing the little blossom bodies I noticed it first became bitter, then slowly increasing taste of what I describe as \"Black Cherry\" flavor, but without any sweetness. It continued to get stronger and more delicious, and I did not want to stop!\n\n\n\n\nThat day I'd chewed (and eventually swallowed) about a dozen blossoms and felt absolutely wonderful; like I had been treated to a real delicacy.\n\n\n\n\nnote: The cherry trees planted and cultiated for their decorative blossoms in the early spring are not the same as the trees that yield commercial cherries. I'm told their fruit is quite sour.\n\n\n\n\nQuestion: What makes cherry blossoms so delicious? Does this delicious molecule (or molecules) have some function in the blossom? Does saliva activate it?\n\n\n\n\nIt's possible that it's stored in structures that take time to break down during chewing, but I got the impression that a chemical reaction was taking place, perhaps a bit like how starch becomes sugar as we continue to chew on bread.\n\n\n\n\n\n\n\n[image: decorative cherry blossoms in Taipei in early February; source: https://i.sstatic.net/RlyKK.jpg] (https://i.sstatic.net/RlyKK.jpg)\n\n\n\n\n[image: decorative cherry blossoms in Taipei in early February; source: https://i.sstatic.net/0L5CU.jpg] (https://i.sstatic.net/0L5CU.jpg)"},{"context_id":"114124","html":"<p>There actually is a <a href=\"https://www.nature.com/articles/s41598-020-80891-0\" rel=\"noreferrer\">study</a> in the Nature magazine <strong>identifying the volatile</strong> (in the sense that they easily evaporate, as most aromatic substances do) <strong>organic compounds in cherry flower essential oils</strong> (basically a liquid cherry flower &quot;extract&quot; in which these volatile organic compounds are enriched by a process similar to distillation) the researchers made from cherry flowers from four different cultivators.</p>\n<p>In the study, you find <a href=\"https://www.nature.com/articles/s41598-020-80891-0/tables/6\" rel=\"noreferrer\">a table</a>.\nIt contains a list of the volatile organic compounds found, including\nhow much they found in the essential oil created from the cherry blossoms from each cultivator, respectively.</p>\n<p>I copied (one copy-paste suffices) the table into a spreadsheet program (LibreOffice Calc), and then added a column with the average share (probably wrt. weight, see study for details) of the respective volatile organic compound found (averaged over the four oils the scientists made from the blossoms from the four different cultivators), and sorted the table by that column.</p>\n<p>The compounds with the largest average share are:</p>\n<div class=\"s-table-container\"><table class=\"s-table\">\n<thead>\n<tr>\n<th>compound</th>\n<th style=\"text-align: right;\">average share [%]</th>\n<th>taste</th>\n</tr>\n</thead>\n<tbody>\n<tr>\n<td>Ethanol</td>\n<td style=\"text-align: right;\">15.8600</td>\n<td><a href=\"https://en.wikipedia.org/wiki/Ethanol\" rel=\"noreferrer\">it's alcohol</a></td>\n</tr>\n<tr>\n<td>(E)-2-Hexenal</td>\n<td style=\"text-align: right;\">11.4725</td>\n<td><a href=\"https://de.wikipedia.org/wiki/2-Hexenal\" rel=\"noreferrer\">like green apples</a></td>\n</tr>\n<tr>\n<td>Benzaldehyde</td>\n<td style=\"text-align: right;\">10.4025</td>\n<td><a href=\"https://en.wikipedia.org/wiki/Benzaldehyde\" rel=\"noreferrer\">like cherries</a></td>\n</tr>\n<tr>\n<td>Dimethyl sulfide</td>\n<td style=\"text-align: right;\">5.7000</td>\n<td><a href=\"https://en.wikipedia.org/wiki/Dimethyl_sulfide\" rel=\"noreferrer\">savory</a></td>\n</tr>\n<tr>\n<td>Acetaldehyde</td>\n<td style=\"text-align: right;\">5.4625</td>\n<td><a href=\"https://beerandbrewing.com/off-flavor-of-the-week-acetaldehyde/\" rel=\"noreferrer\">tart flavor, like green apples or dry cider</a></td>\n</tr>\n<tr>\n<td>Linalool</td>\n<td style=\"text-align: right;\">4.0625</td>\n<td><a href=\"https://shop.perfumersapprentice.com/p-6699-linalool-natural.aspx\" rel=\"noreferrer\">flowery and citrus like flavor</a></td>\n</tr>\n</tbody>\n</table></div>\n<p>Followed by compounds with shares of less than 2.8%.</p>\n<p>Now the question remains which of these are most important for the cherry blossom taste you observed.</p>\n<p>Regarding this, I would like to remark the following:</p>\n<ul>\n<li><strong>benzaldehyde and linalool probably play a major role</strong>, as you described the taste as black cherry like, and according to this <a href=\"https://myfoodjobrocks.com/dark-cherry/\" rel=\"noreferrer\">article</a>, <strong>benzaldehyde, linalool and eugenol are the most important constituents of the cherry taste</strong> (eugenol was not found in the essential oil, and methyleugenol only had a very small share, see the original <a href=\"https://www.nature.com/articles/s41598-020-80891-0/tables/6\" rel=\"noreferrer\">table</a>).</li>\n<li><strong>Ethanol probably only has little effect</strong> on the flavor, as it has not that strong of a flavor to begin with, and may even have appeared in the study in such large quantities just because the blossoms were not handled quickly enough and rotted a little, so that possibly, in fresh blossoms, one would find much less ethanol.</li>\n<li><strong>Dimethyl sulfide possibly only has little effect</strong> on the flavor of fresh blossoms, as it's savory taste doesn't fit the taste you described and the quantity found in the study may similarly actually mostly be the result of the blossoms rotting (<a href=\"https://en.wikipedia.org/wiki/Dimethyl_sulfide\" rel=\"noreferrer\">as dimethyl sulfide indicates bacterial contamination when brewing</a>).</li>\n</ul>\n<p><strong>Explaining the time delay:</strong></p>\n<p>Obviously, the compounds are at first contained in the cells of the blossoms (mostly in the vacuoles of the cells). <strong>It takes time for the chewing to destroy those cells and for the compounds to leave the destroyed cells</strong> and enter your saliva by diffusion, possibly explaining the short time delay.</p>\n<p><strong>Safety of eating blossoms:</strong></p>\n<p>As you see, those blossoms contain a variety of organic compounds, some of which are actually poisonous in still quite small amounts.\n<strong>I don't know in what amount, if any, those cherry blossoms you ate are safe to eat, maybe they are totally fine, maybe they are fine in small enough amounts, and maybe those specific cherry blossoms are downright poisonous.</strong> This may even depend on details, maybe some cherry blossoms are safe to eat and others aren't (considering <a href=\"https://www.nature.com/articles/s41598-020-80891-0/tables/6\" rel=\"noreferrer\">that table</a> for example, one of the cherry blossom essential oils tested had 0.54% coumarin, while another had none, and coumarin is poisonous). <strong>Please ask someone qualified whether the cherry blossoms you eat are safe.</strong></p>\n","text":"There actually is a study (https://www.nature.com/articles/s41598-020-80891-0) in the Nature magazine identifying the volatile (in the sense that they easily evaporate, as most aromatic substances do) organic compounds in cherry flower essential oils (basically a liquid cherry flower \"extract\" in which these volatile organic compounds are enriched by a process similar to distillation) the researchers made from cherry flowers from four different cultivators.\n\n\n\n\nIn the study, you find a table (https://www.nature.com/articles/s41598-020-80891-0/tables/6).\nIt contains a list of the volatile organic compounds found, including\nhow much they found in the essential oil created from the cherry blossoms from each cultivator, respectively.\n\n\n\n\nI copied (one copy-paste suffices) the table into a spreadsheet program (LibreOffice Calc), and then added a column with the average share (probably wrt. weight, see study for details) of the respective volatile organic compound found (averaged over the four oils the scientists made from the blossoms from the four different cultivators), and sorted the table by that column.\n\n\n\n\nThe compounds with the largest average share are:\n\n\n\n\n\n\n\n\n\ncompound\naverage share [%]\ntaste\n\n\n\n\n\n\n\n\n\tEthanol\n\t15.8600\n\tit's alcohol (https://en.wikipedia.org/wiki/Ethanol)\n\n\n\n\n\n\n\t(E)-2-Hexenal\n\t11.4725\n\tlike green apples (https://de.wikipedia.org/wiki/2-Hexenal)\n\n\n\n\n\n\n\tBenzaldehyde\n\t10.4025\n\tlike cherries (https://en.wikipedia.org/wiki/Benzaldehyde)\n\n\n\n\n\n\n\tDimethyl sulfide\n\t5.7000\n\tsavory (https://en.wikipedia.org/wiki/Dimethyl_sulfide)\n\n\n\n\n\n\n\tAcetaldehyde\n\t5.4625\n\ttart flavor, like green apples or dry cider (https://beerandbrewing.com/off-flavor-of-the-week-acetaldehyde/)\n\n\n\n\n\n\n\tLinalool\n\t4.0625\n\tflowery and citrus like flavor (https://shop.perfumersapprentice.com/p-6699-linalool-natural.aspx)\n\n\n\n\n\n\n\n\n\nFollowed by compounds with shares of less than 2.8%.\n\n\n\n\nNow the question remains which of these are most important for the cherry blossom taste you observed.\n\n\n\n\nRegarding this, I would like to remark the following:\n\n\n\n\n\nbenzaldehyde and linalool probably play a major role, as you described the taste as black cherry like, and according to this article (https://myfoodjobrocks.com/dark-cherry/), benzaldehyde, linalool and eugenol are the most important constituents of the cherry taste (eugenol was not found in the essential oil, and methyleugenol only had a very small share, see the original table (https://www.nature.com/articles/s41598-020-80891-0/tables/6)).\n\n\n\n\nEthanol probably only has little effect on the flavor, as it has not that strong of a flavor to begin with, and may even have appeared in the study in such large quantities just because the blossoms were not handled quickly enough and rotted a little, so that possibly, in fresh blossoms, one would find much less ethanol.\n\n\n\n\nDimethyl sulfide possibly only has little effect on the flavor of fresh blossoms, as it's savory taste doesn't fit the taste you described and the quantity found in the study may similarly actually mostly be the result of the blossoms rotting (as dimethyl sulfide indicates bacterial contamination when brewing (https://en.wikipedia.org/wiki/Dimethyl_sulfide)).\n\n\n\n\n\nExplaining the time delay:\n\n\n\n\nObviously, the compounds are at first contained in the cells of the blossoms (mostly in the vacuoles of the cells). It takes time for the chewing to destroy those cells and for the compounds to leave the destroyed cells and enter your saliva by diffusion, possibly explaining the short time delay.\n\n\n\n\nSafety of eating blossoms:\n\n\n\n\nAs you see, those blossoms contain a variety of organic compounds, some of which are actually poisonous in still quite small amounts.\nI don't know in what amount, if any, those cherry blossoms you ate are safe to eat, maybe they are totally fine, maybe they are fine in small enough amounts, and maybe those specific cherry blossoms are downright poisonous. This may even depend on details, maybe some cherry blossoms are safe to eat and others aren't (considering that table (https://www.nature.com/articles/s41598-020-80891-0/tables/6) for example, one of the cherry blossom essential oils tested had 0.54% coumarin, while another had none, and coumarin is poisonous). Please ask someone qualified whether the cherry blossoms you eat are safe."}],"domain":"biology","external_citations":["https://beerandbrewing.com/off-flavor-of-the-week-acetaldehyde/","https://de.wikipedia.org/wiki/2-Hexenal","https://en.wikipedia.org/wiki/Benzaldehyde","https://en.wikipedia.org/wiki/Dimethyl_sulfide","https://en.wikipedia.org/wiki/Ethanol","https://i.sstatic.net/0L5CU.jpg","https://i.sstatic.net/RlyKK.jpg","https://myfoodjobrocks.com/dark-cherry/","https://shop.perfumersapprentice.com/p-6699-linalool-natural.aspx","https://www.nature.com/articles/s41598-020-80891-0","https://www.nature.com/articles/s41598-020-80891-0/tables/6","https://youtu.be/1beZGlaWOvU"],"ground_truth_type":"metadata_grounded","group_id":"cdf2018b4af068aee118d26046f3eb729dd182cabc5ac836117cb06b3e398be3","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-f60ae814f52db18ade75325c","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:08.576606+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1051d4f3e38449f1419d1973ac812b2286659e454a76f89a23fdaa941dfadddb_0.json","raw_sha256":"583dcd577e20d33b29e9f8818a7ab6a1fab039c19ab79927e16096cff23fa61d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=7&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"uhoh","profile_url":"https://biology.stackexchange.com/users/27918/uhoh","user_type":"registered"},"created_at":"2024-02-14T15:12:25+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"D165DD2D-9BB0-4A30-9B51-1E57C63C91DB","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D165DD2D-9BB0-4A30-9B51-1E57C63C91DB/view-source"},{"content_license":null,"contributor":{"display_name":"uhoh","profile_url":"https://biology.stackexchange.com/users/27918/uhoh","user_type":"registered"},"created_at":"2024-02-17T07:37:59+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"7DC323B9-0D63-46BB-B4CC-D88A706546B4","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/7DC323B9-0D63-46BB-B4CC-D88A706546B4/view-source"},{"content_license":null,"contributor":{"display_name":"uhoh","profile_url":"https://biology.stackexchange.com/users/27918/uhoh","user_type":"registered"},"created_at":"2024-02-17T07:37:59+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"DB465CA5-E6DA-4B59-8A39-AFC46F588C8A","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/DB465CA5-E6DA-4B59-8A39-AFC46F588C8A/view-source"},{"content_license":null,"contributor":{"display_name":"uhoh","profile_url":"https://biology.stackexchange.com/users/27918/uhoh","user_type":"registered"},"created_at":"2024-02-20T01:40:44+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"193173CE-305E-43BE-97C0-EFA88980ED38","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/193173CE-305E-43BE-97C0-EFA88980ED38/view-source"},{"content_license":null,"contributor":{"display_name":"uhoh","profile_url":"https://biology.stackexchange.com/users/27918/uhoh","user_type":"registered"},"created_at":"2024-02-20T01:40:44+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"7EC8A583-4834-4135-B7CE-86A680BCFD14","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/7EC8A583-4834-4135-B7CE-86A680BCFD14/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"uhoh","profile_url":"https://biology.stackexchange.com/users/27918/uhoh","user_type":"registered"},"created_at":"2024-02-23T14:58:02+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"9176DF04-5977-459A-868B-A09DEDBB192A","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9176DF04-5977-459A-868B-A09DEDBB192A/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114094","source_record_sha256":"32af60ca61a60cb884f67483357cbec52d12f300819842aac58250e8e398e1ad","source_url":"https://biology.stackexchange.com/questions/114094/what-makes-cherry-blossoms-so-delicious-does-this-delicious-molecule-or-molecu","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What makes cherry blossoms so delicious? Does this delicious molecule (or molecules) have some function in the blossom? Does saliva activate it?\nMy friend showed me a news item about a monkey (or macaque) recently (early February) seen in Taiwan eating cherry blossoms. I assumed it must have been eating caterpillars or other insects that eat the blossoms, but a quick search in google found a related video shot in Japan Monkey Eating Cherry Blossoms in Slow Motion (https://youtu.be/1beZGlaWOvU).\n\n\n\n\nSo a few days ago I tried a few. I pulled off the petals (since the monkey also seemed uninterested in them) and when I first started chewing I tasted nothing but inert vegetable matter.\n\n\n\n\nBut then over about 15 to 20 seconds of chewing the little blossom bodies I noticed it first became bitter, then slowly increasing taste of what I describe as \"Black Cherry\" flavor, but without any sweetness. It continued to get stronger and more delicious, and I did not want to stop!\n\n\n\n\nThat day I'd chewed (and eventually swallowed) about a dozen blossoms and felt absolutely wonderful; like I had been treated to a real delicacy.\n\n\n\n\nnote: The cherry trees planted and cultiated for their decorative blossoms in the early spring are not the same as the trees that yield commercial cherries. I'm told their fruit is quite sour.\n\n\n\n\nQuestion: What makes cherry blossoms so delicious? Does this delicious molecule (or molecules) have some function in the blossom? Does saliva activate it?\n\n\n\n\nIt's possible that it's stored in structures that take time to break down during chewing, but I got the impression that a chemical reaction was taking place, perhaps a bit like how starch becomes sugar as we continue to chew on bread.\n\n\n\n\n\n\n\n[image: decorative cherry blossoms in Taipei in early February; source: https://i.sstatic.net/RlyKK.jpg] (https://i.sstatic.net/RlyKK.jpg)\n\n\n\n\n[image: decorative cherry blossoms in Taipei in early February; source: https://i.sstatic.net/0L5CU.jpg] (https://i.sstatic.net/0L5CU.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114124,"score":9}],"split":"test"}
{"accepted_status":{"accepted_answer_id":114168,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The parameters cited by OP are not in conflict.</p>\n<p>The misconception relates to a disconnect between what the theory predicts and the type of observation we have available. This leads to an unnecessary assumption that the observed substitutions have become fixed, as well as a failure to account for standing variation at the time of divergence.</p>\n<p><a href=\"https://doi-org.slo.idm.oclc.org/10.1016/j.tree.2013.09.009\" rel=\"nofollow noreferrer\">Lanfear et al.</a> correctly states that &quot;the rate of evolution at <em>a site</em> is <span class=\"math-container\">$KU × 1/K = U$</span>&quot;. To find the amount of (this type of) evolution between two populations over time, one would calculate <span class=\"math-container\">$UTG$</span>, where <span class=\"math-container\">$T$</span> is the time in number of generations, and <span class=\"math-container\">$G$</span> is the genome size. However, this is a calculation of <em>neutral</em> substitutions that have become <em>fixed</em> across two diverged <em>populations</em>, and is really most appropriate when <span class=\"math-container\">$T$</span> is much greater than the expected time to fixation (<a href=\"https://en.wikipedia.org/wiki/Coalescent_theory#Time_to_coalescence\" rel=\"nofollow noreferrer\"><span class=\"math-container\">$T&gt;2N$</span></a>, where <span class=\"math-container\">$N$</span> is the effective population size).</p>\n<p>To perfectly test the theory, one would need to census all substitutions in both populations in order to differentiate between substitutions that have become fixed and those that are polymorphic.</p>\n<p>The observation we have here, however, is essentially a single individual from each population.</p>\n<p>When one compares two individual genomes that have been separated, the SNPs observed between them will include:</p>\n<ol>\n<li>sites with a SNP that originated since divergence and has become fixed (what the theory is talking about).</li>\n<li>sites that are polymorphic, with SNPs that originated since divergence.</li>\n<li>sites polymorphic in the original population, where a SNP became fixed in one lineage and lost in the other.</li>\n<li>sites polymorphic in the original population that are still polymorphic.</li>\n</ol>\n<h3>SNPs originating since divergence that have become fixed</h3>\n<p>Even just applying the above calculation, considering only fixed SNPs (or those that will become fixed) provides the same order of magnitude as the observation of 30,000 substitutions in humans since divergence with chimps.</p>\n<p><a href=\"https://doi.org/10.1073/pnas.0701705104\" rel=\"nofollow noreferrer\">Bakewell et al.</a> surveyed 5,215,415 synonymous sites, so we'll use that as <span class=\"math-container\">$G$</span>. Assuming 20 years per generation and 7 million years of divergence <span class=\"math-container\">$7×10^6/20= 3.5×10^5$</span> generations:</p>\n<p><span class=\"math-container\">$UTG = 10^{-8} × (3.5×10^5) × 5,215,415 = 18,253$</span> substitutions (though we don't know which of the 30,000 observed substitutions these are).</p>\n<h3>Sites that are polymorphic with SNPs that originated since divergence.</h3>\n<p>New mutations are entering the population all the time, with every individual.</p>\n<p>Imagine this measurement was taken one generation after divergence, and where the ancestral population was all exactly identical.</p>\n<p>The human genome is <span class=\"math-container\">$3×10^9$</span> nucleotides, so <span class=\"math-container\">$10^{-8} × 1 × (3×10^9) = 30$</span> substitutions. Humans and chimps are diploid, so an individual would have ~<span class=\"math-container\">$30$</span> mutations on each set of <span class=\"math-container\">$3×10^9$</span> nucleotides, or ~<span class=\"math-container\">$60$</span> mutations compared to our hypothetical source population.</p>\n<p>As Lanfear pointed out, each one of these substitutions is unlikely to eventually become fixed (they have probability <span class=\"math-container\">$1/K$</span>), but we're taking the measurement now, so we observe them. Many of them are likely to spread in the population at least a little bit, even if they eventually disappear.</p>\n<p>We also know from Bakewell that both the observed human and chimp genomes contain sites that are not only polymorphic in the population, but polymorphic in the sequenced individuals.</p>\n<h3>Sites polymorphic in the original population, where a SNP became fixed in one population and lost in the other</h3>\n<p>Overlooked by OP is the fact that the most recent common ancestor of humans and chimps (which was a population, not an individual) was not full of identical individuals, but contained the standing genetic variation one sees in any species. This allows for the fixation of alternative alleles between the daughter populations, even in the absence of new substitutions.</p>\n<p>We know in fact this happened. The <a href=\"https://doi.org/10.1038/nature10842\" rel=\"nofollow noreferrer\">gorilla genome</a> showed us that ~30% of the gorilla genome is more closely related to human or chimp than the later are to each other. This is due to a phenomenon called incomplete lineage sorting, which occurs when two speciation events occur over a short span of time (again <span class=\"math-container\">$T&lt;2N$</span>; the gorilla/human/chimp split is thought to have occurred ~10 million years ago). It is caused by variation in the ancestral population that gets differentially sorted into the daughter populations.</p>\n<h3>Sites polymorphic in the original population that are still polymorphic</h3>\n<p>It's possible there are still sites that retain polymorphism within the daughter populations that was present in the ancestral population. A wide survey of human and chimp genomes could find these alleles.</p>\n<p>(This may be rare between humans and chimps. Estimates of the <a href=\"https://doi.org/10.1101%2Fgr.6023607\" rel=\"nofollow noreferrer\">human effective population size</a> are generally <span class=\"math-container\">$&lt;10,000$</span>, so <span class=\"math-container\">$2N=20,000$</span>. Our estimate of ~350,000 generations probably means few sites in the genome have failed coalesce in that time.)</p>\n","answer_id":114168,"answer_text":"The parameters cited by OP are not in conflict.\n\n\n\n\nThe misconception relates to a disconnect between what the theory predicts and the type of observation we have available. This leads to an unnecessary assumption that the observed substitutions have become fixed, as well as a failure to account for standing variation at the time of divergence.\n\n\n\n\nLanfear et al. (https://doi-org.slo.idm.oclc.org/10.1016/j.tree.2013.09.009) correctly states that \"the rate of evolution at a site is $KU × 1/K = U$\". To find the amount of (this type of) evolution between two populations over time, one would calculate $UTG$, where $T$ is the time in number of generations, and $G$ is the genome size. However, this is a calculation of neutral substitutions that have become fixed across two diverged populations, and is really most appropriate when $T$ is much greater than the expected time to fixation ($T>2N$ (https://en.wikipedia.org/wiki/Coalescent_theory#Time_to_coalescence), where $N$ is the effective population size).\n\n\n\n\nTo perfectly test the theory, one would need to census all substitutions in both populations in order to differentiate between substitutions that have become fixed and those that are polymorphic.\n\n\n\n\nThe observation we have here, however, is essentially a single individual from each population.\n\n\n\n\nWhen one compares two individual genomes that have been separated, the SNPs observed between them will include:\n\n\n\n\n\nsites with a SNP that originated since divergence and has become fixed (what the theory is talking about).\n\n\n\n\nsites that are polymorphic, with SNPs that originated since divergence.\n\n\n\n\nsites polymorphic in the original population, where a SNP became fixed in one lineage and lost in the other.\n\n\n\n\nsites polymorphic in the original population that are still polymorphic.\n\n\n\n\n\nSNPs originating since divergence that have become fixed\n\n\n\n\nEven just applying the above calculation, considering only fixed SNPs (or those that will become fixed) provides the same order of magnitude as the observation of 30,000 substitutions in humans since divergence with chimps.\n\n\n\n\nBakewell et al. (https://doi.org/10.1073/pnas.0701705104) surveyed 5,215,415 synonymous sites, so we'll use that as $G$. Assuming 20 years per generation and 7 million years of divergence $7×10^6/20= 3.5×10^5$ generations:\n\n\n\n\n$UTG = 10^{-8} × (3.5×10^5) × 5,215,415 = 18,253$ substitutions (though we don't know which of the 30,000 observed substitutions these are).\n\n\n\n\nSites that are polymorphic with SNPs that originated since divergence.\n\n\n\n\nNew mutations are entering the population all the time, with every individual.\n\n\n\n\nImagine this measurement was taken one generation after divergence, and where the ancestral population was all exactly identical.\n\n\n\n\nThe human genome is $3×10^9$ nucleotides, so $10^{-8} × 1 × (3×10^9) = 30$ substitutions. Humans and chimps are diploid, so an individual would have ~$30$ mutations on each set of $3×10^9$ nucleotides, or ~$60$ mutations compared to our hypothetical source population.\n\n\n\n\nAs Lanfear pointed out, each one of these substitutions is unlikely to eventually become fixed (they have probability $1/K$), but we're taking the measurement now, so we observe them. Many of them are likely to spread in the population at least a little bit, even if they eventually disappear.\n\n\n\n\nWe also know from Bakewell that both the observed human and chimp genomes contain sites that are not only polymorphic in the population, but polymorphic in the sequenced individuals.\n\n\n\n\nSites polymorphic in the original population, where a SNP became fixed in one population and lost in the other\n\n\n\n\nOverlooked by OP is the fact that the most recent common ancestor of humans and chimps (which was a population, not an individual) was not full of identical individuals, but contained the standing genetic variation one sees in any species. This allows for the fixation of alternative alleles between the daughter populations, even in the absence of new substitutions.\n\n\n\n\nWe know in fact this happened. The gorilla genome (https://doi.org/10.1038/nature10842) showed us that ~30% of the gorilla genome is more closely related to human or chimp than the later are to each other. This is due to a phenomenon called incomplete lineage sorting, which occurs when two speciation events occur over a short span of time (again $T<2N$; the gorilla/human/chimp split is thought to have occurred ~10 million years ago). It is caused by variation in the ancestral population that gets differentially sorted into the daughter populations.\n\n\n\n\nSites polymorphic in the original population that are still polymorphic\n\n\n\n\nIt's possible there are still sites that retain polymorphism within the daughter populations that was present in the ancestral population. A wide survey of human and chimp genomes could find these alleles.\n\n\n\n\n(This may be rare between humans and chimps. Estimates of the human effective population size (https://doi.org/10.1101%2Fgr.6023607) are generally $<10,000$, so $2N=20,000$. Our estimate of ~350,000 generations probably means few sites in the genome have failed coalesce in that time.)","answer_url":"https://biology.stackexchange.com/a/114168","author":"Darlingtonia","author_url":"https://biology.stackexchange.com/users/1197/darlingtonia","content_license":"CC BY-SA 4.0","created_at":"2024-02-25T06:21:03+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:30.839943+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2139ae0ecb1bf62b149af3f8e91d7ce461ad269d38020aaf05922333eabb51a1_0.json","raw_sha256":"2610bc07f1691b2794681a23d0459bba24822de1f31c7b48d79495b29b0b1285","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/114428;114427;114412;114410;114399;114395;114391;114386;114385;114381;114378;114377;114376;114374;114372;114371;114370;114361;114354;114353;114348;114342;114331;114329;114324;114321;114319;114307;114305;114304;114299;114298;114295;114290;114281;114277;114273;114266;114256;114239;114238;114222;114216;114213;114211;114207;114197;114192;114185;114180;114178;114175;114174;114173;114172;114169;114161;114156;114155;114148;114145;114144;114139;114136;114135;114127;114119;114117;114114;114111;114110;114103;114098;114096;114094;114089;114085;114078;114076;114069;114067;114065;114058;114055;114048;114045;114038;114031;114028;114027;114025;114021;114020;114012;114006;113998;113997;113988;113986;113983/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114127,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Darlingtonia","profile_url":"https://biology.stackexchange.com/users/1197/darlingtonia","user_type":"registered"},"created_at":"2024-02-25T06:21:03+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"E08B6D01-3846-428B-A1E7-6DE4EBFBF3A6","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E08B6D01-3846-428B-A1E7-6DE4EBFBF3A6/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Devin","author_url":"https://biology.stackexchange.com/users/75790/devin","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Devin","profile_url":"https://biology.stackexchange.com/users/75790/devin","user_type":"registered"},"created_at":"2024-02-19T16:14:10+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"2DC8EB7B-AD68-4511-AD8A-AB38EFD28BDB","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2DC8EB7B-AD68-4511-AD8A-AB38EFD28BDB/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Devin","profile_url":"https://biology.stackexchange.com/users/75790/devin","user_type":"registered"},"created_at":"2024-02-19T21:51:00+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"DEAFB10B-42AB-4F0D-B9D7-AAB6E409E2ED","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DEAFB10B-42AB-4F0D-B9D7-AAB6E409E2ED/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Devin","profile_url":"https://biology.stackexchange.com/users/75790/devin","user_type":"registered"},"created_at":"2024-02-19T21:58:57+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"774D7515-3FED-42C7-AC4C-ED7188024CA4","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/774D7515-3FED-42C7-AC4C-ED7188024CA4/view-source"},{"content_license":null,"contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2024-02-25T13:46:11+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"97674E41-E6C9-403D-92DB-CBBF1A1B58CF","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/97674E41-E6C9-403D-92DB-CBBF1A1B58CF/view-source"}],"url":"https://biology.stackexchange.com/questions/114127/how-to-resolve-the-contradiction-between-the-time-required-for-the-fixation-of-n"},{"author":"Darlingtonia","author_url":"https://biology.stackexchange.com/users/1197/darlingtonia","content_license":"CC BY-SA 4.0","context_id":"114168","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Darlingtonia","profile_url":"https://biology.stackexchange.com/users/1197/darlingtonia","user_type":"registered"},"created_at":"2024-02-25T06:21:03+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"E08B6D01-3846-428B-A1E7-6DE4EBFBF3A6","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E08B6D01-3846-428B-A1E7-6DE4EBFBF3A6/view-source"}],"url":"https://biology.stackexchange.com/a/114168"}],"contexts":[{"context_id":"question","html":"<p>More than thirty thousand synonymous single-nucleotide-substitutions have occurred in protein-coding genes in the human genome since the human lineage diverged from the chimp lineage ~7 million years ago (Bakewell et al, 2007, p.7490). Since, by definition, synonymous substitutions don’t change the amino acid, these substitutions must be selectively neutral mutations. For neutral mutations, the rate of evolution is simply equal to the point mutation rate U, “irrespective of selection at other linked loci, changes in population size, or almost any other conceivable complication” (Lanfear et al, 2014, p.36). This is problematic because U is approximately 10 to the -8 power for humans, which means that it took about a hundred million generations for each of these substitutions to become fixed in the human genome. Since each generation is more than ten years, a hundred million generations is more than a billion years, which is much longer than the ~7 million years since the human lineage diverged from the chimp lineage. How is this to be reconciled?</p>\n<p>Bakewell, M. et al, “More genes underwent positive selection in chimpanzee evolution than in human evolution.” Proceedings of the National Academy of Sciences USA, vol 104, pages 7489–7494, 2007</p>\n<p>Lanfear, R. et al, “Population size and the rate of evolution.”\nTrends in Ecology and Evolution, vol 29, pages 33–40, 2014</p>\n","text":"More than thirty thousand synonymous single-nucleotide-substitutions have occurred in protein-coding genes in the human genome since the human lineage diverged from the chimp lineage ~7 million years ago (Bakewell et al, 2007, p.7490). Since, by definition, synonymous substitutions don’t change the amino acid, these substitutions must be selectively neutral mutations. For neutral mutations, the rate of evolution is simply equal to the point mutation rate U, “irrespective of selection at other linked loci, changes in population size, or almost any other conceivable complication” (Lanfear et al, 2014, p.36). This is problematic because U is approximately 10 to the -8 power for humans, which means that it took about a hundred million generations for each of these substitutions to become fixed in the human genome. Since each generation is more than ten years, a hundred million generations is more than a billion years, which is much longer than the ~7 million years since the human lineage diverged from the chimp lineage. How is this to be reconciled?\n\n\n\n\nBakewell, M. et al, “More genes underwent positive selection in chimpanzee evolution than in human evolution.” Proceedings of the National Academy of Sciences USA, vol 104, pages 7489–7494, 2007\n\n\n\n\nLanfear, R. et al, “Population size and the rate of evolution.”\nTrends in Ecology and Evolution, vol 29, pages 33–40, 2014"},{"context_id":"114168","html":"<p>The parameters cited by OP are not in conflict.</p>\n<p>The misconception relates to a disconnect between what the theory predicts and the type of observation we have available. This leads to an unnecessary assumption that the observed substitutions have become fixed, as well as a failure to account for standing variation at the time of divergence.</p>\n<p><a href=\"https://doi-org.slo.idm.oclc.org/10.1016/j.tree.2013.09.009\" rel=\"nofollow noreferrer\">Lanfear et al.</a> correctly states that &quot;the rate of evolution at <em>a site</em> is <span class=\"math-container\">$KU × 1/K = U$</span>&quot;. To find the amount of (this type of) evolution between two populations over time, one would calculate <span class=\"math-container\">$UTG$</span>, where <span class=\"math-container\">$T$</span> is the time in number of generations, and <span class=\"math-container\">$G$</span> is the genome size. However, this is a calculation of <em>neutral</em> substitutions that have become <em>fixed</em> across two diverged <em>populations</em>, and is really most appropriate when <span class=\"math-container\">$T$</span> is much greater than the expected time to fixation (<a href=\"https://en.wikipedia.org/wiki/Coalescent_theory#Time_to_coalescence\" rel=\"nofollow noreferrer\"><span class=\"math-container\">$T&gt;2N$</span></a>, where <span class=\"math-container\">$N$</span> is the effective population size).</p>\n<p>To perfectly test the theory, one would need to census all substitutions in both populations in order to differentiate between substitutions that have become fixed and those that are polymorphic.</p>\n<p>The observation we have here, however, is essentially a single individual from each population.</p>\n<p>When one compares two individual genomes that have been separated, the SNPs observed between them will include:</p>\n<ol>\n<li>sites with a SNP that originated since divergence and has become fixed (what the theory is talking about).</li>\n<li>sites that are polymorphic, with SNPs that originated since divergence.</li>\n<li>sites polymorphic in the original population, where a SNP became fixed in one lineage and lost in the other.</li>\n<li>sites polymorphic in the original population that are still polymorphic.</li>\n</ol>\n<h3>SNPs originating since divergence that have become fixed</h3>\n<p>Even just applying the above calculation, considering only fixed SNPs (or those that will become fixed) provides the same order of magnitude as the observation of 30,000 substitutions in humans since divergence with chimps.</p>\n<p><a href=\"https://doi.org/10.1073/pnas.0701705104\" rel=\"nofollow noreferrer\">Bakewell et al.</a> surveyed 5,215,415 synonymous sites, so we'll use that as <span class=\"math-container\">$G$</span>. Assuming 20 years per generation and 7 million years of divergence <span class=\"math-container\">$7×10^6/20= 3.5×10^5$</span> generations:</p>\n<p><span class=\"math-container\">$UTG = 10^{-8} × (3.5×10^5) × 5,215,415 = 18,253$</span> substitutions (though we don't know which of the 30,000 observed substitutions these are).</p>\n<h3>Sites that are polymorphic with SNPs that originated since divergence.</h3>\n<p>New mutations are entering the population all the time, with every individual.</p>\n<p>Imagine this measurement was taken one generation after divergence, and where the ancestral population was all exactly identical.</p>\n<p>The human genome is <span class=\"math-container\">$3×10^9$</span> nucleotides, so <span class=\"math-container\">$10^{-8} × 1 × (3×10^9) = 30$</span> substitutions. Humans and chimps are diploid, so an individual would have ~<span class=\"math-container\">$30$</span> mutations on each set of <span class=\"math-container\">$3×10^9$</span> nucleotides, or ~<span class=\"math-container\">$60$</span> mutations compared to our hypothetical source population.</p>\n<p>As Lanfear pointed out, each one of these substitutions is unlikely to eventually become fixed (they have probability <span class=\"math-container\">$1/K$</span>), but we're taking the measurement now, so we observe them. Many of them are likely to spread in the population at least a little bit, even if they eventually disappear.</p>\n<p>We also know from Bakewell that both the observed human and chimp genomes contain sites that are not only polymorphic in the population, but polymorphic in the sequenced individuals.</p>\n<h3>Sites polymorphic in the original population, where a SNP became fixed in one population and lost in the other</h3>\n<p>Overlooked by OP is the fact that the most recent common ancestor of humans and chimps (which was a population, not an individual) was not full of identical individuals, but contained the standing genetic variation one sees in any species. This allows for the fixation of alternative alleles between the daughter populations, even in the absence of new substitutions.</p>\n<p>We know in fact this happened. The <a href=\"https://doi.org/10.1038/nature10842\" rel=\"nofollow noreferrer\">gorilla genome</a> showed us that ~30% of the gorilla genome is more closely related to human or chimp than the later are to each other. This is due to a phenomenon called incomplete lineage sorting, which occurs when two speciation events occur over a short span of time (again <span class=\"math-container\">$T&lt;2N$</span>; the gorilla/human/chimp split is thought to have occurred ~10 million years ago). It is caused by variation in the ancestral population that gets differentially sorted into the daughter populations.</p>\n<h3>Sites polymorphic in the original population that are still polymorphic</h3>\n<p>It's possible there are still sites that retain polymorphism within the daughter populations that was present in the ancestral population. A wide survey of human and chimp genomes could find these alleles.</p>\n<p>(This may be rare between humans and chimps. Estimates of the <a href=\"https://doi.org/10.1101%2Fgr.6023607\" rel=\"nofollow noreferrer\">human effective population size</a> are generally <span class=\"math-container\">$&lt;10,000$</span>, so <span class=\"math-container\">$2N=20,000$</span>. Our estimate of ~350,000 generations probably means few sites in the genome have failed coalesce in that time.)</p>\n","text":"The parameters cited by OP are not in conflict.\n\n\n\n\nThe misconception relates to a disconnect between what the theory predicts and the type of observation we have available. This leads to an unnecessary assumption that the observed substitutions have become fixed, as well as a failure to account for standing variation at the time of divergence.\n\n\n\n\nLanfear et al. (https://doi-org.slo.idm.oclc.org/10.1016/j.tree.2013.09.009) correctly states that \"the rate of evolution at a site is $KU × 1/K = U$\". To find the amount of (this type of) evolution between two populations over time, one would calculate $UTG$, where $T$ is the time in number of generations, and $G$ is the genome size. However, this is a calculation of neutral substitutions that have become fixed across two diverged populations, and is really most appropriate when $T$ is much greater than the expected time to fixation ($T>2N$ (https://en.wikipedia.org/wiki/Coalescent_theory#Time_to_coalescence), where $N$ is the effective population size).\n\n\n\n\nTo perfectly test the theory, one would need to census all substitutions in both populations in order to differentiate between substitutions that have become fixed and those that are polymorphic.\n\n\n\n\nThe observation we have here, however, is essentially a single individual from each population.\n\n\n\n\nWhen one compares two individual genomes that have been separated, the SNPs observed between them will include:\n\n\n\n\n\nsites with a SNP that originated since divergence and has become fixed (what the theory is talking about).\n\n\n\n\nsites that are polymorphic, with SNPs that originated since divergence.\n\n\n\n\nsites polymorphic in the original population, where a SNP became fixed in one lineage and lost in the other.\n\n\n\n\nsites polymorphic in the original population that are still polymorphic.\n\n\n\n\n\nSNPs originating since divergence that have become fixed\n\n\n\n\nEven just applying the above calculation, considering only fixed SNPs (or those that will become fixed) provides the same order of magnitude as the observation of 30,000 substitutions in humans since divergence with chimps.\n\n\n\n\nBakewell et al. (https://doi.org/10.1073/pnas.0701705104) surveyed 5,215,415 synonymous sites, so we'll use that as $G$. Assuming 20 years per generation and 7 million years of divergence $7×10^6/20= 3.5×10^5$ generations:\n\n\n\n\n$UTG = 10^{-8} × (3.5×10^5) × 5,215,415 = 18,253$ substitutions (though we don't know which of the 30,000 observed substitutions these are).\n\n\n\n\nSites that are polymorphic with SNPs that originated since divergence.\n\n\n\n\nNew mutations are entering the population all the time, with every individual.\n\n\n\n\nImagine this measurement was taken one generation after divergence, and where the ancestral population was all exactly identical.\n\n\n\n\nThe human genome is $3×10^9$ nucleotides, so $10^{-8} × 1 × (3×10^9) = 30$ substitutions. Humans and chimps are diploid, so an individual would have ~$30$ mutations on each set of $3×10^9$ nucleotides, or ~$60$ mutations compared to our hypothetical source population.\n\n\n\n\nAs Lanfear pointed out, each one of these substitutions is unlikely to eventually become fixed (they have probability $1/K$), but we're taking the measurement now, so we observe them. Many of them are likely to spread in the population at least a little bit, even if they eventually disappear.\n\n\n\n\nWe also know from Bakewell that both the observed human and chimp genomes contain sites that are not only polymorphic in the population, but polymorphic in the sequenced individuals.\n\n\n\n\nSites polymorphic in the original population, where a SNP became fixed in one population and lost in the other\n\n\n\n\nOverlooked by OP is the fact that the most recent common ancestor of humans and chimps (which was a population, not an individual) was not full of identical individuals, but contained the standing genetic variation one sees in any species. This allows for the fixation of alternative alleles between the daughter populations, even in the absence of new substitutions.\n\n\n\n\nWe know in fact this happened. The gorilla genome (https://doi.org/10.1038/nature10842) showed us that ~30% of the gorilla genome is more closely related to human or chimp than the later are to each other. This is due to a phenomenon called incomplete lineage sorting, which occurs when two speciation events occur over a short span of time (again $T<2N$; the gorilla/human/chimp split is thought to have occurred ~10 million years ago). It is caused by variation in the ancestral population that gets differentially sorted into the daughter populations.\n\n\n\n\nSites polymorphic in the original population that are still polymorphic\n\n\n\n\nIt's possible there are still sites that retain polymorphism within the daughter populations that was present in the ancestral population. A wide survey of human and chimp genomes could find these alleles.\n\n\n\n\n(This may be rare between humans and chimps. Estimates of the human effective population size (https://doi.org/10.1101%2Fgr.6023607) are generally $<10,000$, so $2N=20,000$. Our estimate of ~350,000 generations probably means few sites in the genome have failed coalesce in that time.)"}],"domain":"biology","external_citations":["https://doi-org.slo.idm.oclc.org/10.1016/j.tree.2013.09.009","https://doi.org/10.1038/nature10842","https://doi.org/10.1073/pnas.0701705104","https://doi.org/10.1101%2Fgr.6023607","https://en.wikipedia.org/wiki/Coalescent_theory#Time_to_coalescence"],"ground_truth_type":"metadata_grounded","group_id":"9e1f02e07c797896d5eb198cfe8be2013a79ccbef43152c4b9da181013ffb990","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-66d46918c7f788b3803fc4ff","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:08.576606+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1051d4f3e38449f1419d1973ac812b2286659e454a76f89a23fdaa941dfadddb_0.json","raw_sha256":"583dcd577e20d33b29e9f8818a7ab6a1fab039c19ab79927e16096cff23fa61d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=7&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Devin","profile_url":"https://biology.stackexchange.com/users/75790/devin","user_type":"registered"},"created_at":"2024-02-19T16:14:10+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"2DC8EB7B-AD68-4511-AD8A-AB38EFD28BDB","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2DC8EB7B-AD68-4511-AD8A-AB38EFD28BDB/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Devin","profile_url":"https://biology.stackexchange.com/users/75790/devin","user_type":"registered"},"created_at":"2024-02-19T21:51:00+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"DEAFB10B-42AB-4F0D-B9D7-AAB6E409E2ED","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DEAFB10B-42AB-4F0D-B9D7-AAB6E409E2ED/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Devin","profile_url":"https://biology.stackexchange.com/users/75790/devin","user_type":"registered"},"created_at":"2024-02-19T21:58:57+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"774D7515-3FED-42C7-AC4C-ED7188024CA4","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/774D7515-3FED-42C7-AC4C-ED7188024CA4/view-source"},{"content_license":null,"contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2024-02-25T13:46:11+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"97674E41-E6C9-403D-92DB-CBBF1A1B58CF","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/97674E41-E6C9-403D-92DB-CBBF1A1B58CF/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114127","source_record_sha256":"402a31b3c6d65ea4f32ca8377196d8a0082163ac0573bc0d0d3ba38e5a60ee03","source_url":"https://biology.stackexchange.com/questions/114127/how-to-resolve-the-contradiction-between-the-time-required-for-the-fixation-of-n","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How to resolve the contradiction between the time required for the fixation of neutral mutations and the time available according to the fossil record\nMore than thirty thousand synonymous single-nucleotide-substitutions have occurred in protein-coding genes in the human genome since the human lineage diverged from the chimp lineage ~7 million years ago (Bakewell et al, 2007, p.7490). Since, by definition, synonymous substitutions don’t change the amino acid, these substitutions must be selectively neutral mutations. For neutral mutations, the rate of evolution is simply equal to the point mutation rate U, “irrespective of selection at other linked loci, changes in population size, or almost any other conceivable complication” (Lanfear et al, 2014, p.36). This is problematic because U is approximately 10 to the -8 power for humans, which means that it took about a hundred million generations for each of these substitutions to become fixed in the human genome. Since each generation is more than ten years, a hundred million generations is more than a billion years, which is much longer than the ~7 million years since the human lineage diverged from the chimp lineage. How is this to be reconciled?\n\n\n\n\nBakewell, M. et al, “More genes underwent positive selection in chimpanzee evolution than in human evolution.” Proceedings of the National Academy of Sciences USA, vol 104, pages 7489–7494, 2007\n\n\n\n\nLanfear, R. et al, “Population size and the rate of evolution.”\nTrends in Ecology and Evolution, vol 29, pages 33–40, 2014","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114168,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":114162,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>If you're wanting to store DNA long-term at room temperature, you'll probably want to dry it. DNA extraction methods have been known since 1869. You can then use ethanol to precipitate the DNA, centrifuge it, and dry off the ethanol. The dried DNA pellet is surprisingly stable (though still <a href=\"https://www.nature.com/articles/s41467-021-21587-5#Sec2\" rel=\"nofollow noreferrer\">maybe not great</a> at this time scale, depending on what you want to do with it). Adsorbing the DNA onto a matrix, including silk, can increase preservation.</p>\n<p>You could also try preserving the tissue itself. Two <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461180/\" rel=\"nofollow noreferrer\">good options</a> would be freeze drying the tissue, or preserving it in 95% ethanol. You would not want to store in formalin, as that creates DNA fragmentation and cross-linkages.</p>\n","answer_id":114162,"answer_text":"If you're wanting to store DNA long-term at room temperature, you'll probably want to dry it. DNA extraction methods have been known since 1869. You can then use ethanol to precipitate the DNA, centrifuge it, and dry off the ethanol. The dried DNA pellet is surprisingly stable (though still maybe not great (https://www.nature.com/articles/s41467-021-21587-5#Sec2) at this time scale, depending on what you want to do with it). Adsorbing the DNA onto a matrix, including silk, can increase preservation.\n\n\n\n\nYou could also try preserving the tissue itself. Two good options (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461180/) would be freeze drying the tissue, or preserving it in 95% ethanol. You would not want to store in formalin, as that creates DNA fragmentation and cross-linkages.","answer_url":"https://biology.stackexchange.com/a/114162","author":"Darlingtonia","author_url":"https://biology.stackexchange.com/users/1197/darlingtonia","content_license":"CC BY-SA 4.0","created_at":"2024-02-23T19:25:11+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:30.839943+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2139ae0ecb1bf62b149af3f8e91d7ce461ad269d38020aaf05922333eabb51a1_0.json","raw_sha256":"2610bc07f1691b2794681a23d0459bba24822de1f31c7b48d79495b29b0b1285","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/114428;114427;114412;114410;114399;114395;114391;114386;114385;114381;114378;114377;114376;114374;114372;114371;114370;114361;114354;114353;114348;114342;114331;114329;114324;114321;114319;114307;114305;114304;114299;114298;114295;114290;114281;114277;114273;114266;114256;114239;114238;114222;114216;114213;114211;114207;114197;114192;114185;114180;114178;114175;114174;114173;114172;114169;114161;114156;114155;114148;114145;114144;114139;114136;114135;114127;114119;114117;114114;114111;114110;114103;114098;114096;114094;114089;114085;114078;114076;114069;114067;114065;114058;114055;114048;114045;114038;114031;114028;114027;114025;114021;114020;114012;114006;113998;113997;113988;113986;113983/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114156,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Darlingtonia","profile_url":"https://biology.stackexchange.com/users/1197/darlingtonia","user_type":"registered"},"created_at":"2024-02-23T19:25:11+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"7E911425-9804-4BF5-9207-3D94BE624DE9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7E911425-9804-4BF5-9207-3D94BE624DE9/view-source"}],"score":3},{"answer_html":"<p>For anyone curious, @Darlingtonia's answer is what I needed.  It also gave me the search terms that Google could use to finally find further useful information.  In particular, a paper published at the National Center for Biotechnology Information, linked here.</p>\n<p><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910151/\" rel=\"nofollow noreferrer\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910151/</a></p>\n<p>First paragraph of the abstract:</p>\n<blockquote>\n<p>The globalization of DNA barcoding will require core analytical facilities to develop cost-effective, efficient protocols for the shipment and archival storage of DNA extracts and PCR products. We evaluated three dry-state DNA stabilization systems: commercial Biomatrica® DNAstable® plates, home-made trehalose and polyvinyl alcohol (PVA) plates on 96-well panels of insect DNA stored at 56 °C and at room temperature. Controls included unprotected samples that were stored dry at room temperature and at 56 °C, and diluted samples held at 4 °C and at −20 °C. PCR and selective sequencing were performed over a 4-year interval to test the condition of DNA extracts. Biomatrica® provided better protection of DNA at 56 °C and at room temperature than trehalose and PVA, especially for diluted samples.</p>\n</blockquote>\n","answer_id":114166,"answer_text":"For anyone curious, @Darlingtonia's answer is what I needed.  It also gave me the search terms that Google could use to finally find further useful information.  In particular, a paper published at the National Center for Biotechnology Information, linked here.\n\n\n\n\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910151/ (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910151/)\n\n\n\n\nFirst paragraph of the abstract:\n\n\n\n\n\n\n\nThe globalization of DNA barcoding will require core analytical facilities to develop cost-effective, efficient protocols for the shipment and archival storage of DNA extracts and PCR products. We evaluated three dry-state DNA stabilization systems: commercial Biomatrica® DNAstable® plates, home-made trehalose and polyvinyl alcohol (PVA) plates on 96-well panels of insect DNA stored at 56 °C and at room temperature. Controls included unprotected samples that were stored dry at room temperature and at 56 °C, and diluted samples held at 4 °C and at −20 °C. PCR and selective sequencing were performed over a 4-year interval to test the condition of DNA extracts. Biomatrica® provided better protection of DNA at 56 °C and at room temperature than trehalose and PVA, especially for diluted samples.","answer_url":"https://biology.stackexchange.com/a/114166","author":"CXJ","author_url":"https://biology.stackexchange.com/users/78949/cxj","content_license":"CC BY-SA 4.0","created_at":"2024-02-24T02:32:14+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:30.839943+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2139ae0ecb1bf62b149af3f8e91d7ce461ad269d38020aaf05922333eabb51a1_0.json","raw_sha256":"2610bc07f1691b2794681a23d0459bba24822de1f31c7b48d79495b29b0b1285","source_api":"Stack Exchange API 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4.0","contributor":{"display_name":"Darlingtonia","profile_url":"https://biology.stackexchange.com/users/1197/darlingtonia","user_type":"registered"},"created_at":"2024-02-23T19:25:11+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"7E911425-9804-4BF5-9207-3D94BE624DE9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7E911425-9804-4BF5-9207-3D94BE624DE9/view-source"}],"url":"https://biology.stackexchange.com/a/114162"},{"author":"CXJ","author_url":"https://biology.stackexchange.com/users/78949/cxj","content_license":"CC BY-SA 4.0","context_id":"114166","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"CXJ","profile_url":"https://biology.stackexchange.com/users/78949/cxj","user_type":"registered"},"created_at":"2024-02-24T02:32:14+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"4120770B-F783-437A-BDEA-D11C9F620A5C","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4120770B-F783-437A-BDEA-D11C9F620A5C/view-source"}],"url":"https://biology.stackexchange.com/a/114166"}],"contexts":[{"context_id":"question","html":"<p>Imagine a person in the early half of the 20th century (1900 to 1950) took some kind of sample(s) from a living human body using any technology of the era.  They then stored it using any technology available, but could not use prolonged (70+ years) refrigeration.</p>\n<p>We want to be able to do useful analysis of that sample in the year 2024.  We particularly might want to be able to sequence mtDNA and nucleus DNA, look at telomeres and methylation.  Furthermore, we especially want to be able to try to determine the age of the individual, and even better, from what approximate generation they were (i.e. plus/minus a hundred years).</p>\n<p>Is such sample storage even possible?</p>\n<p>Using my &quot;just enough knowledge to ask stupid questions&quot;:</p>\n<ul>\n<li>Could a sample be preserved in formalin and then immersed in alcohol, all in an air-free sealed container, and preserve the needed DNA strands and/or other biochemistry?</li>\n<li>Could ethanol precipitation of DNA be used on the sample\ncontemporaneously, and that precipitate instead be stored safely for\n70+ years?</li>\n</ul>\n<p>Maybe these other questions apply?</p>\n<ul>\n<li><a href=\"https://biology.stackexchange.com/questions/9089/diy-extraction-and-long-term-storage-of-human-dna-sample?rq=1\">DIY extraction and long term storage of human DNA sample?</a></li>\n<li><a href=\"https://biology.stackexchange.com/questions/3210/how-realistic-is-to-use-dna-for-long-term-storage?rq=1\">How realistic is to use DNA for long term storage?</a></li>\n<li><a href=\"https://biology.stackexchange.com/questions/15236/isopropanol-precipitation-of-dna-duration-and-magnitude-of-cold-storage?rq=1\">Isopropanol precipitation of DNA - duration and magnitude of cold storage</a></li>\n</ul>\n<p>(I'm an old hand at Stack Overflow / Stack Exchange sites, but this is my first post to Biology.  Gentle feedback appreciated.)</p>\n","text":"Imagine a person in the early half of the 20th century (1900 to 1950) took some kind of sample(s) from a living human body using any technology of the era.  They then stored it using any technology available, but could not use prolonged (70+ years) refrigeration.\n\n\n\n\nWe want to be able to do useful analysis of that sample in the year 2024.  We particularly might want to be able to sequence mtDNA and nucleus DNA, look at telomeres and methylation.  Furthermore, we especially want to be able to try to determine the age of the individual, and even better, from what approximate generation they were (i.e. plus/minus a hundred years).\n\n\n\n\nIs such sample storage even possible?\n\n\n\n\nUsing my \"just enough knowledge to ask stupid questions\":\n\n\n\n\n\nCould a sample be preserved in formalin and then immersed in alcohol, all in an air-free sealed container, and preserve the needed DNA strands and/or other biochemistry?\n\n\n\n\nCould ethanol precipitation of DNA be used on the sample\ncontemporaneously, and that precipitate instead be stored safely for\n70+ years?\n\n\n\n\n\nMaybe these other questions apply?\n\n\n\n\n\nDIY extraction and long term storage of human DNA sample? (https://biology.stackexchange.com/questions/9089/diy-extraction-and-long-term-storage-of-human-dna-sample?rq=1)\n\n\n\n\nHow realistic is to use DNA for long term storage? (https://biology.stackexchange.com/questions/3210/how-realistic-is-to-use-dna-for-long-term-storage?rq=1)\n\n\n\n\nIsopropanol precipitation of DNA - duration and magnitude of cold storage (https://biology.stackexchange.com/questions/15236/isopropanol-precipitation-of-dna-duration-and-magnitude-of-cold-storage?rq=1)\n\n\n\n\n\n(I'm an old hand at Stack Overflow / Stack Exchange sites, but this is my first post to Biology.  Gentle feedback appreciated.)"},{"context_id":"114162","html":"<p>If you're wanting to store DNA long-term at room temperature, you'll probably want to dry it. DNA extraction methods have been known since 1869. You can then use ethanol to precipitate the DNA, centrifuge it, and dry off the ethanol. The dried DNA pellet is surprisingly stable (though still <a href=\"https://www.nature.com/articles/s41467-021-21587-5#Sec2\" rel=\"nofollow noreferrer\">maybe not great</a> at this time scale, depending on what you want to do with it). Adsorbing the DNA onto a matrix, including silk, can increase preservation.</p>\n<p>You could also try preserving the tissue itself. Two <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461180/\" rel=\"nofollow noreferrer\">good options</a> would be freeze drying the tissue, or preserving it in 95% ethanol. You would not want to store in formalin, as that creates DNA fragmentation and cross-linkages.</p>\n","text":"If you're wanting to store DNA long-term at room temperature, you'll probably want to dry it. DNA extraction methods have been known since 1869. You can then use ethanol to precipitate the DNA, centrifuge it, and dry off the ethanol. The dried DNA pellet is surprisingly stable (though still maybe not great (https://www.nature.com/articles/s41467-021-21587-5#Sec2) at this time scale, depending on what you want to do with it). Adsorbing the DNA onto a matrix, including silk, can increase preservation.\n\n\n\n\nYou could also try preserving the tissue itself. Two good options (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461180/) would be freeze drying the tissue, or preserving it in 95% ethanol. You would not want to store in formalin, as that creates DNA fragmentation and cross-linkages."},{"context_id":"114166","html":"<p>For anyone curious, @Darlingtonia's answer is what I needed.  It also gave me the search terms that Google could use to finally find further useful information.  In particular, a paper published at the National Center for Biotechnology Information, linked here.</p>\n<p><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910151/\" rel=\"nofollow noreferrer\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910151/</a></p>\n<p>First paragraph of the abstract:</p>\n<blockquote>\n<p>The globalization of DNA barcoding will require core analytical facilities to develop cost-effective, efficient protocols for the shipment and archival storage of DNA extracts and PCR products. We evaluated three dry-state DNA stabilization systems: commercial Biomatrica® DNAstable® plates, home-made trehalose and polyvinyl alcohol (PVA) plates on 96-well panels of insect DNA stored at 56 °C and at room temperature. Controls included unprotected samples that were stored dry at room temperature and at 56 °C, and diluted samples held at 4 °C and at −20 °C. PCR and selective sequencing were performed over a 4-year interval to test the condition of DNA extracts. Biomatrica® provided better protection of DNA at 56 °C and at room temperature than trehalose and PVA, especially for diluted samples.</p>\n</blockquote>\n","text":"For anyone curious, @Darlingtonia's answer is what I needed.  It also gave me the search terms that Google could use to finally find further useful information.  In particular, a paper published at the National Center for Biotechnology Information, linked here.\n\n\n\n\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910151/ (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910151/)\n\n\n\n\nFirst paragraph of the abstract:\n\n\n\n\n\n\n\nThe globalization of DNA barcoding will require core analytical facilities to develop cost-effective, efficient protocols for the shipment and archival storage of DNA extracts and PCR products. We evaluated three dry-state DNA stabilization systems: commercial Biomatrica® DNAstable® plates, home-made trehalose and polyvinyl alcohol (PVA) plates on 96-well panels of insect DNA stored at 56 °C and at room temperature. Controls included unprotected samples that were stored dry at room temperature and at 56 °C, and diluted samples held at 4 °C and at −20 °C. PCR and selective sequencing were performed over a 4-year interval to test the condition of DNA extracts. Biomatrica® provided better protection of DNA at 56 °C and at room temperature than trehalose and PVA, especially for diluted samples."}],"domain":"biology","external_citations":["https://biology.stackexchange.com/questions/15236/isopropanol-precipitation-of-dna-duration-and-magnitude-of-cold-storage?rq=1","https://biology.stackexchange.com/questions/3210/how-realistic-is-to-use-dna-for-long-term-storage?rq=1","https://biology.stackexchange.com/questions/9089/diy-extraction-and-long-term-storage-of-human-dna-sample?rq=1","https://www.nature.com/articles/s41467-021-21587-5#Sec2","https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910151/","https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461180/"],"ground_truth_type":"metadata_grounded","group_id":"82e8180483b4666f986d73a76d87e04b01b1443e4df00266e26ad71744870704","hard_case_family":["multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-8f8136a7841364aef245a643","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:08.576606+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1051d4f3e38449f1419d1973ac812b2286659e454a76f89a23fdaa941dfadddb_0.json","raw_sha256":"583dcd577e20d33b29e9f8818a7ab6a1fab039c19ab79927e16096cff23fa61d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=7&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"CXJ","profile_url":"https://biology.stackexchange.com/users/78949/cxj","user_type":"registered"},"created_at":"2024-02-23T05:15:11+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"10A751EB-E11E-4C19-9DA4-61E80F5D7211","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/10A751EB-E11E-4C19-9DA4-61E80F5D7211/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"CXJ","profile_url":"https://biology.stackexchange.com/users/78949/cxj","user_type":"registered"},"created_at":"2024-02-23T05:47:30+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"683F5A3B-4AEA-4834-90AD-AC56EAFE2478","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/683F5A3B-4AEA-4834-90AD-AC56EAFE2478/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"CXJ","profile_url":"https://biology.stackexchange.com/users/78949/cxj","user_type":"registered"},"created_at":"2024-02-23T05:56:48+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"89C2ACC2-482E-4593-B3AE-4B12894E486F","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/89C2ACC2-482E-4593-B3AE-4B12894E486F/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"cell0","profile_url":"https://biology.stackexchange.com/users/49230/cell0","user_type":"registered"},"created_at":"2024-02-25T23:12:52+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"240BC9F9-B314-4E64-9B89-FAE5363CDC47","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/240BC9F9-B314-4E64-9B89-FAE5363CDC47/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114156","source_record_sha256":"ee97e257b286db30af714b426fe4744c0892b309ecb654e2bc8113aeef63ce57","source_url":"https://biology.stackexchange.com/questions/114156/preserving-a-sample-for-mtdna-and-nuclear-dna-analysis","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Preserving a sample for mtDNA and nuclear DNA analysis\nImagine a person in the early half of the 20th century (1900 to 1950) took some kind of sample(s) from a living human body using any technology of the era.  They then stored it using any technology available, but could not use prolonged (70+ years) refrigeration.\n\n\n\n\nWe want to be able to do useful analysis of that sample in the year 2024.  We particularly might want to be able to sequence mtDNA and nucleus DNA, look at telomeres and methylation.  Furthermore, we especially want to be able to try to determine the age of the individual, and even better, from what approximate generation they were (i.e. plus/minus a hundred years).\n\n\n\n\nIs such sample storage even possible?\n\n\n\n\nUsing my \"just enough knowledge to ask stupid questions\":\n\n\n\n\n\nCould a sample be preserved in formalin and then immersed in alcohol, all in an air-free sealed container, and preserve the needed DNA strands and/or other biochemistry?\n\n\n\n\nCould ethanol precipitation of DNA be used on the sample\ncontemporaneously, and that precipitate instead be stored safely for\n70+ years?\n\n\n\n\n\nMaybe these other questions apply?\n\n\n\n\n\nDIY extraction and long term storage of human DNA sample? (https://biology.stackexchange.com/questions/9089/diy-extraction-and-long-term-storage-of-human-dna-sample?rq=1)\n\n\n\n\nHow realistic is to use DNA for long term storage? (https://biology.stackexchange.com/questions/3210/how-realistic-is-to-use-dna-for-long-term-storage?rq=1)\n\n\n\n\nIsopropanol precipitation of DNA - duration and magnitude of cold storage (https://biology.stackexchange.com/questions/15236/isopropanol-precipitation-of-dna-duration-and-magnitude-of-cold-storage?rq=1)\n\n\n\n\n\n(I'm an old hand at Stack Overflow / Stack Exchange sites, but this is my first post to Biology.  Gentle feedback appreciated.)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114162,"score":3},{"answer_id":114166,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<blockquote>\n<p>What I want to know, is if this is a bad thing, why don't normal evolutionary forces act to prevent this?</p>\n</blockquote>\n<p>You seem to be attributing a moral value to an evolutionary process. So does the article you linked to your post (probably for sensationalism), which is not a scientific way of reasoning. I suggest you read the <a href=\"https://www.nature.com/articles/s41598-020-58997-2#Abs1\" rel=\"nofollow noreferrer\">original article instead</a>. In the abstract, you can read :</p>\n<blockquote>\n<p>The results of our study suggest these forces are not exclusive to the Y chromosome, and chromosomal degeneration may have occurred throughout our evolutionary history. The reduction of recombination could additionally result in rapid fixation through isolation, of specialized functions resulting in a cost-benefit relationship during times of intense selective pressure.</p>\n</blockquote>\n<p>Therefore, this trend is not specific to the Y chromosome, and there is no evidence that the reduction in the number of genes on the Y chromosome has been associated to a decrease in the fitness of humans.</p>\n","answer_id":114200,"answer_text":"What I want to know, is if this is a bad thing, why don't normal evolutionary forces act to prevent this?\n\n\n\n\n\n\n\nYou seem to be attributing a moral value to an evolutionary process. So does the article you linked to your post (probably for sensationalism), which is not a scientific way of reasoning. I suggest you read the original article instead (https://www.nature.com/articles/s41598-020-58997-2#Abs1). In the abstract, you can read :\n\n\n\n\n\n\n\nThe results of our study suggest these forces are not exclusive to the Y chromosome, and chromosomal degeneration may have occurred throughout our evolutionary history. The reduction of recombination could additionally result in rapid fixation through isolation, of specialized functions resulting in a cost-benefit relationship during times of intense selective pressure.\n\n\n\n\n\n\n\nTherefore, this trend is not specific to the Y chromosome, and there is no evidence that the reduction in the number of genes on the Y chromosome has been associated to a decrease in the fitness of humans.","answer_url":"https://biology.stackexchange.com/a/114200","author":"CaroZ","author_url":"https://biology.stackexchange.com/users/26370/caroz","content_license":"CC BY-SA 4.0","created_at":"2024-02-28T09:49:29+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:30.839943+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2139ae0ecb1bf62b149af3f8e91d7ce461ad269d38020aaf05922333eabb51a1_0.json","raw_sha256":"2610bc07f1691b2794681a23d0459bba24822de1f31c7b48d79495b29b0b1285","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/114428;114427;114412;114410;114399;114395;114391;114386;114385;114381;114378;114377;114376;114374;114372;114371;114370;114361;114354;114353;114348;114342;114331;114329;114324;114321;114319;114307;114305;114304;114299;114298;114295;114290;114281;114277;114273;114266;114256;114239;114238;114222;114216;114213;114211;114207;114197;114192;114185;114180;114178;114175;114174;114173;114172;114169;114161;114156;114155;114148;114145;114144;114139;114136;114135;114127;114119;114117;114114;114111;114110;114103;114098;114096;114094;114089;114085;114078;114076;114069;114067;114065;114058;114055;114048;114045;114038;114031;114028;114027;114025;114021;114020;114012;114006;113998;113997;113988;113986;113983/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114197,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"CaroZ","profile_url":"https://biology.stackexchange.com/users/26370/caroz","user_type":"registered"},"created_at":"2024-02-28T09:49:29+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"501EE5DC-0633-43DD-9100-BFC8F1FBCD1A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/501EE5DC-0633-43DD-9100-BFC8F1FBCD1A/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"KDP","author_url":"https://biology.stackexchange.com/users/80058/kdp","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"KDP","profile_url":"https://biology.stackexchange.com/users/80058/kdp","user_type":"registered"},"created_at":"2024-02-28T09:21:53+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"D4651F89-C465-4807-AE32-47B5224254B3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D4651F89-C465-4807-AE32-47B5224254B3/view-source"}],"url":"https://biology.stackexchange.com/questions/114197/evolution-of-the-human-y-chromosome"},{"author":"CaroZ","author_url":"https://biology.stackexchange.com/users/26370/caroz","content_license":"CC BY-SA 4.0","context_id":"114200","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"CaroZ","profile_url":"https://biology.stackexchange.com/users/26370/caroz","user_type":"registered"},"created_at":"2024-02-28T09:49:29+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"501EE5DC-0633-43DD-9100-BFC8F1FBCD1A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/501EE5DC-0633-43DD-9100-BFC8F1FBCD1A/view-source"}],"url":"https://biology.stackexchange.com/a/114200"}],"contexts":[{"context_id":"question","html":"<p><a href=\"https://www.msn.com/en-gb/health/medical/humans-could-become-extinct-unless-we-change-sex-as-we-know-it/ar-BB1iYe7z?ocid=msedgntp&amp;pc=U531&amp;cvid=b0a7ae8bfa4f47dcb87bd0ca2e5f3e9f&amp;ei=71\" rel=\"nofollow noreferrer\">This recent news article</a> suggests the number of genes in human male Y chromosome has steadily been reducing in the Y chromosome for a long time and is in danger of dying out all together.</p>\n<p>What I want to know, is if this is a bad thing, why don't normal evolutionary forces act to prevent this? For example if some individual is born in the future with a further reduced gene count in their Y chromosome and this reduces or eliminates their fertility, they will will have less offspring and that trait will die out. Why would the human race evolve in a way that is disadvantages to reproduction, when that is the main driving force of evolution?</p>\n","text":"This recent news article (https://www.msn.com/en-gb/health/medical/humans-could-become-extinct-unless-we-change-sex-as-we-know-it/ar-BB1iYe7z?ocid=msedgntp&pc=U531&cvid=b0a7ae8bfa4f47dcb87bd0ca2e5f3e9f&ei=71) suggests the number of genes in human male Y chromosome has steadily been reducing in the Y chromosome for a long time and is in danger of dying out all together.\n\n\n\n\nWhat I want to know, is if this is a bad thing, why don't normal evolutionary forces act to prevent this? For example if some individual is born in the future with a further reduced gene count in their Y chromosome and this reduces or eliminates their fertility, they will will have less offspring and that trait will die out. Why would the human race evolve in a way that is disadvantages to reproduction, when that is the main driving force of evolution?"},{"context_id":"114200","html":"<blockquote>\n<p>What I want to know, is if this is a bad thing, why don't normal evolutionary forces act to prevent this?</p>\n</blockquote>\n<p>You seem to be attributing a moral value to an evolutionary process. So does the article you linked to your post (probably for sensationalism), which is not a scientific way of reasoning. I suggest you read the <a href=\"https://www.nature.com/articles/s41598-020-58997-2#Abs1\" rel=\"nofollow noreferrer\">original article instead</a>. In the abstract, you can read :</p>\n<blockquote>\n<p>The results of our study suggest these forces are not exclusive to the Y chromosome, and chromosomal degeneration may have occurred throughout our evolutionary history. The reduction of recombination could additionally result in rapid fixation through isolation, of specialized functions resulting in a cost-benefit relationship during times of intense selective pressure.</p>\n</blockquote>\n<p>Therefore, this trend is not specific to the Y chromosome, and there is no evidence that the reduction in the number of genes on the Y chromosome has been associated to a decrease in the fitness of humans.</p>\n","text":"What I want to know, is if this is a bad thing, why don't normal evolutionary forces act to prevent this?\n\n\n\n\n\n\n\nYou seem to be attributing a moral value to an evolutionary process. So does the article you linked to your post (probably for sensationalism), which is not a scientific way of reasoning. I suggest you read the original article instead (https://www.nature.com/articles/s41598-020-58997-2#Abs1). In the abstract, you can read :\n\n\n\n\n\n\n\nThe results of our study suggest these forces are not exclusive to the Y chromosome, and chromosomal degeneration may have occurred throughout our evolutionary history. The reduction of recombination could additionally result in rapid fixation through isolation, of specialized functions resulting in a cost-benefit relationship during times of intense selective pressure.\n\n\n\n\n\n\n\nTherefore, this trend is not specific to the Y chromosome, and there is no evidence that the reduction in the number of genes on the Y chromosome has been associated to a decrease in the fitness of humans."}],"domain":"biology","external_citations":["https://www.msn.com/en-gb/health/medical/humans-could-become-extinct-unless-we-change-sex-as-we-know-it/ar-BB1iYe7z?ocid=msedgntp&pc=U531&cvid=b0a7ae8bfa4f47dcb87bd0ca2e5f3e9f&ei=71","https://www.nature.com/articles/s41598-020-58997-2#Abs1"],"ground_truth_type":"metadata_grounded","group_id":"d7d0d070e7e59307fb84c0866a3ea12a24dd1d302bf301a0c8d23577dcbf0ac5","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-adf0fd64c1e37c30a4f3a9a0","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:08.576606+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1051d4f3e38449f1419d1973ac812b2286659e454a76f89a23fdaa941dfadddb_0.json","raw_sha256":"583dcd577e20d33b29e9f8818a7ab6a1fab039c19ab79927e16096cff23fa61d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=7&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"KDP","profile_url":"https://biology.stackexchange.com/users/80058/kdp","user_type":"registered"},"created_at":"2024-02-28T09:21:53+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"D4651F89-C465-4807-AE32-47B5224254B3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D4651F89-C465-4807-AE32-47B5224254B3/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114197","source_record_sha256":"71b3d9345e92d69e714b36f1187f74ddaefd6754593c21366eddc41cd41fcd04","source_url":"https://biology.stackexchange.com/questions/114197/evolution-of-the-human-y-chromosome","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Evolution of the human Y chromosome\nThis recent news article (https://www.msn.com/en-gb/health/medical/humans-could-become-extinct-unless-we-change-sex-as-we-know-it/ar-BB1iYe7z?ocid=msedgntp&pc=U531&cvid=b0a7ae8bfa4f47dcb87bd0ca2e5f3e9f&ei=71) suggests the number of genes in human male Y chromosome has steadily been reducing in the Y chromosome for a long time and is in danger of dying out all together.\n\n\n\n\nWhat I want to know, is if this is a bad thing, why don't normal evolutionary forces act to prevent this? For example if some individual is born in the future with a further reduced gene count in their Y chromosome and this reduces or eliminates their fertility, they will will have less offspring and that trait will die out. Why would the human race evolve in a way that is disadvantages to reproduction, when that is the main driving force of evolution?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114200,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":114306,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p><a href=\"https://en.wikipedia.org/wiki/Splanchnic\" rel=\"nofollow noreferrer\">Splanchnic</a> refers to all the abdominal cavity organs, not just the liver.</p>\n<p>The <a href=\"https://en.wikipedia.org/wiki/Portal_vein\" rel=\"nofollow noreferrer\">portal vein</a> system carries blood from these organs to the liver instead of directly back to the heart. The more blood flows to these organs, the more goes through the portal system. Vasodilation increases blood flow because there is less resistance when the vessels are wider.</p>\n<p>This is all a compensatory mechanism gone a bit wild; there's not enough flow through the portal system. Normally, arterial tone sets flow, so normally if there's not enough flow it's because the arteries need to relax. As they relax it does increase flow, but because it isn't actually the arteries that are the problem (the problem is the pathology in the liver) there is even more hypertension in the portal system.</p>\n<p>Remember, too, that veins are <em>low-pressure</em> vessels. Hypertension in the veins is a problem at much lower pressures than normal pressure in the arteries.</p>\n","answer_id":114306,"answer_text":"Splanchnic (https://en.wikipedia.org/wiki/Splanchnic) refers to all the abdominal cavity organs, not just the liver.\n\n\n\n\nThe portal vein (https://en.wikipedia.org/wiki/Portal_vein) system carries blood from these organs to the liver instead of directly back to the heart. The more blood flows to these organs, the more goes through the portal system. Vasodilation increases blood flow because there is less resistance when the vessels are wider.\n\n\n\n\nThis is all a compensatory mechanism gone a bit wild; there's not enough flow through the portal system. Normally, arterial tone sets flow, so normally if there's not enough flow it's because the arteries need to relax. As they relax it does increase flow, but because it isn't actually the arteries that are the problem (the problem is the pathology in the liver) there is even more hypertension in the portal system.\n\n\n\n\nRemember, too, that veins are low-pressure vessels. Hypertension in the veins is a problem at much lower pressures than normal pressure in the arteries.","answer_url":"https://biology.stackexchange.com/a/114306","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2024-03-12T17:52:59+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:30.839943+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2139ae0ecb1bf62b149af3f8e91d7ce461ad269d38020aaf05922333eabb51a1_0.json","raw_sha256":"2610bc07f1691b2794681a23d0459bba24822de1f31c7b48d79495b29b0b1285","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/114428;114427;114412;114410;114399;114395;114391;114386;114385;114381;114378;114377;114376;114374;114372;114371;114370;114361;114354;114353;114348;114342;114331;114329;114324;114321;114319;114307;114305;114304;114299;114298;114295;114290;114281;114277;114273;114266;114256;114239;114238;114222;114216;114213;114211;114207;114197;114192;114185;114180;114178;114175;114174;114173;114172;114169;114161;114156;114155;114148;114145;114144;114139;114136;114135;114127;114119;114117;114114;114111;114110;114103;114098;114096;114094;114089;114085;114078;114076;114069;114067;114065;114058;114055;114048;114045;114038;114031;114028;114027;114025;114021;114020;114012;114006;113998;113997;113988;113986;113983/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114305,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2024-03-12T17:52:59+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"D018AC35-AAFF-425B-8A43-24ADD09DDB6D","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D018AC35-AAFF-425B-8A43-24ADD09DDB6D/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Drita Raci","author_url":"https://biology.stackexchange.com/users/70297/drita-raci","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Drita Raci","profile_url":"https://biology.stackexchange.com/users/70297/drita-raci","user_type":"registered"},"created_at":"2024-03-12T17:18:14+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"4D84B2CC-C2E0-4505-9DDC-A0C8E31CBF58","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4D84B2CC-C2E0-4505-9DDC-A0C8E31CBF58/view-source"}],"url":"https://biology.stackexchange.com/questions/114305/portal-hypertension"},{"author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","context_id":"114306","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2024-03-12T17:52:59+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"D018AC35-AAFF-425B-8A43-24ADD09DDB6D","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D018AC35-AAFF-425B-8A43-24ADD09DDB6D/view-source"}],"url":"https://biology.stackexchange.com/a/114306"}],"contexts":[{"context_id":"question","html":"<p>&quot;Portal hypertension is more frequent and manifests in more complex ways in chronic liver failure than in acute liver failure (Fig. 14.7). It stems from increased vascular resistance coupled with increased portal blood flow. The increased resistance to portal flow is at the level of the sinusoids and is caused by contraction of vascular smooth muscle cells and myofibroblasts, and disruption of blood flow by scarring and the formation of parenchymal nodules. Increase in portal venous blood flow is due to arterial vasodilation. The increased splanchnic arterial blood flow in turn leads to increased venous efflux into the portal venous system.&quot; Robbins &amp; Kumar Basic Pathology.</p>\n<p>In liver cirrhosis, the blood neither from the hepatic artery nor from the portal vein are able to enter the liver normally, hence blood backs up in both, right? With the following: &quot;Increase in portal venous blood flow is due to arterial vasodilation&quot;, how does the arterial vasodilation cause an increase in portal venous blood flow? Which arteries is it talking about? If for example the hepatic arteries are in vasodilation, more blood fits them hence less blood would go into the portal venous system, so how would there be an increase in the portal venous blood flow? Am I simply missing the picture of the circulatory system around the liver?</p>\n<p>Moreover, with &quot;The increased splanchnic arterial blood flow in turn leads to increased venous efflux into the portal venous system&quot;, why did the splanchnic arterial blood flow increase? Venous efflux from where and why into the portal venous system?</p>\n<p>Many thanks for any help!</p>\n","text":"\"Portal hypertension is more frequent and manifests in more complex ways in chronic liver failure than in acute liver failure (Fig. 14.7). It stems from increased vascular resistance coupled with increased portal blood flow. The increased resistance to portal flow is at the level of the sinusoids and is caused by contraction of vascular smooth muscle cells and myofibroblasts, and disruption of blood flow by scarring and the formation of parenchymal nodules. Increase in portal venous blood flow is due to arterial vasodilation. The increased splanchnic arterial blood flow in turn leads to increased venous efflux into the portal venous system.\" Robbins & Kumar Basic Pathology.\n\n\n\n\nIn liver cirrhosis, the blood neither from the hepatic artery nor from the portal vein are able to enter the liver normally, hence blood backs up in both, right? With the following: \"Increase in portal venous blood flow is due to arterial vasodilation\", how does the arterial vasodilation cause an increase in portal venous blood flow? Which arteries is it talking about? If for example the hepatic arteries are in vasodilation, more blood fits them hence less blood would go into the portal venous system, so how would there be an increase in the portal venous blood flow? Am I simply missing the picture of the circulatory system around the liver?\n\n\n\n\nMoreover, with \"The increased splanchnic arterial blood flow in turn leads to increased venous efflux into the portal venous system\", why did the splanchnic arterial blood flow increase? Venous efflux from where and why into the portal venous system?\n\n\n\n\nMany thanks for any help!"},{"context_id":"114306","html":"<p><a href=\"https://en.wikipedia.org/wiki/Splanchnic\" rel=\"nofollow noreferrer\">Splanchnic</a> refers to all the abdominal cavity organs, not just the liver.</p>\n<p>The <a href=\"https://en.wikipedia.org/wiki/Portal_vein\" rel=\"nofollow noreferrer\">portal vein</a> system carries blood from these organs to the liver instead of directly back to the heart. The more blood flows to these organs, the more goes through the portal system. Vasodilation increases blood flow because there is less resistance when the vessels are wider.</p>\n<p>This is all a compensatory mechanism gone a bit wild; there's not enough flow through the portal system. Normally, arterial tone sets flow, so normally if there's not enough flow it's because the arteries need to relax. As they relax it does increase flow, but because it isn't actually the arteries that are the problem (the problem is the pathology in the liver) there is even more hypertension in the portal system.</p>\n<p>Remember, too, that veins are <em>low-pressure</em> vessels. Hypertension in the veins is a problem at much lower pressures than normal pressure in the arteries.</p>\n","text":"Splanchnic (https://en.wikipedia.org/wiki/Splanchnic) refers to all the abdominal cavity organs, not just the liver.\n\n\n\n\nThe portal vein (https://en.wikipedia.org/wiki/Portal_vein) system carries blood from these organs to the liver instead of directly back to the heart. The more blood flows to these organs, the more goes through the portal system. Vasodilation increases blood flow because there is less resistance when the vessels are wider.\n\n\n\n\nThis is all a compensatory mechanism gone a bit wild; there's not enough flow through the portal system. Normally, arterial tone sets flow, so normally if there's not enough flow it's because the arteries need to relax. As they relax it does increase flow, but because it isn't actually the arteries that are the problem (the problem is the pathology in the liver) there is even more hypertension in the portal system.\n\n\n\n\nRemember, too, that veins are low-pressure vessels. Hypertension in the veins is a problem at much lower pressures than normal pressure in the arteries."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Portal_vein","https://en.wikipedia.org/wiki/Splanchnic"],"ground_truth_type":"metadata_grounded","group_id":"f83f423870049837d59b7945a77061bfc63e508931566b0f467fa14b18955830","hard_case_family":["multiple_sources"],"id":"RHM-1743eef18e2ee515580c7d18","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:08.576606+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1051d4f3e38449f1419d1973ac812b2286659e454a76f89a23fdaa941dfadddb_0.json","raw_sha256":"583dcd577e20d33b29e9f8818a7ab6a1fab039c19ab79927e16096cff23fa61d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=7&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Drita Raci","profile_url":"https://biology.stackexchange.com/users/70297/drita-raci","user_type":"registered"},"created_at":"2024-03-12T17:18:14+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"4D84B2CC-C2E0-4505-9DDC-A0C8E31CBF58","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4D84B2CC-C2E0-4505-9DDC-A0C8E31CBF58/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114305","source_record_sha256":"1bd8911c75b0dd91eb7a101a4e4290989e56d8c2c21b839c77ee8e3bb1486b94","source_url":"https://biology.stackexchange.com/questions/114305/portal-hypertension","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Portal hypertension\n\"Portal hypertension is more frequent and manifests in more complex ways in chronic liver failure than in acute liver failure (Fig. 14.7). It stems from increased vascular resistance coupled with increased portal blood flow. The increased resistance to portal flow is at the level of the sinusoids and is caused by contraction of vascular smooth muscle cells and myofibroblasts, and disruption of blood flow by scarring and the formation of parenchymal nodules. Increase in portal venous blood flow is due to arterial vasodilation. The increased splanchnic arterial blood flow in turn leads to increased venous efflux into the portal venous system.\" Robbins & Kumar Basic Pathology.\n\n\n\n\nIn liver cirrhosis, the blood neither from the hepatic artery nor from the portal vein are able to enter the liver normally, hence blood backs up in both, right? With the following: \"Increase in portal venous blood flow is due to arterial vasodilation\", how does the arterial vasodilation cause an increase in portal venous blood flow? Which arteries is it talking about? If for example the hepatic arteries are in vasodilation, more blood fits them hence less blood would go into the portal venous system, so how would there be an increase in the portal venous blood flow? Am I simply missing the picture of the circulatory system around the liver?\n\n\n\n\nMoreover, with \"The increased splanchnic arterial blood flow in turn leads to increased venous efflux into the portal venous system\", why did the splanchnic arterial blood flow increase? Venous efflux from where and why into the portal venous system?\n\n\n\n\nMany thanks for any help!","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114306,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":114357,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The passage is saying that if you get enough of a nutrient in your diet, you don't need to synthesize it.</p>\n<p>If you don't need to synthesize a nutrient, you don't need to waste energy on the machinery to synthesize it.</p>\n<p>Even if you switch off the process that makes the machinery, even just keeping and copying the instructions for making that machinery is a waste.</p>\n","answer_id":114355,"answer_text":"The passage is saying that if you get enough of a nutrient in your diet, you don't need to synthesize it.\n\n\n\n\nIf you don't need to synthesize a nutrient, you don't need to waste energy on the machinery to synthesize it.\n\n\n\n\nEven if you switch off the process that makes the machinery, even just keeping and copying the instructions for making that machinery is a waste.","answer_url":"https://biology.stackexchange.com/a/114355","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2024-03-22T15:31:53+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:30.839943+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2139ae0ecb1bf62b149af3f8e91d7ce461ad269d38020aaf05922333eabb51a1_0.json","raw_sha256":"2610bc07f1691b2794681a23d0459bba24822de1f31c7b48d79495b29b0b1285","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/114428;114427;114412;114410;114399;114395;114391;114386;114385;114381;114378;114377;114376;114374;114372;114371;114370;114361;114354;114353;114348;114342;114331;114329;114324;114321;114319;114307;114305;114304;114299;114298;114295;114290;114281;114277;114273;114266;114256;114239;114238;114222;114216;114213;114211;114207;114197;114192;114185;114180;114178;114175;114174;114173;114172;114169;114161;114156;114155;114148;114145;114144;114139;114136;114135;114127;114119;114117;114114;114111;114110;114103;114098;114096;114094;114089;114085;114078;114076;114069;114067;114065;114058;114055;114048;114045;114038;114031;114028;114027;114025;114021;114020;114012;114006;113998;113997;113988;113986;113983/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114354,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2024-03-22T15:31:53+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"577039E1-AC3E-45A1-9C98-54786D96E497","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/577039E1-AC3E-45A1-9C98-54786D96E497/view-source"}],"score":6},{"answer_html":"<p>It’s a very dubious argument in my opinion.</p>\n<p>Whenever I see a question on this list arguing that higher organisms could save energy and DNA by such-and-such a hypothetical construct I want to scream. Think ‘junk’ DNA, introns, gene duplication, plant polyploidy and goodness knows how many other apparently inefficient and wasteful aspects of higher organisms that should never have appeared if these arguments held true. And the invalidity of the underlying assumption — that higher animals are competing like bacteria for the most efficient growth — never seems to occur to the proponents.</p>\n<p>I‘m no geneticist, but I gather that it is thought that genetic changes can spread in a population even if they convey no advantage, as long as they are not deleterious.</p>\n<p>The more I see of Harper, the less I like it. Not a biochemistry book for biochemists, and too many authors with only narrow expertise, lacking editing on what they write.</p>\n","answer_id":114357,"answer_text":"It’s a very dubious argument in my opinion.\n\n\n\n\nWhenever I see a question on this list arguing that higher organisms could save energy and DNA by such-and-such a hypothetical construct I want to scream. Think ‘junk’ DNA, introns, gene duplication, plant polyploidy and goodness knows how many other apparently inefficient and wasteful aspects of higher organisms that should never have appeared if these arguments held true. And the invalidity of the underlying assumption — that higher animals are competing like bacteria for the most efficient growth — never seems to occur to the proponents.\n\n\n\n\nI‘m no geneticist, but I gather that it is thought that genetic changes can spread in a population even if they convey no advantage, as long as they are not deleterious.\n\n\n\n\nThe more I see of Harper, the less I like it. Not a biochemistry book for biochemists, and too many authors with only narrow expertise, lacking editing on what they write.","answer_url":"https://biology.stackexchange.com/a/114357","author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","created_at":"2024-03-22T23:09:20+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:30.839943+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2139ae0ecb1bf62b149af3f8e91d7ce461ad269d38020aaf05922333eabb51a1_0.json","raw_sha256":"2610bc07f1691b2794681a23d0459bba24822de1f31c7b48d79495b29b0b1285","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/114428;114427;114412;114410;114399;114395;114391;114386;114385;114381;114378;114377;114376;114374;114372;114371;114370;114361;114354;114353;114348;114342;114331;114329;114324;114321;114319;114307;114305;114304;114299;114298;114295;114290;114281;114277;114273;114266;114256;114239;114238;114222;114216;114213;114211;114207;114197;114192;114185;114180;114178;114175;114174;114173;114172;114169;114161;114156;114155;114148;114145;114144;114139;114136;114135;114127;114119;114117;114114;114111;114110;114103;114098;114096;114094;114089;114085;114078;114076;114069;114067;114065;114058;114055;114048;114045;114038;114031;114028;114027;114025;114021;114020;114012;114006;113998;113997;113988;113986;113983/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114354,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2024-03-22T23:09:20+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"9E7ED099-2578-4C1C-8175-BC368D5F49ED","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9E7ED099-2578-4C1C-8175-BC368D5F49ED/view-source"}],"score":19},{"answer_html":"<p>I don't see the cost of the synthetization machinery as relevant (in this case), either. There is selection pressure to <strong>turn off</strong> the production if it's not needed, since leaving it running would consume resources to produce something of which there is enough which thus are not available to produce something that is missing, leaving the next processes which rely on the products unable to run, since it is missing all other raw materials except one being overabundant. This may well make several percent of difference in fitness.</p>\n<p>However, the cost of replicating the extra gene just in case someone might need it is an additional burden somewhere around a percent of a percent of a percent of cost: a selection pressure exists, but it is significantly lower. It will still lead to loss of the gene, but it will take <strong>thousands</strong> of times the number of generations to lose an useless gene compared to a detrimental gene, so it's not a significant effect.</p>\n<p>Also consider that a mutation usually changes the gene, it does not remove it, so the cost remains unchanged: the change that makes humans unable to synthetisize vitamin C is merely due to a <strong>defective</strong> gene, not due to a <strong>lost</strong> gene.</p>\n<p>It's more of a case of &quot;<strong>use it or lose it</strong>&quot;: a mutation that causes loss of the ability to synthesize it would be a disadvantage if the product is not available otherwise. But if it is available from food then there is no deletrious effect: the organism can survive in spite of losing this gene, so there is no selection pressure requiring to retain it. Therefore, a mutation that stops it from working may spread through the population.</p>\n<p>Still, the food situation can regularly change (for example, the source being seasonal), so the disadvantage is merely mitigated, thus a selection pressure against it still exists: if during the long time it takes to select against the useless gene a situation occurs where it is useful (like a year with bad weather), it will be strongly enough selected in favor to offset its uselessness.</p>\n<p>What is additionally required is a <strong>bottleneck</strong> in which the population shrinks so significantly that the survivors coincidentally lack that gene to produce it. Since losing the gene was not harmful, lacking it could spread to a sufficient proportion in the population.</p>\n<p>Then the <strong>founder effect</strong> in a subpopulation isolated from the main population would make that gene exceptionless in that subpopulation, coupled with the extinction of the remaining population or speciation of the new subpopulation leads to the species universally lacking that gene.</p>\n","answer_id":114369,"answer_text":"I don't see the cost of the synthetization machinery as relevant (in this case), either. There is selection pressure to turn off the production if it's not needed, since leaving it running would consume resources to produce something of which there is enough which thus are not available to produce something that is missing, leaving the next processes which rely on the products unable to run, since it is missing all other raw materials except one being overabundant. This may well make several percent of difference in fitness.\n\n\n\n\nHowever, the cost of replicating the extra gene just in case someone might need it is an additional burden somewhere around a percent of a percent of a percent of cost: a selection pressure exists, but it is significantly lower. It will still lead to loss of the gene, but it will take thousands of times the number of generations to lose an useless gene compared to a detrimental gene, so it's not a significant effect.\n\n\n\n\nAlso consider that a mutation usually changes the gene, it does not remove it, so the cost remains unchanged: the change that makes humans unable to synthetisize vitamin C is merely due to a defective gene, not due to a lost gene.\n\n\n\n\nIt's more of a case of \"use it or lose it\": a mutation that causes loss of the ability to synthesize it would be a disadvantage if the product is not available otherwise. But if it is available from food then there is no deletrious effect: the organism can survive in spite of losing this gene, so there is no selection pressure requiring to retain it. Therefore, a mutation that stops it from working may spread through the population.\n\n\n\n\nStill, the food situation can regularly change (for example, the source being seasonal), so the disadvantage is merely mitigated, thus a selection pressure against it still exists: if during the long time it takes to select against the useless gene a situation occurs where it is useful (like a year with bad weather), it will be strongly enough selected in favor to offset its uselessness.\n\n\n\n\nWhat is additionally required is a bottleneck in which the population shrinks so significantly that the survivors coincidentally lack that gene to produce it. Since losing the gene was not harmful, lacking it could spread to a sufficient proportion in the population.\n\n\n\n\nThen the founder effect in a subpopulation isolated from the main population would make that gene exceptionless in that subpopulation, coupled with the extinction of the remaining population or speciation of the new subpopulation leads to the species universally lacking that gene.","answer_url":"https://biology.stackexchange.com/a/114369","author":"user66554","author_url":"https://biology.stackexchange.com/users/14628/user66554","content_license":"CC BY-SA 4.0","created_at":"2024-03-25T09:19:29+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:30.839943+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2139ae0ecb1bf62b149af3f8e91d7ce461ad269d38020aaf05922333eabb51a1_0.json","raw_sha256":"2610bc07f1691b2794681a23d0459bba24822de1f31c7b48d79495b29b0b1285","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/114428;114427;114412;114410;114399;114395;114391;114386;114385;114381;114378;114377;114376;114374;114372;114371;114370;114361;114354;114353;114348;114342;114331;114329;114324;114321;114319;114307;114305;114304;114299;114298;114295;114290;114281;114277;114273;114266;114256;114239;114238;114222;114216;114213;114211;114207;114197;114192;114185;114180;114178;114175;114174;114173;114172;114169;114161;114156;114155;114148;114145;114144;114139;114136;114135;114127;114119;114117;114114;114111;114110;114103;114098;114096;114094;114089;114085;114078;114076;114069;114067;114065;114058;114055;114048;114045;114038;114031;114028;114027;114025;114021;114020;114012;114006;113998;113997;113988;113986;113983/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114354,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user66554","profile_url":"https://biology.stackexchange.com/users/14628/user66554","user_type":"registered"},"created_at":"2024-03-25T09:19:29+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"87321CDD-57AA-4A5D-961D-CF6B61751579","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/87321CDD-57AA-4A5D-961D-CF6B61751579/view-source"}],"score":2},{"answer_html":"<p>The question seems confused. Non-essential aminoacids (in the traditional sense, counting only aminoacids that take part in proteins) are only non-essential because we have biosynthetic pathways that make them. Lose the biosynthetic pathway for such a non-essential aminoacid, it becomes essential.</p>\n","answer_id":114422,"answer_text":"The question seems confused. Non-essential aminoacids (in the traditional sense, counting only aminoacids that take part in proteins) are only non-essential because we have biosynthetic pathways that make them. Lose the biosynthetic pathway for such a non-essential aminoacid, it becomes essential.","answer_url":"https://biology.stackexchange.com/a/114422","author":"terry-s","author_url":"https://biology.stackexchange.com/users/43627/terry-s","content_license":"CC BY-SA 4.0","created_at":"2024-04-01T21:33:52+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:32.233008+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/29e10377e709be0879cc174e9be11ba5513feaafd20aa842a20668af70c6d683_0.json","raw_sha256":"535e870bb8fe62b3db0c0b66043a398cf2f6d26fcd7ad4a13a2a7e2a09999ee9","source_api":"Stack Exchange API 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Why?</p>\n<p>Because if the diet contains ample quantities of a nutrient, retention of the ability to biosynthesize it represents information of <em>negative</em> survival value, <strong>because ATP and nutrients not required to synthesize “unnecessary” DNA-even if specific encoded genes are no longer expressed.</strong></p>\n</blockquote>\n<p>I could not understand the part that I have emboldened.</p>\n","text":"In my textbook \"Harper's illustrated biochemistry\" chapter 27 it is written that\n\n\n\n\n\n\n\nThe existence of nutritional requirements suggests that dependence on an external source of a specific nutrient can be of greater survival value than ability to biosynthesize it. Why?\n\n\n\n\nBecause if the diet contains ample quantities of a nutrient, retention of the ability to biosynthesize it represents information of negative survival value, because ATP and nutrients not required to synthesize “unnecessary” DNA-even if specific encoded genes are no longer expressed.\n\n\n\n\n\n\n\nI could not understand the part that I have emboldened."},{"context_id":"114355","html":"<p>The passage is saying that if you get enough of a nutrient in your diet, you don't need to synthesize it.</p>\n<p>If you don't need to synthesize a nutrient, you don't need to waste energy on the machinery to synthesize it.</p>\n<p>Even if you switch off the process that makes the machinery, even just keeping and copying the instructions for making that machinery is a waste.</p>\n","text":"The passage is saying that if you get enough of a nutrient in your diet, you don't need to synthesize it.\n\n\n\n\nIf you don't need to synthesize a nutrient, you don't need to waste energy on the machinery to synthesize it.\n\n\n\n\nEven if you switch off the process that makes the machinery, even just keeping and copying the instructions for making that machinery is a waste."},{"context_id":"114357","html":"<p>It’s a very dubious argument in my opinion.</p>\n<p>Whenever I see a question on this list arguing that higher organisms could save energy and DNA by such-and-such a hypothetical construct I want to scream. Think ‘junk’ DNA, introns, gene duplication, plant polyploidy and goodness knows how many other apparently inefficient and wasteful aspects of higher organisms that should never have appeared if these arguments held true. And the invalidity of the underlying assumption — that higher animals are competing like bacteria for the most efficient growth — never seems to occur to the proponents.</p>\n<p>I‘m no geneticist, but I gather that it is thought that genetic changes can spread in a population even if they convey no advantage, as long as they are not deleterious.</p>\n<p>The more I see of Harper, the less I like it. Not a biochemistry book for biochemists, and too many authors with only narrow expertise, lacking editing on what they write.</p>\n","text":"It’s a very dubious argument in my opinion.\n\n\n\n\nWhenever I see a question on this list arguing that higher organisms could save energy and DNA by such-and-such a hypothetical construct I want to scream. Think ‘junk’ DNA, introns, gene duplication, plant polyploidy and goodness knows how many other apparently inefficient and wasteful aspects of higher organisms that should never have appeared if these arguments held true. And the invalidity of the underlying assumption — that higher animals are competing like bacteria for the most efficient growth — never seems to occur to the proponents.\n\n\n\n\nI‘m no geneticist, but I gather that it is thought that genetic changes can spread in a population even if they convey no advantage, as long as they are not deleterious.\n\n\n\n\nThe more I see of Harper, the less I like it. Not a biochemistry book for biochemists, and too many authors with only narrow expertise, lacking editing on what they write."},{"context_id":"114369","html":"<p>I don't see the cost of the synthetization machinery as relevant (in this case), either. There is selection pressure to <strong>turn off</strong> the production if it's not needed, since leaving it running would consume resources to produce something of which there is enough which thus are not available to produce something that is missing, leaving the next processes which rely on the products unable to run, since it is missing all other raw materials except one being overabundant. This may well make several percent of difference in fitness.</p>\n<p>However, the cost of replicating the extra gene just in case someone might need it is an additional burden somewhere around a percent of a percent of a percent of cost: a selection pressure exists, but it is significantly lower. It will still lead to loss of the gene, but it will take <strong>thousands</strong> of times the number of generations to lose an useless gene compared to a detrimental gene, so it's not a significant effect.</p>\n<p>Also consider that a mutation usually changes the gene, it does not remove it, so the cost remains unchanged: the change that makes humans unable to synthetisize vitamin C is merely due to a <strong>defective</strong> gene, not due to a <strong>lost</strong> gene.</p>\n<p>It's more of a case of &quot;<strong>use it or lose it</strong>&quot;: a mutation that causes loss of the ability to synthesize it would be a disadvantage if the product is not available otherwise. But if it is available from food then there is no deletrious effect: the organism can survive in spite of losing this gene, so there is no selection pressure requiring to retain it. Therefore, a mutation that stops it from working may spread through the population.</p>\n<p>Still, the food situation can regularly change (for example, the source being seasonal), so the disadvantage is merely mitigated, thus a selection pressure against it still exists: if during the long time it takes to select against the useless gene a situation occurs where it is useful (like a year with bad weather), it will be strongly enough selected in favor to offset its uselessness.</p>\n<p>What is additionally required is a <strong>bottleneck</strong> in which the population shrinks so significantly that the survivors coincidentally lack that gene to produce it. Since losing the gene was not harmful, lacking it could spread to a sufficient proportion in the population.</p>\n<p>Then the <strong>founder effect</strong> in a subpopulation isolated from the main population would make that gene exceptionless in that subpopulation, coupled with the extinction of the remaining population or speciation of the new subpopulation leads to the species universally lacking that gene.</p>\n","text":"I don't see the cost of the synthetization machinery as relevant (in this case), either. There is selection pressure to turn off the production if it's not needed, since leaving it running would consume resources to produce something of which there is enough which thus are not available to produce something that is missing, leaving the next processes which rely on the products unable to run, since it is missing all other raw materials except one being overabundant. This may well make several percent of difference in fitness.\n\n\n\n\nHowever, the cost of replicating the extra gene just in case someone might need it is an additional burden somewhere around a percent of a percent of a percent of cost: a selection pressure exists, but it is significantly lower. It will still lead to loss of the gene, but it will take thousands of times the number of generations to lose an useless gene compared to a detrimental gene, so it's not a significant effect.\n\n\n\n\nAlso consider that a mutation usually changes the gene, it does not remove it, so the cost remains unchanged: the change that makes humans unable to synthetisize vitamin C is merely due to a defective gene, not due to a lost gene.\n\n\n\n\nIt's more of a case of \"use it or lose it\": a mutation that causes loss of the ability to synthesize it would be a disadvantage if the product is not available otherwise. But if it is available from food then there is no deletrious effect: the organism can survive in spite of losing this gene, so there is no selection pressure requiring to retain it. Therefore, a mutation that stops it from working may spread through the population.\n\n\n\n\nStill, the food situation can regularly change (for example, the source being seasonal), so the disadvantage is merely mitigated, thus a selection pressure against it still exists: if during the long time it takes to select against the useless gene a situation occurs where it is useful (like a year with bad weather), it will be strongly enough selected in favor to offset its uselessness.\n\n\n\n\nWhat is additionally required is a bottleneck in which the population shrinks so significantly that the survivors coincidentally lack that gene to produce it. Since losing the gene was not harmful, lacking it could spread to a sufficient proportion in the population.\n\n\n\n\nThen the founder effect in a subpopulation isolated from the main population would make that gene exceptionless in that subpopulation, coupled with the extinction of the remaining population or speciation of the new subpopulation leads to the species universally lacking that gene."},{"context_id":"114422","html":"<p>The question seems confused. Non-essential aminoacids (in the traditional sense, counting only aminoacids that take part in proteins) are only non-essential because we have biosynthetic pathways that make them. Lose the biosynthetic pathway for such a non-essential aminoacid, it becomes essential.</p>\n","text":"The question seems confused. Non-essential aminoacids (in the traditional sense, counting only aminoacids that take part in proteins) are only non-essential because we have biosynthetic pathways that make them. Lose the biosynthetic pathway for such a non-essential aminoacid, it becomes essential."}],"domain":"biology","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"22cbe7613468be52c7382402102c55107f88c92909d62872dd785e1fa693fd3d","hard_case_family":["multiple_answer_candidates"],"id":"RHM-d4dfc6a8f374cf60bf8178d3","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:08.576606+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1051d4f3e38449f1419d1973ac812b2286659e454a76f89a23fdaa941dfadddb_0.json","raw_sha256":"583dcd577e20d33b29e9f8818a7ab6a1fab039c19ab79927e16096cff23fa61d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=7&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lakshya Kumar Singh","profile_url":"https://biology.stackexchange.com/users/69135/lakshya-kumar-singh","user_type":"registered"},"created_at":"2024-03-22T14:50:47+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"1FDBF832-1562-4410-B736-35A35E7919A6","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/1FDBF832-1562-4410-B736-35A35E7919A6/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-03-22T22:57:28+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"606C2639-1A88-4A57-913C-8967E7701F21","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/606C2639-1A88-4A57-913C-8967E7701F21/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2024-04-01T12:31:03+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"63A67BBD-8291-4752-B598-AEDFE8195AC5","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/63A67BBD-8291-4752-B598-AEDFE8195AC5/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2024-04-01T12:31:03+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"ABAB603F-7A26-480B-BC5C-EB0C011D7174","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/ABAB603F-7A26-480B-BC5C-EB0C011D7174/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114354","source_record_sha256":"5722369c01cf2fa74245fed6684573569d902e3bc84d3efb85fd48aacceb8c4c","source_url":"https://biology.stackexchange.com/questions/114354/why-is-the-retention-of-ability-to-synthesize-non-essential-amino-acids-of-negat","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Why is the retention of ability to synthesize non essential amino acids of negative survival value?\nIn my textbook \"Harper's illustrated biochemistry\" chapter 27 it is written that\n\n\n\n\n\n\n\nThe existence of nutritional requirements suggests that dependence on an external source of a specific nutrient can be of greater survival value than ability to biosynthesize it. Why?\n\n\n\n\nBecause if the diet contains ample quantities of a nutrient, retention of the ability to biosynthesize it represents information of negative survival value, because ATP and nutrients not required to synthesize “unnecessary” DNA-even if specific encoded genes are no longer expressed.\n\n\n\n\n\n\n\nI could not understand the part that I have emboldened.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114355,"score":6},{"answer_id":114357,"score":19},{"answer_id":114369,"score":2},{"answer_id":114422,"score":0}],"split":"test"}
{"accepted_status":{"accepted_answer_id":114468,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The easy answer is to use acidified SDS 10 Percent in 0,01 N HCl. I added this directly, to my media and did not have any problems with crystal removal anymore. The acid will remove the coloring of the indicator. The triplet accuracy increased enormously in comparison to the DMSO approach. I would not recommend the DMSO technique at all, because you might ruin all your work. At least if media removal is involved. But you need to incubate overnight as stated in various protocols if using SDS.Also additional mixing with a pipette or a plate shaker might help if you have a gradient of color in your wells. On the other hand maybe it would be possible to add acidified DMSO, or DMF or an alkohol in acidified Form without the need to remove media.</p>\n<p>See this publication for an overview of MTT, MTS, XTT, WSF-1, WSF-8 and different advantages and cons of each variant: <a href=\"https://onlinelibrary.wiley.com/doi/10.1002/fft2.44\" rel=\"nofollow noreferrer\">https://onlinelibrary.wiley.com/doi/10.1002/fft2.44</a></p>\n<p>Edit: If you have air bubbles, use gently a heat gun. The bubbles will disappear instantly.</p>\n","answer_id":114468,"answer_text":"The easy answer is to use acidified SDS 10 Percent in 0,01 N HCl. I added this directly, to my media and did not have any problems with crystal removal anymore. The acid will remove the coloring of the indicator. The triplet accuracy increased enormously in comparison to the DMSO approach. I would not recommend the DMSO technique at all, because you might ruin all your work. At least if media removal is involved. But you need to incubate overnight as stated in various protocols if using SDS.Also additional mixing with a pipette or a plate shaker might help if you have a gradient of color in your wells. On the other hand maybe it would be possible to add acidified DMSO, or DMF or an alkohol in acidified Form without the need to remove media.\n\n\n\n\nSee this publication for an overview of MTT, MTS, XTT, WSF-1, WSF-8 and different advantages and cons of each variant: https://onlinelibrary.wiley.com/doi/10.1002/fft2.44 (https://onlinelibrary.wiley.com/doi/10.1002/fft2.44)\n\n\n\n\nEdit: If you have air bubbles, use gently a heat gun. The bubbles will disappear instantly.","answer_url":"https://biology.stackexchange.com/a/114468","author":"raptorlane","author_url":"https://biology.stackexchange.com/users/77746/raptorlane","content_license":"CC BY-SA 4.0","created_at":"2024-04-09T18:49:27+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:27.977583+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1cbf95322a17dce0fd00a109179063ffe60bcd4bddc6e720f0ca398ee7aa9da8_0.json","raw_sha256":"a096c86028a279b01346143890b4827bd8ed05afc0a76bd7c8bcb840211dc20e","source_api":"Stack Exchange API 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4.0","contributor":{"display_name":"raptorlane","profile_url":"https://biology.stackexchange.com/users/77746/raptorlane","user_type":"registered"},"created_at":"2024-08-12T16:08:05+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"25008C26-3203-4F75-9E38-BCBDC1EAF1B9","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/25008C26-3203-4F75-9E38-BCBDC1EAF1B9/view-source"}],"url":"https://biology.stackexchange.com/a/114468"}],"contexts":[{"context_id":"question","html":"<p>I am testing two compounds against 3 cell lines to determine cell viability. Two lines grow in Eagle media, one in DMEM (+10 Percent bovine serum) which contain phenyl red indicator.\nI prepared 3 plates to let the compounds take effect for up to 96h. For each time point I treat the plate with MTT for 4 h, then remove the media, than add DMSO and incubate for 15 min. On the first plate it appeared to be a positive correlation between increasing concentration and decreasing cell viability. However on the second plate the trend is not as obvious. I would also assume that cell viability is reduced more than at the first time point which is not the case in a clear way or I can't see it from the data until mow. You find an image of the first plate here</p>\n<p><a href=\"https://i.sstatic.net/InPpW.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/InPpW.jpg\" alt=\"enter image description here\" /></a></p>\n<p>On the plate columns 1-4 are cell line 1 (with increasing compound concentration), 5-8 cell line 2 and 9-12 is cell line 3. Rows A-C are triplicates of compound 1, rows D-F are triplicates of compound 2, and G+H and is just media as negative control.</p>\n<p>For me the plate does not look good with bare eye: The first row is off completely and from column 1-4 the intensity should either decrease or at least stay steady.</p>\n<p>I am assuming the problem could be related to multiple factors:</p>\n<ol>\n<li><p>During media removal always some crystals will be sucked in by the pipette. I tried to avoid this by centrifuging the crystals to create a more stiff layer but this did not work well. Also tilting the plates a little bit did not work nicely.</p>\n</li>\n<li><p>When you're too careful not to suck any crystals in on the other hand media will remain in the well which will change concentration and also show some absorbance  due to the indicator.</p>\n</li>\n</ol>\n<p>I am wondering how your experiences are with with these issues with the MTT assay? I personally find it to be a huge design flaw, that you need to remove the media, witch will lead to possible problems with the quantification.</p>\n<p>The alternative works with 10 Percent SDS in 0.01 HCl overnight to dissolve the formazan. I am also wondering if you can share experiences on this modification as well. I am likely to do this for the 3rd plate to see if the overall structure of the data is more consistent.</p>\n<p>Alternatively, should I switch to XTT, WSF-1, MSF etc.?</p>\n","text":"I am testing two compounds against 3 cell lines to determine cell viability. Two lines grow in Eagle media, one in DMEM (+10 Percent bovine serum) which contain phenyl red indicator.\nI prepared 3 plates to let the compounds take effect for up to 96h. For each time point I treat the plate with MTT for 4 h, then remove the media, than add DMSO and incubate for 15 min. On the first plate it appeared to be a positive correlation between increasing concentration and decreasing cell viability. However on the second plate the trend is not as obvious. I would also assume that cell viability is reduced more than at the first time point which is not the case in a clear way or I can't see it from the data until mow. You find an image of the first plate here\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/InPpW.jpg] (https://i.sstatic.net/InPpW.jpg)\n\n\n\n\nOn the plate columns 1-4 are cell line 1 (with increasing compound concentration), 5-8 cell line 2 and 9-12 is cell line 3. Rows A-C are triplicates of compound 1, rows D-F are triplicates of compound 2, and G+H and is just media as negative control.\n\n\n\n\nFor me the plate does not look good with bare eye: The first row is off completely and from column 1-4 the intensity should either decrease or at least stay steady.\n\n\n\n\nI am assuming the problem could be related to multiple factors:\n\n\n\n\n\n\n\nDuring media removal always some crystals will be sucked in by the pipette. I tried to avoid this by centrifuging the crystals to create a more stiff layer but this did not work well. Also tilting the plates a little bit did not work nicely.\n\n\n\n\n\n\n\n\n\nWhen you're too careful not to suck any crystals in on the other hand media will remain in the well which will change concentration and also show some absorbance  due to the indicator.\n\n\n\n\n\n\n\n\nI am wondering how your experiences are with with these issues with the MTT assay? I personally find it to be a huge design flaw, that you need to remove the media, witch will lead to possible problems with the quantification.\n\n\n\n\nThe alternative works with 10 Percent SDS in 0.01 HCl overnight to dissolve the formazan. I am also wondering if you can share experiences on this modification as well. I am likely to do this for the 3rd plate to see if the overall structure of the data is more consistent.\n\n\n\n\nAlternatively, should I switch to XTT, WSF-1, MSF etc.?"},{"context_id":"114468","html":"<p>The easy answer is to use acidified SDS 10 Percent in 0,01 N HCl. I added this directly, to my media and did not have any problems with crystal removal anymore. The acid will remove the coloring of the indicator. The triplet accuracy increased enormously in comparison to the DMSO approach. I would not recommend the DMSO technique at all, because you might ruin all your work. At least if media removal is involved. But you need to incubate overnight as stated in various protocols if using SDS.Also additional mixing with a pipette or a plate shaker might help if you have a gradient of color in your wells. On the other hand maybe it would be possible to add acidified DMSO, or DMF or an alkohol in acidified Form without the need to remove media.</p>\n<p>See this publication for an overview of MTT, MTS, XTT, WSF-1, WSF-8 and different advantages and cons of each variant: <a href=\"https://onlinelibrary.wiley.com/doi/10.1002/fft2.44\" rel=\"nofollow noreferrer\">https://onlinelibrary.wiley.com/doi/10.1002/fft2.44</a></p>\n<p>Edit: If you have air bubbles, use gently a heat gun. The bubbles will disappear instantly.</p>\n","text":"The easy answer is to use acidified SDS 10 Percent in 0,01 N HCl. I added this directly, to my media and did not have any problems with crystal removal anymore. The acid will remove the coloring of the indicator. The triplet accuracy increased enormously in comparison to the DMSO approach. I would not recommend the DMSO technique at all, because you might ruin all your work. At least if media removal is involved. But you need to incubate overnight as stated in various protocols if using SDS.Also additional mixing with a pipette or a plate shaker might help if you have a gradient of color in your wells. On the other hand maybe it would be possible to add acidified DMSO, or DMF or an alkohol in acidified Form without the need to remove media.\n\n\n\n\nSee this publication for an overview of MTT, MTS, XTT, WSF-1, WSF-8 and different advantages and cons of each variant: https://onlinelibrary.wiley.com/doi/10.1002/fft2.44 (https://onlinelibrary.wiley.com/doi/10.1002/fft2.44)\n\n\n\n\nEdit: If you have air bubbles, use gently a heat gun. The bubbles will disappear instantly."}],"domain":"biology","external_citations":["https://i.sstatic.net/InPpW.jpg","https://onlinelibrary.wiley.com/doi/10.1002/fft2.44"],"ground_truth_type":"metadata_grounded","group_id":"80501d1c64ba89cd17d8c32bc590827e390ebd122fa8124c93a2e755f15c8a9f","hard_case_family":["multiple_sources"],"id":"RHM-7e33b065d68fffd3853faece","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:07.165481+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/b97a755f39b54a1e8a057fa5e484426784aa17a1971c6ef0ca759105de983078_0.json","raw_sha256":"4c9dcc077d306d60a8b8a237ad3f9b3144c0d5885fa62ef1bfdd55d2fbbdaf6a","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=6&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"raptorlane","profile_url":"https://biology.stackexchange.com/users/77746/raptorlane","user_type":"registered"},"created_at":"2024-04-06T22:50:55+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"75F4E194-3AD5-4EC3-A35E-A53EEEB3035A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/75F4E194-3AD5-4EC3-A35E-A53EEEB3035A/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"raptorlane","profile_url":"https://biology.stackexchange.com/users/77746/raptorlane","user_type":"registered"},"created_at":"2024-04-06T23:04:37+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"78DC5608-69B6-43F2-920C-882B8DD05F1E","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/78DC5608-69B6-43F2-920C-882B8DD05F1E/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"raptorlane","profile_url":"https://biology.stackexchange.com/users/77746/raptorlane","user_type":"registered"},"created_at":"2024-04-09T21:46:24+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"17045A98-C1DC-42B2-AA93-D64CBBD718BA","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/17045A98-C1DC-42B2-AA93-D64CBBD718BA/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114451","source_record_sha256":"a68d32b251059d339839f422841eaef3a625d4e215a58c89a2b682a0561c7ca8","source_url":"https://biology.stackexchange.com/questions/114451/cell-viability-assay-problems-with-mtt-assay-in-the-solubilization-step","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Cell viability assay: Problems with MTT assay in the solubilization step\nI am testing two compounds against 3 cell lines to determine cell viability. Two lines grow in Eagle media, one in DMEM (+10 Percent bovine serum) which contain phenyl red indicator.\nI prepared 3 plates to let the compounds take effect for up to 96h. For each time point I treat the plate with MTT for 4 h, then remove the media, than add DMSO and incubate for 15 min. On the first plate it appeared to be a positive correlation between increasing concentration and decreasing cell viability. However on the second plate the trend is not as obvious. I would also assume that cell viability is reduced more than at the first time point which is not the case in a clear way or I can't see it from the data until mow. You find an image of the first plate here\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/InPpW.jpg] (https://i.sstatic.net/InPpW.jpg)\n\n\n\n\nOn the plate columns 1-4 are cell line 1 (with increasing compound concentration), 5-8 cell line 2 and 9-12 is cell line 3. Rows A-C are triplicates of compound 1, rows D-F are triplicates of compound 2, and G+H and is just media as negative control.\n\n\n\n\nFor me the plate does not look good with bare eye: The first row is off completely and from column 1-4 the intensity should either decrease or at least stay steady.\n\n\n\n\nI am assuming the problem could be related to multiple factors:\n\n\n\n\n\n\n\nDuring media removal always some crystals will be sucked in by the pipette. I tried to avoid this by centrifuging the crystals to create a more stiff layer but this did not work well. Also tilting the plates a little bit did not work nicely.\n\n\n\n\n\n\n\n\n\nWhen you're too careful not to suck any crystals in on the other hand media will remain in the well which will change concentration and also show some absorbance  due to the indicator.\n\n\n\n\n\n\n\n\nI am wondering how your experiences are with with these issues with the MTT assay? I personally find it to be a huge design flaw, that you need to remove the media, witch will lead to possible problems with the quantification.\n\n\n\n\nThe alternative works with 10 Percent SDS in 0.01 HCl overnight to dissolve the formazan. I am also wondering if you can share experiences on this modification as well. I am likely to do this for the 3rd plate to see if the overall structure of the data is more consistent.\n\n\n\n\nAlternatively, should I switch to XTT, WSF-1, MSF etc.?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114468,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I would suggest looking into the field of <a href=\"https://www.nature.com/scitable/topicpage/the-complexity-of-gene-expression-protein-interaction-34575/\" rel=\"nofollow noreferrer\">organismal complexity</a>.</p>\n<p>One could turn the question on its head: why does a worm, which apparently has the raw materials to get as complex as a human, stay a worm?</p>\n<p>One answer would be that the human developmental process is much longer and more elaborate than the worm's. We might for example have <a href=\"https://www.nature.com/scitable/topicpage/transcription-factors-and-transcriptional-control-in-eukaryotic-1046/\" rel=\"nofollow noreferrer\">a more elaborate process of gene regulation throughout development</a> that lets us keep developing longer- so the question is not how many genes, but what combinations of the genes we have can be turned on or off together. The number of possible combinations is very large when you have 20K genes!</p>\n<p>More answers might have to do with the number of gene-gene or protein-protein interactions, that might underlie complexity in the way you mean. For example, from the source I linked:</p>\n<blockquote>\n<p>Using bioinformatics, the team estimated that 650,000 protein interactions occur in humans; this number is approximately three times more than that in the roundworm and 10 times more than that in the fruit fly. Moreover, it seems that a single protein can have dozens, if not hundreds, of different interactions.</p>\n</blockquote>\n<p>So when we say &quot;complexity&quot; what we might mean is number of gene-gene interactions, not the number of genes.</p>\n<p>A fun aside, plants <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203354/\" rel=\"nofollow noreferrer\">tend to have more transcription factors</a> (which basically turn genes off and on and lead to interactions). Higher plants also usually <a href=\"https://www.google.com/url?sa=t&amp;source=web&amp;rct=j&amp;opi=89978449&amp;url=https://pubmed.ncbi.nlm.nih.gov/26130755/&amp;ved=2ahUKEwidz5SYoseFAxULMDQIHdX_AXcQFnoECDYQAQ&amp;usg=AOvVaw3Fr7DxORwp3LrJEbFu1Gi8\" rel=\"nofollow noreferrer\">develop continuously throughout their lives and can dedifferentiate their cells fairly readily</a>. So if we're looking in this way, there might be an argument that plants are a lot more complex than humans, even while having similar numbers of genes!</p>\n<p>Here is for example a tabulation of the number of transcription factors in various eukaryotes from <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203354/\" rel=\"nofollow noreferrer\">this paper</a> (apologies for not taking the time to retranscribe this image). Over time we've described/annotated more TFs in the various species of course, but even with the disproportionate effort on humans, plants still have more. For example, at last count <a href=\"https://planttfdb.gao-lab.org/download.php\" rel=\"nofollow noreferrer\">soybean had almost 4000 TFs</a>, whereas humans have around <a href=\"https://www.cell.com/cell/pdf/S0092-8674(18)30106-5.pdf\" rel=\"nofollow noreferrer\">1600</a>.</p>\n<p><a href=\"https://i.sstatic.net/AQ8UE.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/AQ8UE.jpg\" alt=\"Tabulation of TF numbers in different families overlaid on an evolutionary tree showing higher TF numbers in various lineages\" /></a></p>\n<p>That's not to say that this is the <em>right</em> measure of complexity. What you mean by complexity will differ depending on what you are interested in!</p>\n","answer_id":114509,"answer_text":"I would suggest looking into the field of organismal complexity (https://www.nature.com/scitable/topicpage/the-complexity-of-gene-expression-protein-interaction-34575/).\n\n\n\n\nOne could turn the question on its head: why does a worm, which apparently has the raw materials to get as complex as a human, stay a worm?\n\n\n\n\nOne answer would be that the human developmental process is much longer and more elaborate than the worm's. We might for example have a more elaborate process of gene regulation throughout development (https://www.nature.com/scitable/topicpage/transcription-factors-and-transcriptional-control-in-eukaryotic-1046/) that lets us keep developing longer- so the question is not how many genes, but what combinations of the genes we have can be turned on or off together. The number of possible combinations is very large when you have 20K genes!\n\n\n\n\nMore answers might have to do with the number of gene-gene or protein-protein interactions, that might underlie complexity in the way you mean. For example, from the source I linked:\n\n\n\n\n\n\n\nUsing bioinformatics, the team estimated that 650,000 protein interactions occur in humans; this number is approximately three times more than that in the roundworm and 10 times more than that in the fruit fly. Moreover, it seems that a single protein can have dozens, if not hundreds, of different interactions.\n\n\n\n\n\n\n\nSo when we say \"complexity\" what we might mean is number of gene-gene interactions, not the number of genes.\n\n\n\n\nA fun aside, plants tend to have more transcription factors (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203354/) (which basically turn genes off and on and lead to interactions). Higher plants also usually develop continuously throughout their lives and can dedifferentiate their cells fairly readily (https://www.google.com/url?sa=t&source=web&rct=j&opi=89978449&url=https://pubmed.ncbi.nlm.nih.gov/26130755/&ved=2ahUKEwidz5SYoseFAxULMDQIHdX_AXcQFnoECDYQAQ&usg=AOvVaw3Fr7DxORwp3LrJEbFu1Gi8). So if we're looking in this way, there might be an argument that plants are a lot more complex than humans, even while having similar numbers of genes!\n\n\n\n\nHere is for example a tabulation of the number of transcription factors in various eukaryotes from this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203354/) (apologies for not taking the time to retranscribe this image). Over time we've described/annotated more TFs in the various species of course, but even with the disproportionate effort on humans, plants still have more. For example, at last count soybean had almost 4000 TFs (https://planttfdb.gao-lab.org/download.php), whereas humans have around 1600 (https://www.cell.com/cell/pdf/S0092-8674(18)30106-5.pdf).\n\n\n\n\n[image: Tabulation of TF numbers in different families overlaid on an evolutionary tree showing higher TF numbers in various lineages; source: https://i.sstatic.net/AQ8UE.jpg] (https://i.sstatic.net/AQ8UE.jpg)\n\n\n\n\nThat's not to say that this is the right measure of complexity. What you mean by complexity will differ depending on what you are interested in!","answer_url":"https://biology.stackexchange.com/a/114509","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2024-04-16T17:35:33+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:27.977583+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1cbf95322a17dce0fd00a109179063ffe60bcd4bddc6e720f0ca398ee7aa9da8_0.json","raw_sha256":"a096c86028a279b01346143890b4827bd8ed05afc0a76bd7c8bcb840211dc20e","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/114983;114969;114966;114963;114939;114936;114918;114909;114904;114899;114888;114885;114881;114875;114874;114873;114872;114864;114857;114850;114846;114841;114834;114827;114821;114819;114813;114804;114791;114784;114768;114765;114762;114760;114758;114755;114745;114741;114739;114738;114732;114730;114726;114714;114706;114695;114691;114690;114686;114683;114677;114675;114666;114660;114656;114653;114642;114641;114632;114628;114620;114618;114613;114601;114599;114597;114581;114577;114573;114567;114558;114555;114553;114552;114547;114545;114543;114542;114541;114539;114529;114524;114516;114502;114501;114498;114495;114492;114481;114476;114474;114470;114453;114451;114449;114448;114446;114440;114438;114435/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114501,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-04-16T17:35:33+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"28D3658A-53BF-4982-87F9-ACA28595D3F7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/28D3658A-53BF-4982-87F9-ACA28595D3F7/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-04-16T20:10:48+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"BCF3B99C-8D62-4DBB-B2DF-C0F4D9176AB8","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/BCF3B99C-8D62-4DBB-B2DF-C0F4D9176AB8/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"tree","author_url":"https://biology.stackexchange.com/users/80300/tree","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"tree","profile_url":"https://biology.stackexchange.com/users/80300/tree","user_type":"registered"},"created_at":"2024-04-15T18:52:38+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"0F687A08-3079-471B-A167-8132321766AB","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0F687A08-3079-471B-A167-8132321766AB/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-04-16T20:11:34+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"D457B163-01AB-435D-AEDF-40132FF1D395","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D457B163-01AB-435D-AEDF-40132FF1D395/view-source"}],"url":"https://biology.stackexchange.com/questions/114501/no-of-genes-and-organismal-complexity"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"114509","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-04-16T17:35:33+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"28D3658A-53BF-4982-87F9-ACA28595D3F7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/28D3658A-53BF-4982-87F9-ACA28595D3F7/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-04-16T20:10:48+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"BCF3B99C-8D62-4DBB-B2DF-C0F4D9176AB8","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/BCF3B99C-8D62-4DBB-B2DF-C0F4D9176AB8/view-source"}],"url":"https://biology.stackexchange.com/a/114509"}],"contexts":[{"context_id":"question","html":"<p>Why do humans contain trillions of cells arranged in many complex organs, and worms contain many less cells and less organs, but we and the worm have a similar number of genes? See for example Table 1 <a href=\"https://www.nature.com/scitable/topicpage/eukaryotic-genome-complexity-437/\" rel=\"nofollow noreferrer\">here</a>.</p>\n<p>I know that the number of genes does not correlate well with organismal complexity, and the size of the genome is unrelated to the metabolic, developmental, and behavioural complexity. But I am curious WHY?</p>\n","text":"Why do humans contain trillions of cells arranged in many complex organs, and worms contain many less cells and less organs, but we and the worm have a similar number of genes? See for example Table 1 here (https://www.nature.com/scitable/topicpage/eukaryotic-genome-complexity-437/).\n\n\n\n\nI know that the number of genes does not correlate well with organismal complexity, and the size of the genome is unrelated to the metabolic, developmental, and behavioural complexity. But I am curious WHY?"},{"context_id":"114509","html":"<p>I would suggest looking into the field of <a href=\"https://www.nature.com/scitable/topicpage/the-complexity-of-gene-expression-protein-interaction-34575/\" rel=\"nofollow noreferrer\">organismal complexity</a>.</p>\n<p>One could turn the question on its head: why does a worm, which apparently has the raw materials to get as complex as a human, stay a worm?</p>\n<p>One answer would be that the human developmental process is much longer and more elaborate than the worm's. We might for example have <a href=\"https://www.nature.com/scitable/topicpage/transcription-factors-and-transcriptional-control-in-eukaryotic-1046/\" rel=\"nofollow noreferrer\">a more elaborate process of gene regulation throughout development</a> that lets us keep developing longer- so the question is not how many genes, but what combinations of the genes we have can be turned on or off together. The number of possible combinations is very large when you have 20K genes!</p>\n<p>More answers might have to do with the number of gene-gene or protein-protein interactions, that might underlie complexity in the way you mean. For example, from the source I linked:</p>\n<blockquote>\n<p>Using bioinformatics, the team estimated that 650,000 protein interactions occur in humans; this number is approximately three times more than that in the roundworm and 10 times more than that in the fruit fly. Moreover, it seems that a single protein can have dozens, if not hundreds, of different interactions.</p>\n</blockquote>\n<p>So when we say &quot;complexity&quot; what we might mean is number of gene-gene interactions, not the number of genes.</p>\n<p>A fun aside, plants <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203354/\" rel=\"nofollow noreferrer\">tend to have more transcription factors</a> (which basically turn genes off and on and lead to interactions). Higher plants also usually <a href=\"https://www.google.com/url?sa=t&amp;source=web&amp;rct=j&amp;opi=89978449&amp;url=https://pubmed.ncbi.nlm.nih.gov/26130755/&amp;ved=2ahUKEwidz5SYoseFAxULMDQIHdX_AXcQFnoECDYQAQ&amp;usg=AOvVaw3Fr7DxORwp3LrJEbFu1Gi8\" rel=\"nofollow noreferrer\">develop continuously throughout their lives and can dedifferentiate their cells fairly readily</a>. So if we're looking in this way, there might be an argument that plants are a lot more complex than humans, even while having similar numbers of genes!</p>\n<p>Here is for example a tabulation of the number of transcription factors in various eukaryotes from <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203354/\" rel=\"nofollow noreferrer\">this paper</a> (apologies for not taking the time to retranscribe this image). Over time we've described/annotated more TFs in the various species of course, but even with the disproportionate effort on humans, plants still have more. For example, at last count <a href=\"https://planttfdb.gao-lab.org/download.php\" rel=\"nofollow noreferrer\">soybean had almost 4000 TFs</a>, whereas humans have around <a href=\"https://www.cell.com/cell/pdf/S0092-8674(18)30106-5.pdf\" rel=\"nofollow noreferrer\">1600</a>.</p>\n<p><a href=\"https://i.sstatic.net/AQ8UE.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/AQ8UE.jpg\" alt=\"Tabulation of TF numbers in different families overlaid on an evolutionary tree showing higher TF numbers in various lineages\" /></a></p>\n<p>That's not to say that this is the <em>right</em> measure of complexity. What you mean by complexity will differ depending on what you are interested in!</p>\n","text":"I would suggest looking into the field of organismal complexity (https://www.nature.com/scitable/topicpage/the-complexity-of-gene-expression-protein-interaction-34575/).\n\n\n\n\nOne could turn the question on its head: why does a worm, which apparently has the raw materials to get as complex as a human, stay a worm?\n\n\n\n\nOne answer would be that the human developmental process is much longer and more elaborate than the worm's. We might for example have a more elaborate process of gene regulation throughout development (https://www.nature.com/scitable/topicpage/transcription-factors-and-transcriptional-control-in-eukaryotic-1046/) that lets us keep developing longer- so the question is not how many genes, but what combinations of the genes we have can be turned on or off together. The number of possible combinations is very large when you have 20K genes!\n\n\n\n\nMore answers might have to do with the number of gene-gene or protein-protein interactions, that might underlie complexity in the way you mean. For example, from the source I linked:\n\n\n\n\n\n\n\nUsing bioinformatics, the team estimated that 650,000 protein interactions occur in humans; this number is approximately three times more than that in the roundworm and 10 times more than that in the fruit fly. Moreover, it seems that a single protein can have dozens, if not hundreds, of different interactions.\n\n\n\n\n\n\n\nSo when we say \"complexity\" what we might mean is number of gene-gene interactions, not the number of genes.\n\n\n\n\nA fun aside, plants tend to have more transcription factors (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203354/) (which basically turn genes off and on and lead to interactions). Higher plants also usually develop continuously throughout their lives and can dedifferentiate their cells fairly readily (https://www.google.com/url?sa=t&source=web&rct=j&opi=89978449&url=https://pubmed.ncbi.nlm.nih.gov/26130755/&ved=2ahUKEwidz5SYoseFAxULMDQIHdX_AXcQFnoECDYQAQ&usg=AOvVaw3Fr7DxORwp3LrJEbFu1Gi8). So if we're looking in this way, there might be an argument that plants are a lot more complex than humans, even while having similar numbers of genes!\n\n\n\n\nHere is for example a tabulation of the number of transcription factors in various eukaryotes from this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203354/) (apologies for not taking the time to retranscribe this image). Over time we've described/annotated more TFs in the various species of course, but even with the disproportionate effort on humans, plants still have more. For example, at last count soybean had almost 4000 TFs (https://planttfdb.gao-lab.org/download.php), whereas humans have around 1600 (https://www.cell.com/cell/pdf/S0092-8674(18)30106-5.pdf).\n\n\n\n\n[image: Tabulation of TF numbers in different families overlaid on an evolutionary tree showing higher TF numbers in various lineages; source: https://i.sstatic.net/AQ8UE.jpg] (https://i.sstatic.net/AQ8UE.jpg)\n\n\n\n\nThat's not to say that this is the right measure of complexity. What you mean by complexity will differ depending on what you are interested in!"}],"domain":"biology","external_citations":["https://i.sstatic.net/AQ8UE.jpg","https://planttfdb.gao-lab.org/download.php","https://www.cell.com/cell/pdf/S0092-8674(18)30106-5.pdf","https://www.google.com/url?sa=t&source=web&rct=j&opi=89978449&url=https://pubmed.ncbi.nlm.nih.gov/26130755/&ved=2ahUKEwidz5SYoseFAxULMDQIHdX_AXcQFnoECDYQAQ&usg=AOvVaw3Fr7DxORwp3LrJEbFu1Gi8","https://www.nature.com/scitable/topicpage/eukaryotic-genome-complexity-437/","https://www.nature.com/scitable/topicpage/the-complexity-of-gene-expression-protein-interaction-34575/","https://www.nature.com/scitable/topicpage/transcription-factors-and-transcriptional-control-in-eukaryotic-1046/","https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203354/"],"ground_truth_type":"metadata_grounded","group_id":"fae91ce083d912c8f52857f9f06ef18581f07cb574fa0627f334e7fe61f0d1e3","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-7fd99159c72042f839d3a5c6","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:07.165481+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/b97a755f39b54a1e8a057fa5e484426784aa17a1971c6ef0ca759105de983078_0.json","raw_sha256":"4c9dcc077d306d60a8b8a237ad3f9b3144c0d5885fa62ef1bfdd55d2fbbdaf6a","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=6&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"tree","profile_url":"https://biology.stackexchange.com/users/80300/tree","user_type":"registered"},"created_at":"2024-04-15T18:52:38+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"0F687A08-3079-471B-A167-8132321766AB","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0F687A08-3079-471B-A167-8132321766AB/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-04-16T20:11:34+00:00","raw_file":"raw/codex_api_v1/b602368e34ed1079a83bbba1a32b92a27d14f606a32491790edbb641b7174400_1790824069729218500_0.json","raw_sha256":"344e5c131b2fccd9065fd8d099aa324193d0a48a71360ff64b27810a4ec54fba","revision_guid":"D457B163-01AB-435D-AEDF-40132FF1D395","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D457B163-01AB-435D-AEDF-40132FF1D395/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114501","source_record_sha256":"d72179ab11217835eb7a450e01f80f66b05e52b2489e834e44efdb00bd254ff3","source_url":"https://biology.stackexchange.com/questions/114501/no-of-genes-and-organismal-complexity","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"No. of genes and organismal complexity?\nWhy do humans contain trillions of cells arranged in many complex organs, and worms contain many less cells and less organs, but we and the worm have a similar number of genes? See for example Table 1 here (https://www.nature.com/scitable/topicpage/eukaryotic-genome-complexity-437/).\n\n\n\n\nI know that the number of genes does not correlate well with organismal complexity, and the size of the genome is unrelated to the metabolic, developmental, and behavioural complexity. But I am curious WHY?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114509,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>While David has a point that for specific genes you should look at in vivo data, significant amounts of work has been done to identify representative transcripts, often using direct experimental evidence.</p>\n<p>One such effort is <a href=\"https://www.ncbi.nlm.nih.gov/refseq/MANE/\" rel=\"nofollow noreferrer\">MANE-Select</a>. When in doubt, or specifically when doing high-throughput or computational work, I would choose the MANE-Select transcript.</p>\n<p>The idea behind it is to find a single transcript that is agreed upon by NCBI and ENSEMBL and to go through various steps of automated and manual curation to provide a &quot;ground truth&quot; expression product for a particular gene.</p>\n<p>In vivo data includes techniques such as 5' RACE and CAGE to identify transcript coordinates that broadly agree with transcription starts and stops, among other steps.</p>\n<p>Note: MANE-Select is only for human genes so far as I know.</p>\n","answer_id":114712,"answer_text":"While David has a point that for specific genes you should look at in vivo data, significant amounts of work has been done to identify representative transcripts, often using direct experimental evidence.\n\n\n\n\nOne such effort is MANE-Select (https://www.ncbi.nlm.nih.gov/refseq/MANE/). When in doubt, or specifically when doing high-throughput or computational work, I would choose the MANE-Select transcript.\n\n\n\n\nThe idea behind it is to find a single transcript that is agreed upon by NCBI and ENSEMBL and to go through various steps of automated and manual curation to provide a \"ground truth\" expression product for a particular gene.\n\n\n\n\nIn vivo data includes techniques such as 5' RACE and CAGE to identify transcript coordinates that broadly agree with transcription starts and stops, among other steps.\n\n\n\n\nNote: MANE-Select is only for human genes so far as I know.","answer_url":"https://biology.stackexchange.com/a/114712","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2024-05-16T22:00:12+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:27.977583+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1cbf95322a17dce0fd00a109179063ffe60bcd4bddc6e720f0ca398ee7aa9da8_0.json","raw_sha256":"a096c86028a279b01346143890b4827bd8ed05afc0a76bd7c8bcb840211dc20e","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/114983;114969;114966;114963;114939;114936;114918;114909;114904;114899;114888;114885;114881;114875;114874;114873;114872;114864;114857;114850;114846;114841;114834;114827;114821;114819;114813;114804;114791;114784;114768;114765;114762;114760;114758;114755;114745;114741;114739;114738;114732;114730;114726;114714;114706;114695;114691;114690;114686;114683;114677;114675;114666;114660;114656;114653;114642;114641;114632;114628;114620;114618;114613;114601;114599;114597;114581;114577;114573;114567;114558;114555;114553;114552;114547;114545;114543;114542;114541;114539;114529;114524;114516;114502;114501;114498;114495;114492;114481;114476;114474;114470;114453;114451;114449;114448;114446;114440;114438;114435/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114706,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-05-16T22:00:12+00:00","raw_file":"raw/codex_api_v1/282295cb58dc6e06535acb3b0271f00300dd2b6c85e78f47464472e253aa1cdd_1790824077120302400_0.json","raw_sha256":"93650624b92f65499fe4854f330ed8fd8aceb1ad0cb02a65e5016e49e4b22c69","revision_guid":"02EDA1A2-6307-448D-B781-32A924D8D537","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/02EDA1A2-6307-448D-B781-32A924D8D537/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"qwerty","author_url":"https://biology.stackexchange.com/users/80926/qwerty","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"qwerty","profile_url":"https://biology.stackexchange.com/users/80926/qwerty","user_type":"registered"},"created_at":"2024-05-16T14:16:47+00:00","raw_file":"raw/codex_api_v1/282295cb58dc6e06535acb3b0271f00300dd2b6c85e78f47464472e253aa1cdd_1790824077120302400_0.json","raw_sha256":"93650624b92f65499fe4854f330ed8fd8aceb1ad0cb02a65e5016e49e4b22c69","revision_guid":"74A4A768-594F-4416-B97A-E7B036205A02","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/74A4A768-594F-4416-B97A-E7B036205A02/view-source"}],"url":"https://biology.stackexchange.com/questions/114706/identification-of-most-active-gene-protein-isoform"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"114712","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-05-16T22:00:12+00:00","raw_file":"raw/codex_api_v1/282295cb58dc6e06535acb3b0271f00300dd2b6c85e78f47464472e253aa1cdd_1790824077120302400_0.json","raw_sha256":"93650624b92f65499fe4854f330ed8fd8aceb1ad0cb02a65e5016e49e4b22c69","revision_guid":"02EDA1A2-6307-448D-B781-32A924D8D537","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/02EDA1A2-6307-448D-B781-32A924D8D537/view-source"}],"url":"https://biology.stackexchange.com/a/114712"}],"contexts":[{"context_id":"question","html":"<p>I am investigating a gene, and on ensemble, it has multiple variants. How can i know which gene or protein isoform is most active?</p>\n","text":"I am investigating a gene, and on ensemble, it has multiple variants. How can i know which gene or protein isoform is most active?"},{"context_id":"114712","html":"<p>While David has a point that for specific genes you should look at in vivo data, significant amounts of work has been done to identify representative transcripts, often using direct experimental evidence.</p>\n<p>One such effort is <a href=\"https://www.ncbi.nlm.nih.gov/refseq/MANE/\" rel=\"nofollow noreferrer\">MANE-Select</a>. When in doubt, or specifically when doing high-throughput or computational work, I would choose the MANE-Select transcript.</p>\n<p>The idea behind it is to find a single transcript that is agreed upon by NCBI and ENSEMBL and to go through various steps of automated and manual curation to provide a &quot;ground truth&quot; expression product for a particular gene.</p>\n<p>In vivo data includes techniques such as 5' RACE and CAGE to identify transcript coordinates that broadly agree with transcription starts and stops, among other steps.</p>\n<p>Note: MANE-Select is only for human genes so far as I know.</p>\n","text":"While David has a point that for specific genes you should look at in vivo data, significant amounts of work has been done to identify representative transcripts, often using direct experimental evidence.\n\n\n\n\nOne such effort is MANE-Select (https://www.ncbi.nlm.nih.gov/refseq/MANE/). When in doubt, or specifically when doing high-throughput or computational work, I would choose the MANE-Select transcript.\n\n\n\n\nThe idea behind it is to find a single transcript that is agreed upon by NCBI and ENSEMBL and to go through various steps of automated and manual curation to provide a \"ground truth\" expression product for a particular gene.\n\n\n\n\nIn vivo data includes techniques such as 5' RACE and CAGE to identify transcript coordinates that broadly agree with transcription starts and stops, among other steps.\n\n\n\n\nNote: MANE-Select is only for human genes so far as I know."}],"domain":"biology","external_citations":["https://www.ncbi.nlm.nih.gov/refseq/MANE/"],"ground_truth_type":"metadata_grounded","group_id":"8cd5f0e8119524d8080fd3d1b448d5e6570a2dfb4255ff0c69a69280d6e14c17","hard_case_family":["no_accepted_answer"],"id":"RHM-d105432ba09b6f66273f2e82","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:07.165481+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/b97a755f39b54a1e8a057fa5e484426784aa17a1971c6ef0ca759105de983078_0.json","raw_sha256":"4c9dcc077d306d60a8b8a237ad3f9b3144c0d5885fa62ef1bfdd55d2fbbdaf6a","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=6&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"qwerty","profile_url":"https://biology.stackexchange.com/users/80926/qwerty","user_type":"registered"},"created_at":"2024-05-16T14:16:47+00:00","raw_file":"raw/codex_api_v1/282295cb58dc6e06535acb3b0271f00300dd2b6c85e78f47464472e253aa1cdd_1790824077120302400_0.json","raw_sha256":"93650624b92f65499fe4854f330ed8fd8aceb1ad0cb02a65e5016e49e4b22c69","revision_guid":"74A4A768-594F-4416-B97A-E7B036205A02","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/74A4A768-594F-4416-B97A-E7B036205A02/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114706","source_record_sha256":"4e0dc9d76806c72d5a214858a1f27e687ba04ef747db6daad9b1a83d00ee00d5","source_url":"https://biology.stackexchange.com/questions/114706/identification-of-most-active-gene-protein-isoform","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"identification of most Active gene/protein isoform\nI am investigating a gene, and on ensemble, it has multiple variants. How can i know which gene or protein isoform is most active?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114712,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":114749,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>This is almost certainly <a href=\"https://en.wikipedia.org/wiki/Poison_ivy\" rel=\"nofollow noreferrer\">poison ivy</a>. When you said the leaves had a greasy feel, alarm bells started ringing and I hit up Google, and the images I got for poison ivy bore a very close resemblance to what you have here. Quite frankly, I'm surprised you didn't get a rash from a an exposure 12 days ago...</p>\n","answer_id":114747,"answer_text":"This is almost certainly poison ivy (https://en.wikipedia.org/wiki/Poison_ivy). When you said the leaves had a greasy feel, alarm bells started ringing and I hit up Google, and the images I got for poison ivy bore a very close resemblance to what you have here. Quite frankly, I'm surprised you didn't get a rash from a an exposure 12 days ago...","answer_url":"https://biology.stackexchange.com/a/114747","author":"Sir Thinksalot","author_url":"https://biology.stackexchange.com/users/77161/sir-thinksalot","content_license":"CC BY-SA 4.0","created_at":"2024-05-22T15:50:55+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:27.977583+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1cbf95322a17dce0fd00a109179063ffe60bcd4bddc6e720f0ca398ee7aa9da8_0.json","raw_sha256":"a096c86028a279b01346143890b4827bd8ed05afc0a76bd7c8bcb840211dc20e","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/114983;114969;114966;114963;114939;114936;114918;114909;114904;114899;114888;114885;114881;114875;114874;114873;114872;114864;114857;114850;114846;114841;114834;114827;114821;114819;114813;114804;114791;114784;114768;114765;114762;114760;114758;114755;114745;114741;114739;114738;114732;114730;114726;114714;114706;114695;114691;114690;114686;114683;114677;114675;114666;114660;114656;114653;114642;114641;114632;114628;114620;114618;114613;114601;114599;114597;114581;114577;114573;114567;114558;114555;114553;114552;114547;114545;114543;114542;114541;114539;114529;114524;114516;114502;114501;114498;114495;114492;114481;114476;114474;114470;114453;114451;114449;114448;114446;114440;114438;114435/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114745,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Sir Thinksalot","profile_url":"https://biology.stackexchange.com/users/77161/sir-thinksalot","user_type":"registered"},"created_at":"2024-05-22T15:50:55+00:00","raw_file":"raw/codex_api_v1/41500cf35bca9ae31b7ea454bad8679af7e3276d71713db5d1815d84a971bb0e_1790824088925435600_0.json","raw_sha256":"a764902131a161e2a7978a1f607c4912689efa157d70c2752a5b31e3a042aacb","revision_guid":"42439CA3-66CD-428F-8EFD-9C7AB840A94A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/42439CA3-66CD-428F-8EFD-9C7AB840A94A/view-source"}],"score":-4},{"answer_html":"<p>This appears to be <em><a href=\"https://www.wildflower.org/plants/result.php?id_plant=arnu2\" rel=\"nofollow noreferrer\">Aralia nudicaulus</a></em>, wild sarsaparilla. It has a main stem that branches in three, with compound leaves with 3-5 (7) serrate leaflets. It occurs in your area.</p>\n<p><a href=\"https://i.sstatic.net/lGHk5xT9.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/lGHk5xT9.jpg\" alt=\"enter image description here\" /></a>\n<br/>From <a href=\"http://www.wildflowersofontario.ca\" rel=\"nofollow noreferrer\">Wildflowers of Ontario</a></p>\n","answer_id":114749,"answer_text":"This appears to be Aralia nudicaulus (https://www.wildflower.org/plants/result.php?id_plant=arnu2), wild sarsaparilla. It has a main stem that branches in three, with compound leaves with 3-5 (7) serrate leaflets. It occurs in your area.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/lGHk5xT9.jpg] (https://i.sstatic.net/lGHk5xT9.jpg)\n\nFrom Wildflowers of Ontario (http://www.wildflowersofontario.ca)","answer_url":"https://biology.stackexchange.com/a/114749","author":"Eonema","author_url":"https://biology.stackexchange.com/users/61325/eonema","content_license":"CC BY-SA 4.0","created_at":"2024-05-22T22:35:27+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:27.977583+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1cbf95322a17dce0fd00a109179063ffe60bcd4bddc6e720f0ca398ee7aa9da8_0.json","raw_sha256":"a096c86028a279b01346143890b4827bd8ed05afc0a76bd7c8bcb840211dc20e","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/114983;114969;114966;114963;114939;114936;114918;114909;114904;114899;114888;114885;114881;114875;114874;114873;114872;114864;114857;114850;114846;114841;114834;114827;114821;114819;114813;114804;114791;114784;114768;114765;114762;114760;114758;114755;114745;114741;114739;114738;114732;114730;114726;114714;114706;114695;114691;114690;114686;114683;114677;114675;114666;114660;114656;114653;114642;114641;114632;114628;114620;114618;114613;114601;114599;114597;114581;114577;114573;114567;114558;114555;114553;114552;114547;114545;114543;114542;114541;114539;114529;114524;114516;114502;114501;114498;114495;114492;114481;114476;114474;114470;114453;114451;114449;114448;114446;114440;114438;114435/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114745,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Eonema","profile_url":"https://biology.stackexchange.com/users/61325/eonema","user_type":"registered"},"created_at":"2024-05-22T22:35:27+00:00","raw_file":"raw/codex_api_v1/41500cf35bca9ae31b7ea454bad8679af7e3276d71713db5d1815d84a971bb0e_1790824088925435600_0.json","raw_sha256":"a764902131a161e2a7978a1f607c4912689efa157d70c2752a5b31e3a042aacb","revision_guid":"EE750266-12C0-4644-BB04-AEB1C61A8D5B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/EE750266-12C0-4644-BB04-AEB1C61A8D5B/view-source"}],"score":4}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"User1974","author_url":"https://biology.stackexchange.com/users/31741/user1974","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"User1974","profile_url":"https://biology.stackexchange.com/users/31741/user1974","user_type":"registered"},"created_at":"2024-05-22T14:37:57+00:00","raw_file":"raw/codex_api_v1/282295cb58dc6e06535acb3b0271f00300dd2b6c85e78f47464472e253aa1cdd_1790824077120302400_0.json","raw_sha256":"93650624b92f65499fe4854f330ed8fd8aceb1ad0cb02a65e5016e49e4b22c69","revision_guid":"E6ABAF31-DC37-45D3-A514-E0B53A6CFC7D","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E6ABAF31-DC37-45D3-A514-E0B53A6CFC7D/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"User1974","profile_url":"https://biology.stackexchange.com/users/31741/user1974","user_type":"registered"},"created_at":"2024-05-22T20:23:05+00:00","raw_file":"raw/codex_api_v1/282295cb58dc6e06535acb3b0271f00300dd2b6c85e78f47464472e253aa1cdd_1790824077120302400_0.json","raw_sha256":"93650624b92f65499fe4854f330ed8fd8aceb1ad0cb02a65e5016e49e4b22c69","revision_guid":"EC8868EB-7D69-4825-B9F3-23E383AA14D5","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/EC8868EB-7D69-4825-B9F3-23E383AA14D5/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"User1974","profile_url":"https://biology.stackexchange.com/users/31741/user1974","user_type":"registered"},"created_at":"2024-05-22T20:28:35+00:00","raw_file":"raw/codex_api_v1/282295cb58dc6e06535acb3b0271f00300dd2b6c85e78f47464472e253aa1cdd_1790824077120302400_0.json","raw_sha256":"93650624b92f65499fe4854f330ed8fd8aceb1ad0cb02a65e5016e49e4b22c69","revision_guid":"A41C900F-2C0C-4D1F-8F1F-912022B67C40","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A41C900F-2C0C-4D1F-8F1F-912022B67C40/view-source"}],"url":"https://biology.stackexchange.com/questions/114745/ontario-plant-with-3-5-leaflets-per-compound-leaf"},{"author":"Sir Thinksalot","author_url":"https://biology.stackexchange.com/users/77161/sir-thinksalot","content_license":"CC BY-SA 4.0","context_id":"114747","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Sir Thinksalot","profile_url":"https://biology.stackexchange.com/users/77161/sir-thinksalot","user_type":"registered"},"created_at":"2024-05-22T15:50:55+00:00","raw_file":"raw/codex_api_v1/41500cf35bca9ae31b7ea454bad8679af7e3276d71713db5d1815d84a971bb0e_1790824088925435600_0.json","raw_sha256":"a764902131a161e2a7978a1f607c4912689efa157d70c2752a5b31e3a042aacb","revision_guid":"42439CA3-66CD-428F-8EFD-9C7AB840A94A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/42439CA3-66CD-428F-8EFD-9C7AB840A94A/view-source"}],"url":"https://biology.stackexchange.com/a/114747"},{"author":"Eonema","author_url":"https://biology.stackexchange.com/users/61325/eonema","content_license":"CC BY-SA 4.0","context_id":"114749","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Eonema","profile_url":"https://biology.stackexchange.com/users/61325/eonema","user_type":"registered"},"created_at":"2024-05-22T22:35:27+00:00","raw_file":"raw/codex_api_v1/41500cf35bca9ae31b7ea454bad8679af7e3276d71713db5d1815d84a971bb0e_1790824088925435600_0.json","raw_sha256":"a764902131a161e2a7978a1f607c4912689efa157d70c2752a5b31e3a042aacb","revision_guid":"EE750266-12C0-4644-BB04-AEB1C61A8D5B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/EE750266-12C0-4644-BB04-AEB1C61A8D5B/view-source"}],"url":"https://biology.stackexchange.com/a/114749"}],"contexts":[{"context_id":"question","html":"<p>This plant has 3-5 leaflets per compound leaf. It caught my eye because, at first, I thought it resembled poison ivy. But I don't think it's poison ivy.</p>\n<p>What species is it?</p>\n<ul>\n<li>Date: May 11, 2024</li>\n<li>Location: Norwood, Ontario, Canada; full shade along forest trail edge</li>\n<li>Height: 1 foot</li>\n<li>Description: New leaves looked somewhat greasy, dark green/dark red, compound, serrated, opposite</li>\n</ul>\n<p>Unfortunately, I can't go back to get clearer pictures.</p>\n<p><a href=\"https://i.sstatic.net/O9Nqo2r1.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/O9Nqo2r1.jpg\" alt=\"enter image description here\" /></a></p>\n<p><a href=\"https://i.sstatic.net/nSYjtOTP.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/nSYjtOTP.jpg\" alt=\"enter image description here\" /></a></p>\n","text":"This plant has 3-5 leaflets per compound leaf. It caught my eye because, at first, I thought it resembled poison ivy. But I don't think it's poison ivy.\n\n\n\n\nWhat species is it?\n\n\n\n\n\nDate: May 11, 2024\n\n\n\n\nLocation: Norwood, Ontario, Canada; full shade along forest trail edge\n\n\n\n\nHeight: 1 foot\n\n\n\n\nDescription: New leaves looked somewhat greasy, dark green/dark red, compound, serrated, opposite\n\n\n\n\n\nUnfortunately, I can't go back to get clearer pictures.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/O9Nqo2r1.jpg] (https://i.sstatic.net/O9Nqo2r1.jpg)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/nSYjtOTP.jpg] (https://i.sstatic.net/nSYjtOTP.jpg)"},{"context_id":"114747","html":"<p>This is almost certainly <a href=\"https://en.wikipedia.org/wiki/Poison_ivy\" rel=\"nofollow noreferrer\">poison ivy</a>. When you said the leaves had a greasy feel, alarm bells started ringing and I hit up Google, and the images I got for poison ivy bore a very close resemblance to what you have here. Quite frankly, I'm surprised you didn't get a rash from a an exposure 12 days ago...</p>\n","text":"This is almost certainly poison ivy (https://en.wikipedia.org/wiki/Poison_ivy). When you said the leaves had a greasy feel, alarm bells started ringing and I hit up Google, and the images I got for poison ivy bore a very close resemblance to what you have here. Quite frankly, I'm surprised you didn't get a rash from a an exposure 12 days ago..."},{"context_id":"114749","html":"<p>This appears to be <em><a href=\"https://www.wildflower.org/plants/result.php?id_plant=arnu2\" rel=\"nofollow noreferrer\">Aralia nudicaulus</a></em>, wild sarsaparilla. It has a main stem that branches in three, with compound leaves with 3-5 (7) serrate leaflets. It occurs in your area.</p>\n<p><a href=\"https://i.sstatic.net/lGHk5xT9.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/lGHk5xT9.jpg\" alt=\"enter image description here\" /></a>\n<br/>From <a href=\"http://www.wildflowersofontario.ca\" rel=\"nofollow noreferrer\">Wildflowers of Ontario</a></p>\n","text":"This appears to be Aralia nudicaulus (https://www.wildflower.org/plants/result.php?id_plant=arnu2), wild sarsaparilla. It has a main stem that branches in three, with compound leaves with 3-5 (7) serrate leaflets. It occurs in your area.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/lGHk5xT9.jpg] (https://i.sstatic.net/lGHk5xT9.jpg)\n\nFrom Wildflowers of Ontario (http://www.wildflowersofontario.ca)"}],"domain":"biology","external_citations":["http://www.wildflowersofontario.ca","https://en.wikipedia.org/wiki/Poison_ivy","https://i.sstatic.net/O9Nqo2r1.jpg","https://i.sstatic.net/lGHk5xT9.jpg","https://i.sstatic.net/nSYjtOTP.jpg","https://www.wildflower.org/plants/result.php?id_plant=arnu2"],"ground_truth_type":"metadata_grounded","group_id":"1cf1e654d146be2c853b31f2d6516b497f9f0046adffdf573606bbead4242961","hard_case_family":["multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-712c22c78144181580936628","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:07.165481+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/b97a755f39b54a1e8a057fa5e484426784aa17a1971c6ef0ca759105de983078_0.json","raw_sha256":"4c9dcc077d306d60a8b8a237ad3f9b3144c0d5885fa62ef1bfdd55d2fbbdaf6a","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=6&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"User1974","profile_url":"https://biology.stackexchange.com/users/31741/user1974","user_type":"registered"},"created_at":"2024-05-22T14:37:57+00:00","raw_file":"raw/codex_api_v1/282295cb58dc6e06535acb3b0271f00300dd2b6c85e78f47464472e253aa1cdd_1790824077120302400_0.json","raw_sha256":"93650624b92f65499fe4854f330ed8fd8aceb1ad0cb02a65e5016e49e4b22c69","revision_guid":"E6ABAF31-DC37-45D3-A514-E0B53A6CFC7D","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E6ABAF31-DC37-45D3-A514-E0B53A6CFC7D/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"User1974","profile_url":"https://biology.stackexchange.com/users/31741/user1974","user_type":"registered"},"created_at":"2024-05-22T20:23:05+00:00","raw_file":"raw/codex_api_v1/282295cb58dc6e06535acb3b0271f00300dd2b6c85e78f47464472e253aa1cdd_1790824077120302400_0.json","raw_sha256":"93650624b92f65499fe4854f330ed8fd8aceb1ad0cb02a65e5016e49e4b22c69","revision_guid":"EC8868EB-7D69-4825-B9F3-23E383AA14D5","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/EC8868EB-7D69-4825-B9F3-23E383AA14D5/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"User1974","profile_url":"https://biology.stackexchange.com/users/31741/user1974","user_type":"registered"},"created_at":"2024-05-22T20:28:35+00:00","raw_file":"raw/codex_api_v1/282295cb58dc6e06535acb3b0271f00300dd2b6c85e78f47464472e253aa1cdd_1790824077120302400_0.json","raw_sha256":"93650624b92f65499fe4854f330ed8fd8aceb1ad0cb02a65e5016e49e4b22c69","revision_guid":"A41C900F-2C0C-4D1F-8F1F-912022B67C40","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A41C900F-2C0C-4D1F-8F1F-912022B67C40/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114745","source_record_sha256":"1f5232c00022fb3c898f6a5f6b9229702e5541697c706d7e0d9a4cb2ece7482a","source_url":"https://biology.stackexchange.com/questions/114745/ontario-plant-with-3-5-leaflets-per-compound-leaf","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Ontario plant with 3-5 leaflets per compound leaf\nThis plant has 3-5 leaflets per compound leaf. It caught my eye because, at first, I thought it resembled poison ivy. But I don't think it's poison ivy.\n\n\n\n\nWhat species is it?\n\n\n\n\n\nDate: May 11, 2024\n\n\n\n\nLocation: Norwood, Ontario, Canada; full shade along forest trail edge\n\n\n\n\nHeight: 1 foot\n\n\n\n\nDescription: New leaves looked somewhat greasy, dark green/dark red, compound, serrated, opposite\n\n\n\n\n\nUnfortunately, I can't go back to get clearer pictures.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/O9Nqo2r1.jpg] (https://i.sstatic.net/O9Nqo2r1.jpg)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/nSYjtOTP.jpg] (https://i.sstatic.net/nSYjtOTP.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114747,"score":-4},{"answer_id":114749,"score":4}],"split":"test"}
{"accepted_status":{"accepted_answer_id":114764,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Your belief is wrong; axons form synapses along their lengths. I'm most familiar with these being referred to as <em>en passant</em> boutons. See for example this image and description from: <a href=\"https://synapseweb.clm.utexas.edu/axons\" rel=\"noreferrer\">https://synapseweb.clm.utexas.edu/axons</a></p>\n<p><a href=\"https://i.sstatic.net/ZL4hogxm.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/ZL4hogxm.png\" alt=\"enter image description here\" /></a></p>\n<p>To clarify, though, this is something that would happen in the terminal field of an axon; in other places an axon is entirely an axon of passage making no synapses at all. The specific anatomy is going to depend on the exact type of neuron and it's origin and target(s).</p>\n","answer_id":114764,"answer_text":"Your belief is wrong; axons form synapses along their lengths. I'm most familiar with these being referred to as en passant boutons. See for example this image and description from: https://synapseweb.clm.utexas.edu/axons (https://synapseweb.clm.utexas.edu/axons)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/ZL4hogxm.png] (https://i.sstatic.net/ZL4hogxm.png)\n\n\n\n\nTo clarify, though, this is something that would happen in the terminal field of an axon; in other places an axon is entirely an axon of passage making no synapses at all. The specific anatomy is going to depend on the exact type of neuron and it's origin and target(s).","answer_url":"https://biology.stackexchange.com/a/114764","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2024-05-27T12:18:03+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:27.977583+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1cbf95322a17dce0fd00a109179063ffe60bcd4bddc6e720f0ca398ee7aa9da8_0.json","raw_sha256":"a096c86028a279b01346143890b4827bd8ed05afc0a76bd7c8bcb840211dc20e","source_api":"Stack Exchange API 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Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2024-05-27T12:18:03+00:00","raw_file":"raw/codex_api_v1/41500cf35bca9ae31b7ea454bad8679af7e3276d71713db5d1815d84a971bb0e_1790824088925435600_0.json","raw_sha256":"a764902131a161e2a7978a1f607c4912689efa157d70c2752a5b31e3a042aacb","revision_guid":"4ECB79D3-F71B-4F58-B247-1FAEFEE7780F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4ECB79D3-F71B-4F58-B247-1FAEFEE7780F/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2024-05-27T12:23:32+00:00","raw_file":"raw/codex_api_v1/41500cf35bca9ae31b7ea454bad8679af7e3276d71713db5d1815d84a971bb0e_1790824088925435600_0.json","raw_sha256":"a764902131a161e2a7978a1f607c4912689efa157d70c2752a5b31e3a042aacb","revision_guid":"78CCBB67-8F13-4D1A-8302-F3BD7DBF0D29","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/78CCBB67-8F13-4D1A-8302-F3BD7DBF0D29/view-source"}],"url":"https://biology.stackexchange.com/a/114764"}],"contexts":[{"context_id":"question","html":"<p>An image from Terrence Sejnowski's lab is around since at least 2015 when it appeared in an <a href=\"https://www.biorxiv.org/content/10.1101/016329v1.full.pdf\" rel=\"nofollow noreferrer\">article about hippocampal spine head sizes</a> and only recently (May 2024) in an <a href=\"https://direct.mit.edu/neco/article/36/5/781/120323/Synaptic-Information-Storage-Capacity-Measured\" rel=\"nofollow noreferrer\">article about synaptic information storage capacity</a>:</p>\n<p><a href=\"https://i.sstatic.net/wiobAx2Y.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/wiobAx2Y.png\" alt=\"neuron image from Sejnowski lab\" /></a></p>\n<p><sup>Visualization of a pair of spines (an SDSA pair) (with gray necks) from\nthe same dendrite (yellow) and the postsynaptic density (PSD) associated area\n(red, indicated by white arrows) formed by the same axon (black stippling) with\npresynaptic vesicles (white spheres)</sup></p>\n<p>What I wonder about in this image is the appearance of the axon. It is neither a regular tube with a somehow fixed diameter nor an obvious terminal. It has several junctions/synapses along its length, while I believed an axon forms synapses only at its ends. Can someone please clarify? Which part of an axon do I see, and how realistic is it supposed to be?</p>\n","text":"An image from Terrence Sejnowski's lab is around since at least 2015 when it appeared in an article about hippocampal spine head sizes (https://www.biorxiv.org/content/10.1101/016329v1.full.pdf) and only recently (May 2024) in an article about synaptic information storage capacity (https://direct.mit.edu/neco/article/36/5/781/120323/Synaptic-Information-Storage-Capacity-Measured):\n\n\n\n\n[image: neuron image from Sejnowski lab; source: https://i.sstatic.net/wiobAx2Y.png] (https://i.sstatic.net/wiobAx2Y.png)\n\n\n\n\nVisualization of a pair of spines (an SDSA pair) (with gray necks) from\nthe same dendrite (yellow) and the postsynaptic density (PSD) associated area\n(red, indicated by white arrows) formed by the same axon (black stippling) with\npresynaptic vesicles (white spheres)\n\n\n\n\nWhat I wonder about in this image is the appearance of the axon. It is neither a regular tube with a somehow fixed diameter nor an obvious terminal. It has several junctions/synapses along its length, while I believed an axon forms synapses only at its ends. Can someone please clarify? Which part of an axon do I see, and how realistic is it supposed to be?"},{"context_id":"114764","html":"<p>Your belief is wrong; axons form synapses along their lengths. I'm most familiar with these being referred to as <em>en passant</em> boutons. See for example this image and description from: <a href=\"https://synapseweb.clm.utexas.edu/axons\" rel=\"noreferrer\">https://synapseweb.clm.utexas.edu/axons</a></p>\n<p><a href=\"https://i.sstatic.net/ZL4hogxm.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/ZL4hogxm.png\" alt=\"enter image description here\" /></a></p>\n<p>To clarify, though, this is something that would happen in the terminal field of an axon; in other places an axon is entirely an axon of passage making no synapses at all. The specific anatomy is going to depend on the exact type of neuron and it's origin and target(s).</p>\n","text":"Your belief is wrong; axons form synapses along their lengths. I'm most familiar with these being referred to as en passant boutons. See for example this image and description from: https://synapseweb.clm.utexas.edu/axons (https://synapseweb.clm.utexas.edu/axons)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/ZL4hogxm.png] (https://i.sstatic.net/ZL4hogxm.png)\n\n\n\n\nTo clarify, though, this is something that would happen in the terminal field of an axon; in other places an axon is entirely an axon of passage making no synapses at all. The specific anatomy is going to depend on the exact type of neuron and it's origin and target(s)."}],"domain":"biology","external_citations":["https://direct.mit.edu/neco/article/36/5/781/120323/Synaptic-Information-Storage-Capacity-Measured","https://i.sstatic.net/ZL4hogxm.png","https://i.sstatic.net/wiobAx2Y.png","https://synapseweb.clm.utexas.edu/axons","https://www.biorxiv.org/content/10.1101/016329v1.full.pdf"],"ground_truth_type":"metadata_grounded","group_id":"980f8a59d635030741294af1ba7dc9052a4c8e394963d4c29dd3f8f2338f9e7a","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-2d363a78f2352665d98496ed","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:07.165481+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/b97a755f39b54a1e8a057fa5e484426784aa17a1971c6ef0ca759105de983078_0.json","raw_sha256":"4c9dcc077d306d60a8b8a237ad3f9b3144c0d5885fa62ef1bfdd55d2fbbdaf6a","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=6&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; 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no LLM truth labels"},"query":"Enigmatic picture of an axon\nAn image from Terrence Sejnowski's lab is around since at least 2015 when it appeared in an article about hippocampal spine head sizes (https://www.biorxiv.org/content/10.1101/016329v1.full.pdf) and only recently (May 2024) in an article about synaptic information storage capacity (https://direct.mit.edu/neco/article/36/5/781/120323/Synaptic-Information-Storage-Capacity-Measured):\n\n\n\n\n[image: neuron image from Sejnowski lab; source: https://i.sstatic.net/wiobAx2Y.png] (https://i.sstatic.net/wiobAx2Y.png)\n\n\n\n\nVisualization of a pair of spines (an SDSA pair) (with gray necks) from\nthe same dendrite (yellow) and the postsynaptic density (PSD) associated area\n(red, indicated by white arrows) formed by the same axon (black stippling) with\npresynaptic vesicles (white spheres)\n\n\n\n\nWhat I wonder about in this image is the appearance of the axon. It is neither a regular tube with a somehow fixed diameter nor an obvious terminal. It has several junctions/synapses along its length, while I believed an axon forms synapses only at its ends. Can someone please clarify? Which part of an axon do I see, and how realistic is it supposed to be?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114764,"score":7}],"split":"test"}
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They occasionally feed on pollen as well.\n\n\n\n\nhttps://link.springer.com/chapter/10.1007/978-3-030-29654-4_14 (https://link.springer.com/chapter/10.1007/978-3-030-29654-4_14)","answer_url":"https://biology.stackexchange.com/a/114814","author":"MadaboutMonarchs","author_url":"https://biology.stackexchange.com/users/80327/madaboutmonarchs","content_license":"CC BY-SA 4.0","created_at":"2024-06-05T04:27:04+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:27.977583+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/1cbf95322a17dce0fd00a109179063ffe60bcd4bddc6e720f0ca398ee7aa9da8_0.json","raw_sha256":"a096c86028a279b01346143890b4827bd8ed05afc0a76bd7c8bcb840211dc20e","source_api":"Stack Exchange API 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BY-SA 4.0","contributor":{"display_name":"MadaboutMonarchs","profile_url":"https://biology.stackexchange.com/users/80327/madaboutmonarchs","user_type":"registered"},"created_at":"2024-06-05T14:14:01+00:00","raw_file":"raw/codex_api_v1/b71692d4db54b1fd919e08bbd0e4d956635bb827b0cfa306c28bd8ef9b9590f2_1790824086740368100_0.json","raw_sha256":"fa87ea0a08a62d73a8b2c94b9665153275b3cd424a985b194879915043e1dde4","revision_guid":"E1B94205-6FFA-4AAD-82BB-61E59D1286CC","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E1B94205-6FFA-4AAD-82BB-61E59D1286CC/view-source"}],"url":"https://biology.stackexchange.com/a/114814"}],"contexts":[{"context_id":"question","html":"<p>There are many species of wasps, some of them are consuming other insects and meat. But do those wasps that eat insects also eat nectar from flowers? Are there known species of wasps that are solely carnivores?</p>\n<p><a href=\"https://www.whatsthatbug.com/what-do-wasps-eat/\" rel=\"nofollow noreferrer\">An article about what wasps eat</a> says that</p>\n<blockquote>\n<p>most adult wasps feed primarily on sugary substances like nectar.</p>\n</blockquote>\n<p>However I don't know if they refer to all known species of wasps and if that means there some wasps that do not eat nectar.</p>\n","text":"There are many species of wasps, some of them are consuming other insects and meat. But do those wasps that eat insects also eat nectar from flowers? Are there known species of wasps that are solely carnivores?\n\n\n\n\nAn article about what wasps eat (https://www.whatsthatbug.com/what-do-wasps-eat/) says that\n\n\n\n\n\n\n\nmost adult wasps feed primarily on sugary substances like nectar.\n\n\n\n\n\n\n\nHowever I don't know if they refer to all known species of wasps and if that means there some wasps that do not eat nectar."},{"context_id":"114814","html":"<p>Vespid wasps that consume other insects, etc. do so during their larval stage, but feed almost exclusively on sugars as adults. Those sugars primarily come from flower nectar, but they can also come from things like aphid honeydew. They occasionally feed on pollen as well.</p>\n<p><a href=\"https://link.springer.com/chapter/10.1007/978-3-030-29654-4_14\" rel=\"nofollow noreferrer\">https://link.springer.com/chapter/10.1007/978-3-030-29654-4_14</a></p>\n","text":"Vespid wasps that consume other insects, etc. do so during their larval stage, but feed almost exclusively on sugars as adults. Those sugars primarily come from flower nectar, but they can also come from things like aphid honeydew. They occasionally feed on pollen as well.\n\n\n\n\nhttps://link.springer.com/chapter/10.1007/978-3-030-29654-4_14 (https://link.springer.com/chapter/10.1007/978-3-030-29654-4_14)"}],"domain":"biology","external_citations":["https://link.springer.com/chapter/10.1007/978-3-030-29654-4_14","https://www.whatsthatbug.com/what-do-wasps-eat/"],"ground_truth_type":"metadata_grounded","group_id":"0359573b56889b7a84b3cfe93785a992b43fca8b03e574bb79f7f677423f6cd6","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-008d2d39eb9664093ffbe678","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:07.165481+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/b97a755f39b54a1e8a057fa5e484426784aa17a1971c6ef0ca759105de983078_0.json","raw_sha256":"4c9dcc077d306d60a8b8a237ad3f9b3144c0d5885fa62ef1bfdd55d2fbbdaf6a","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=6&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user81138","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-06-04T21:47:14+00:00","raw_file":"raw/codex_api_v1/b71692d4db54b1fd919e08bbd0e4d956635bb827b0cfa306c28bd8ef9b9590f2_1790824086740368100_0.json","raw_sha256":"fa87ea0a08a62d73a8b2c94b9665153275b3cd424a985b194879915043e1dde4","revision_guid":"08E2732D-98C9-4975-BF3A-FC54D950D613","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/08E2732D-98C9-4975-BF3A-FC54D950D613/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user81138","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-06-04T22:22:03+00:00","raw_file":"raw/codex_api_v1/b71692d4db54b1fd919e08bbd0e4d956635bb827b0cfa306c28bd8ef9b9590f2_1790824086740368100_0.json","raw_sha256":"fa87ea0a08a62d73a8b2c94b9665153275b3cd424a985b194879915043e1dde4","revision_guid":"DE2A0DA9-C359-433F-BB6B-70450777D1FC","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DE2A0DA9-C359-433F-BB6B-70450777D1FC/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user81138","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-06-05T15:40:53+00:00","raw_file":"raw/codex_api_v1/b71692d4db54b1fd919e08bbd0e4d956635bb827b0cfa306c28bd8ef9b9590f2_1790824086740368100_0.json","raw_sha256":"fa87ea0a08a62d73a8b2c94b9665153275b3cd424a985b194879915043e1dde4","revision_guid":"D3F2ABCE-9BFE-4526-80BB-7455E170CE4B","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D3F2ABCE-9BFE-4526-80BB-7455E170CE4B/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114813","source_record_sha256":"c0cedd659e447e425626ef001e2c2cfbe9bcec81720d581604af9e283b1cefb7","source_url":"https://biology.stackexchange.com/questions/114813/do-all-species-of-wasps-eat-nectar","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Do all species of wasps eat nectar?\nThere are many species of wasps, some of them are consuming other insects and meat. But do those wasps that eat insects also eat nectar from flowers? Are there known species of wasps that are solely carnivores?\n\n\n\n\nAn article about what wasps eat (https://www.whatsthatbug.com/what-do-wasps-eat/) says that\n\n\n\n\n\n\n\nmost adult wasps feed primarily on sugary substances like nectar.\n\n\n\n\n\n\n\nHowever I don't know if they refer to all known species of wasps and if that means there some wasps that do not eat nectar.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114814,"score":-1}],"split":"test"}
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And radioactive decay — a zeroth order process — is surely random.","answer_url":"https://biology.stackexchange.com/a/114893","author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","created_at":"2024-06-20T18:41:29+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:29.530612+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/3ec390b88d6fcaad2351183fd6d84ec73799b065a6f093dbbc0eea59e94500ce_0.json","raw_sha256":"a2f08981a2307fb8f456a33e92a38855de4bf9e165d024d5b20a23d9f8d656e1","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/114983;114969;114966;114963;114939;114936;114918;114909;114904;114899;114888;114885;114881;114875;114874;114873;114872;114864;114857;114850;114846;114841;114834;114827;114821;114819;114813;114804;114791;114784;114768;114765;114762;114760;114758;114755;114745;114741;114739;114738;114732;114730;114726;114714;114706;114695;114691;114690;114686;114683;114677;114675;114666;114660;114656;114653;114642;114641;114632;114628;114620;114618;114613;114601;114599;114597;114581;114577;114573;114567;114558;114555;114553;114552;114547;114545;114543;114542;114541;114539;114529;114524;114516;114502;114501;114498;114495;114492;114481;114476;114474;114470;114453;114451;114449;114448;114446;114440;114438;114435/answers?filter=withbody&order=asc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; 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If I were human or a computer, I would use a random generator (coin flips, dice, pretty sophisticated algorithms in the case of a computer) to perform the random assortment.</p>\n<p>How does this work during meiosis? What random generator mechanics are being used? It is not sufficient to say the assortment is random. Randomness needs to be accomplished by a mechanism.</p>\n","text":"How does the random assortment of chromosomes during meiosis occur?\n\n\n\n\nI am a mathematician, not a biologist, and I am surprised that it is difficult to find an answer to this question online (AI chatbots are also clueless). If I were human or a computer, I would use a random generator (coin flips, dice, pretty sophisticated algorithms in the case of a computer) to perform the random assortment.\n\n\n\n\nHow does this work during meiosis? What random generator mechanics are being used? It is not sufficient to say the assortment is random. Randomness needs to be accomplished by a mechanism."},{"context_id":"114893","html":"<p>God does play dice! And I am not aware that he needs to invoke his powers to ensure that there is a one-in-six chance of throwing a six.</p>\n<p>So I don’t accept the unsubstantiated assertion in the question. Is there a mechanism to determine which atom of radioactive carbon-14 in a population is the one that decays? And radioactive decay — a zeroth order process — is surely random.</p>\n","text":"God does play dice! And I am not aware that he needs to invoke his powers to ensure that there is a one-in-six chance of throwing a six.\n\n\n\n\nSo I don’t accept the unsubstantiated assertion in the question. Is there a mechanism to determine which atom of radioactive carbon-14 in a population is the one that decays? And radioactive decay — a zeroth order process — is surely random."}],"domain":"biology","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"2e4a9e23f0e91067ad98505bfa8a502a9ab1791bfefff868aef09c59fe999d41","hard_case_family":["no_accepted_answer"],"id":"RHM-8f8a8532fb9866c3d17e7b54","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:07.165481+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/b97a755f39b54a1e8a057fa5e484426784aa17a1971c6ef0ca759105de983078_0.json","raw_sha256":"4c9dcc077d306d60a8b8a237ad3f9b3144c0d5885fa62ef1bfdd55d2fbbdaf6a","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=6&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lawrence Fields","profile_url":"https://biology.stackexchange.com/users/81788/lawrence-fields","user_type":"registered"},"created_at":"2024-06-18T19:54:26+00:00","raw_file":"raw/codex_api_v1/b71692d4db54b1fd919e08bbd0e4d956635bb827b0cfa306c28bd8ef9b9590f2_1790824086740368100_0.json","raw_sha256":"fa87ea0a08a62d73a8b2c94b9665153275b3cd424a985b194879915043e1dde4","revision_guid":"3488073E-08D2-4AB8-88FE-EA7073277E30","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3488073E-08D2-4AB8-88FE-EA7073277E30/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-06-18T22:46:31+00:00","raw_file":"raw/codex_api_v1/b71692d4db54b1fd919e08bbd0e4d956635bb827b0cfa306c28bd8ef9b9590f2_1790824086740368100_0.json","raw_sha256":"fa87ea0a08a62d73a8b2c94b9665153275b3cd424a985b194879915043e1dde4","revision_guid":"EAD0DADD-A0BC-465E-845A-26C2E7E1F295","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/EAD0DADD-A0BC-465E-845A-26C2E7E1F295/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lawrence Fields","profile_url":"https://biology.stackexchange.com/users/81788/lawrence-fields","user_type":"registered"},"created_at":"2024-06-20T03:32:48+00:00","raw_file":"raw/codex_api_v1/b71692d4db54b1fd919e08bbd0e4d956635bb827b0cfa306c28bd8ef9b9590f2_1790824086740368100_0.json","raw_sha256":"fa87ea0a08a62d73a8b2c94b9665153275b3cd424a985b194879915043e1dde4","revision_guid":"EF129D8B-2F94-458A-B6C1-0215444F04F3","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/EF129D8B-2F94-458A-B6C1-0215444F04F3/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2024-06-20T18:23:16+00:00","raw_file":"raw/codex_api_v1/b71692d4db54b1fd919e08bbd0e4d956635bb827b0cfa306c28bd8ef9b9590f2_1790824086740368100_0.json","raw_sha256":"fa87ea0a08a62d73a8b2c94b9665153275b3cd424a985b194879915043e1dde4","revision_guid":"1325E0EB-3884-41DA-806B-58055ACE2C21","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/1325E0EB-3884-41DA-806B-58055ACE2C21/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"114885","source_record_sha256":"31e4b9cb9c9d00d906b84b9c2ad9a89cdc3e3ae06b2da3d8d3647de4cbd7fc00","source_url":"https://biology.stackexchange.com/questions/114885/mechanism-of-random-assortment-of-chromosomes","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Mechanism of random assortment of chromosomes\nHow does the random assortment of chromosomes during meiosis occur?\n\n\n\n\nI am a mathematician, not a biologist, and I am surprised that it is difficult to find an answer to this question online (AI chatbots are also clueless). If I were human or a computer, I would use a random generator (coin flips, dice, pretty sophisticated algorithms in the case of a computer) to perform the random assortment.\n\n\n\n\nHow does this work during meiosis? What random generator mechanics are being used? It is not sufficient to say the assortment is random. Randomness needs to be accomplished by a mechanism.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114893,"score":-1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I would suggest looking <a href=\"https://opig.stats.ox.ac.uk/webapps/plabdab\" rel=\"nofollow noreferrer\">here</a> at the PLAbDAb database, this appears to be an up-to-date antibody database including sequences.</p>\n<p>I ran a quick query for &quot;GPCR&quot; and <a href=\"https://opig.stats.ox.ac.uk/webapps/plabdab/results/keyword/20240801_0043943/\" rel=\"nofollow noreferrer\">got a number of results including protein sequences</a>.</p>\n","answer_id":115083,"answer_text":"I would suggest looking here (https://opig.stats.ox.ac.uk/webapps/plabdab) at the PLAbDAb database, this appears to be an up-to-date antibody database including sequences.\n\n\n\n\nI ran a quick query for \"GPCR\" and got a number of results including protein sequences (https://opig.stats.ox.ac.uk/webapps/plabdab/results/keyword/20240801_0043943/).","answer_url":"https://biology.stackexchange.com/a/115083","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2024-08-01T17:43:11+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:25.304620+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/7fe0b66593eb4c0f175024453138b8bd50811f1580a079ffb990af38e09cd1cf_0.json","raw_sha256":"b0a655f3b4c9626cf981180b3ac018a4a26330c5ab9b925b3df78bedd8169a84","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/115493;115490;115488;115483;115479;115477;115456;115453;115452;115447;115445;115444;115436;115431;115427;115413;115404;115403;115396;115391;115389;115388;115386;115383;115382;115379;115367;115365;115355;115340;115334;115328;115321;115314;115309;115304;115296;115295;115292;115283;115272;115270;115269;115265;115264;115260;115255;115252;115243;115235;115233;115225;115218;115215;115214;115213;115207;115204;115179;115177;115170;115167;115165;115164;115154;115149;115137;115131;115129;115115;115107;115099;115095;115094;115093;115085;115082;115081;115077;115076;115075;115074;115073;115072;115063;115044;115039;115035;115030;115025;115022;115019;115016;115012;115003;115002;114997;114993;114991;114987/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":115063,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-08-01T17:43:11+00:00","raw_file":"raw/codex_api_v1/d27b3e16c09e1430a099a72b8b6dd2aeca3c9f4116d2c57936f72acccbad600e_1790824094070868300_0.json","raw_sha256":"75ae5a3acd2d5ed1aadac056a0d6e41f6b40d63445afc68b8af4b71a0282b5d9","revision_guid":"123A93B6-18E1-480F-A55D-8D6CCEB494EB","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/123A93B6-18E1-480F-A55D-8D6CCEB494EB/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"user141154","author_url":"https://biology.stackexchange.com/users/84543/user141154","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user141154","profile_url":"https://biology.stackexchange.com/users/84543/user141154","user_type":"registered"},"created_at":"2024-07-28T13:13:20+00:00","raw_file":"raw/codex_api_v1/d27b3e16c09e1430a099a72b8b6dd2aeca3c9f4116d2c57936f72acccbad600e_1790824094070868300_0.json","raw_sha256":"75ae5a3acd2d5ed1aadac056a0d6e41f6b40d63445afc68b8af4b71a0282b5d9","revision_guid":"FE1DC793-961F-4BE6-A78B-560F1D56A39F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FE1DC793-961F-4BE6-A78B-560F1D56A39F/view-source"}],"url":"https://biology.stackexchange.com/questions/115063/finding-antibodies-sequence-online"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"115083","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-08-01T17:43:11+00:00","raw_file":"raw/codex_api_v1/d27b3e16c09e1430a099a72b8b6dd2aeca3c9f4116d2c57936f72acccbad600e_1790824094070868300_0.json","raw_sha256":"75ae5a3acd2d5ed1aadac056a0d6e41f6b40d63445afc68b8af4b71a0282b5d9","revision_guid":"123A93B6-18E1-480F-A55D-8D6CCEB494EB","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/123A93B6-18E1-480F-A55D-8D6CCEB494EB/view-source"}],"url":"https://biology.stackexchange.com/a/115083"}],"contexts":[{"context_id":"question","html":"<p>Not sure if this is the right section to ask this question but here we go.</p>\n<p>I want to find human GPCR antibody sequences online and download them. I had some trouble finding good platforms with good filters and downloading the results.</p>\n<p>How do you go about finding protein/antibody sequences online? Is there a universal database for proteins? Are there different smaller databases that specialize in antibodies?</p>\n<p>How should I go about this?</p>\n<p>Thank you!</p>\n","text":"Not sure if this is the right section to ask this question but here we go.\n\n\n\n\nI want to find human GPCR antibody sequences online and download them. I had some trouble finding good platforms with good filters and downloading the results.\n\n\n\n\nHow do you go about finding protein/antibody sequences online? Is there a universal database for proteins? Are there different smaller databases that specialize in antibodies?\n\n\n\n\nHow should I go about this?\n\n\n\n\nThank you!"},{"context_id":"115083","html":"<p>I would suggest looking <a href=\"https://opig.stats.ox.ac.uk/webapps/plabdab\" rel=\"nofollow noreferrer\">here</a> at the PLAbDAb database, this appears to be an up-to-date antibody database including sequences.</p>\n<p>I ran a quick query for &quot;GPCR&quot; and <a href=\"https://opig.stats.ox.ac.uk/webapps/plabdab/results/keyword/20240801_0043943/\" rel=\"nofollow noreferrer\">got a number of results including protein sequences</a>.</p>\n","text":"I would suggest looking here (https://opig.stats.ox.ac.uk/webapps/plabdab) at the PLAbDAb database, this appears to be an up-to-date antibody database including sequences.\n\n\n\n\nI ran a quick query for \"GPCR\" and got a number of results including protein sequences (https://opig.stats.ox.ac.uk/webapps/plabdab/results/keyword/20240801_0043943/)."}],"domain":"biology","external_citations":["https://opig.stats.ox.ac.uk/webapps/plabdab","https://opig.stats.ox.ac.uk/webapps/plabdab/results/keyword/20240801_0043943/"],"ground_truth_type":"metadata_grounded","group_id":"76301d910f51740a2978af7e3bfc318289a313b99388e45fb44cec0e1f79d1ce","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-f6f0699f9ef9702034c24fc5","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:05.762873+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/04ed2aa314c5d877c5d79e42620d1f80988a21de8d429a22d8c6af5280cfd6e8_0.json","raw_sha256":"6dd355b99094bb9ba2c965ee7dd7b0e95f92a8078d3b2b85b64196fcb6cf717c","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=5&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user141154","profile_url":"https://biology.stackexchange.com/users/84543/user141154","user_type":"registered"},"created_at":"2024-07-28T13:13:20+00:00","raw_file":"raw/codex_api_v1/d27b3e16c09e1430a099a72b8b6dd2aeca3c9f4116d2c57936f72acccbad600e_1790824094070868300_0.json","raw_sha256":"75ae5a3acd2d5ed1aadac056a0d6e41f6b40d63445afc68b8af4b71a0282b5d9","revision_guid":"FE1DC793-961F-4BE6-A78B-560F1D56A39F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FE1DC793-961F-4BE6-A78B-560F1D56A39F/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115063","source_record_sha256":"05e35be4909b835ec6bc2232815a8742c2d375c20c7ae25171420f8a400e7f61","source_url":"https://biology.stackexchange.com/questions/115063/finding-antibodies-sequence-online","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Finding antibodies sequence online\nNot sure if this is the right section to ask this question but here we go.\n\n\n\n\nI want to find human GPCR antibody sequences online and download them. I had some trouble finding good platforms with good filters and downloading the results.\n\n\n\n\nHow do you go about finding protein/antibody sequences online? Is there a universal database for proteins? Are there different smaller databases that specialize in antibodies?\n\n\n\n\nHow should I go about this?\n\n\n\n\nThank you!","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115083,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The below is speculative, but I believe it to be approximately, if not entirely, correct.</p>\n<p>The origin of this 'unit of reporting' appears to stem from the original attempts of Kety &amp; Schmidt to provide the first quantitative measurement of cerebral blood flow (CBF). There are a few papers spanning several years...with the first one coming out in 1945...but the most relevant one that provides some insight is here: <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC439518/\" rel=\"nofollow noreferrer\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC439518/</a>.</p>\n<p>They provide a logical derivation that uses some basic calculus and laws of incompressible fluid flow to produce the following equation:</p>\n<p><span class=\"math-container\">$$\\text{CBF}(\\tau)=\\frac{\\frac{Q_B(\\tau)}{W}}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}$$</span></p>\n<p>, where <span class=\"math-container\">$Q_B(\\tau)$</span> denotes the number of N2O atoms in the brain (we will use the SI unit <span class=\"math-container\">$\\text{mol}$</span> to report this value), <span class=\"math-container\">$W$</span> denotes the whole weight of the brain, and <span class=\"math-container\">$A$</span> and <span class=\"math-container\">$V$</span> represent the arterial and venous concentrations of N2O, respectively. The authors' derivation to <em>this point</em> in the paper is well explained, and the corresponding physical dimensions of CBF are easily tracked as being: <span class=\"math-container\">$\\displaystyle \\frac{\\text{volume}}{\\text{time}\\cdot\\text{mass}}$</span>.  If we choose centimeters cubed (<span class=\"math-container\">$\\text{cc}$</span>) as our unit of volume, minutes (<span class=\"math-container\">$\\text{min}$</span>) as our unit of time, and grams (<span class=\"math-container\">$\\text{g}$</span>) as our unit of mass, then the dimension are more specifically written as: <span class=\"math-container\">$\\displaystyle \\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}$</span>. So far, so good...but where does the <span class=\"math-container\">$\\frac{1}{\\text{100 g}}$</span> come from?</p>\n<p>Their derivation continues with the following claim:</p>\n<blockquote>\n<p>For long enough <span class=\"math-container\">$\\tau^*$</span>, <span class=\"math-container\">$\\frac{Q_B(\\tau^*)}{W}=V_{\\tau^*}S$</span>, where <span class=\"math-container\">$S$</span> is the partitioning coefficient of N2O between the brain tissue and brain vasculature.</p>\n</blockquote>\n<p>With no additional explanation, they then write:</p>\n<blockquote>\n<p>By substituting appropriately and multiplying through by 100, one obtains a value for cerebral blood flow in convenient units: <span class=\"math-container\">\\begin{align} \\text{CBF}(\\tau^*)=\\frac{100 V_{\\tau^*}S}{\\int_0^{\\tau^*}[A(t)-V(t)]dt}\\end{align}</span> where CBF is expressed as cc. of blood flow per <span class=\"math-container\">$100$</span> g. of brain per minute</p>\n</blockquote>\n<p>These final steps are missing quite a bit of explanation...so here is my attempt at justifying the steps. Firstly, returning to the claim that:</p>\n<p><span class=\"math-container\">$$\\frac{Q_B(\\tau^*)}{W}=V_{\\tau^*}S \\quad (\\dagger_1)$$</span>, you should immediately see that the physical dimensions do not match up (and therefore, the equality is invalid). On the left side we have <span class=\"math-container\">$\\displaystyle\\frac{\\text{mol}}{\\text{g}}$</span>, and on the right side, we have <span class=\"math-container\">$\\displaystyle\\frac{\\text{mol}}{\\text{cc}}$</span>. Importantly, though, we can write out these units a tad more informatively:</p>\n<ol>\n<li><p><span class=\"math-container\">$\\displaystyle\\frac{\\text{mol of N2O in brain tissue}}{\\text{g of brain tissue}}$</span></p>\n</li>\n<li><p><span class=\"math-container\">$\\displaystyle\\frac{\\text{mol of N2O in brain vasculature}}{\\text{cc of brain vasculature}}$</span></p>\n</li>\n</ol>\n<p>Next, note that <span class=\"math-container\">$S$</span>, by definition, has units that can be represented as:</p>\n<p><span class=\"math-container\">$$\\frac{\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}}{\\frac{ \\text{mol of N2O in brain vasculature}}{ \\text{cc of brain vasculature}}}$$</span></p>\n<p>Now, returning to <span class=\"math-container\">$(\\dagger_1)$</span>, if we write out our more descriptive units we have:</p>\n<p><span class=\"math-container\">\\begin{align}\\frac{Q_B(\\tau^*)}{W}\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{g brain tissue}}&amp;=V_{\\tau^*}S \\frac{\\text{mol of N2O in brain vasculature}}{\\text{cc of brain vasculature}} \\cdot \\frac{\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}}{\\frac{ \\text{mol of N2O in brain vasculature}}{ \\text{cc of brain vasculature}}}\\\\&amp;=V_{\\tau^*}S\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}\\end{align}</span></p>\n<p>Notice that we still have this issue of physical dimension mismatch...<strong>however</strong>, if we <strong>approximate the density of the brain tissue</strong> as being largely similarly to <strong>water</strong>, then we know that water has the density of <span class=\"math-container\">$~1.0 \\frac{\\text{g}}{\\text{cc}}$</span>...so we assert:</p>\n<p><span class=\"math-container\">$$\\text{density of brain tissue is approximately } 1.0 \\frac{\\text{g of brain tissue}}{\\text{cc of brain tissue}}$$</span></p>\n<p>Accordingly, if we multiply <span class=\"math-container\">$V_{\\tau^*}S\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}$</span> by the inverse of the brain density, we have:</p>\n<p><span class=\"math-container\">$$V_{\\tau^*}S\\cdot 1\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}} \\cdot \\frac{\\text{cc of brain tissue}}{\\text{g of brain tissue}}=V_{\\tau^*}S \\frac{\\text{mol of N2O in brain tissue}}{\\text{g of brain tissue}}$$</span></p>\n<p><strong>Therefore</strong>, the more correct way of writing <span class=\"math-container\">$(\\dagger_1)$</span> is:</p>\n<p><span class=\"math-container\">$\\frac{Q_B(\\tau^*)}{W}=V_{\\tau^*}S \\cdot \\rho^{-1}_{\\text{brain}} \\quad \\color{green}{(\\dagger_2)}$</span></p>\n<p>At this point, if we substitute the <span class=\"math-container\">$\\color{green}{(\\dagger_2)}$</span> expression in for the CBF formula, we have:</p>\n<p><span class=\"math-container\">$$\\text{CBF}(\\tau^*)=\\frac{V_{\\tau^*}S \\cdot \\rho^{-1}_{\\text{brain}}}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}\\right)$$</span></p>\n<p>I suppose as long as you remember what the units are, given that the magnitude of <span class=\"math-container\">$\\rho^{-1}_{\\text{brain}}$</span> is approximately <span class=\"math-container\">$1.0$</span>, we can drop it from the equation and write:</p>\n<p><span class=\"math-container\">$$\\text{CBF}(\\tau^*)=\\frac{V_{\\tau^*}S}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}\\right) \\quad (\\dagger_3)$$</span></p>\n<p><strong>NOW</strong>, to answer the question of where does the <span class=\"math-container\">$\\frac{1}{100 \\text{g}}$</span> come from...honestly, I feel like it is completely arbitrary and have no sense as to why this choice was made. As far as I can tell, Kety &amp; Schmidt could have just as easily left the equation in its <span class=\"math-container\">$(\\dagger_3)$</span> form. However, for some reason that hopefully someone out there can figure out, they decided to multiply <span class=\"math-container\">$(\\dagger_3)$</span> by unity in the form of <span class=\"math-container\">$\\frac{100}{100}$</span>, which then allowed them to rewrite <span class=\"math-container\">$(\\dagger_3)$</span> as:</p>\n<p><span class=\"math-container\">\\begin{align}\\text{CBF}(\\tau^*)&amp;=\\frac{100}{100}\\times\\frac{V_{\\tau^*}S}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}\\right)\\\\&amp;=\\frac{100V_{\\tau^*}S}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{100 g}}\\right)\\end{align}</span></p>\n","answer_id":115117,"answer_text":"The below is speculative, but I believe it to be approximately, if not entirely, correct.\n\n\n\n\nThe origin of this 'unit of reporting' appears to stem from the original attempts of Kety & Schmidt to provide the first quantitative measurement of cerebral blood flow (CBF). There are a few papers spanning several years...with the first one coming out in 1945...but the most relevant one that provides some insight is here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC439518/ (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC439518/).\n\n\n\n\nThey provide a logical derivation that uses some basic calculus and laws of incompressible fluid flow to produce the following equation:\n\n\n\n\n$$\\text{CBF}(\\tau)=\\frac{\\frac{Q_B(\\tau)}{W}}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}$$\n\n\n\n\n, where $Q_B(\\tau)$ denotes the number of N2O atoms in the brain (we will use the SI unit $\\text{mol}$ to report this value), $W$ denotes the whole weight of the brain, and $A$ and $V$ represent the arterial and venous concentrations of N2O, respectively. The authors' derivation to this point in the paper is well explained, and the corresponding physical dimensions of CBF are easily tracked as being: $\\displaystyle \\frac{\\text{volume}}{\\text{time}\\cdot\\text{mass}}$.  If we choose centimeters cubed ($\\text{cc}$) as our unit of volume, minutes ($\\text{min}$) as our unit of time, and grams ($\\text{g}$) as our unit of mass, then the dimension are more specifically written as: $\\displaystyle \\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}$. So far, so good...but where does the $\\frac{1}{\\text{100 g}}$ come from?\n\n\n\n\nTheir derivation continues with the following claim:\n\n\n\n\n\n\n\nFor long enough $\\tau^*$, $\\frac{Q_B(\\tau^*)}{W}=V_{\\tau^*}S$, where $S$ is the partitioning coefficient of N2O between the brain tissue and brain vasculature.\n\n\n\n\n\n\n\nWith no additional explanation, they then write:\n\n\n\n\n\n\n\nBy substituting appropriately and multiplying through by 100, one obtains a value for cerebral blood flow in convenient units: \\begin{align} \\text{CBF}(\\tau^*)=\\frac{100 V_{\\tau^*}S}{\\int_0^{\\tau^*}[A(t)-V(t)]dt}\\end{align} where CBF is expressed as cc. of blood flow per $100$ g. of brain per minute\n\n\n\n\n\n\n\nThese final steps are missing quite a bit of explanation...so here is my attempt at justifying the steps. Firstly, returning to the claim that:\n\n\n\n\n$$\\frac{Q_B(\\tau^*)}{W}=V_{\\tau^*}S \\quad (\\dagger_1)$$, you should immediately see that the physical dimensions do not match up (and therefore, the equality is invalid). On the left side we have $\\displaystyle\\frac{\\text{mol}}{\\text{g}}$, and on the right side, we have $\\displaystyle\\frac{\\text{mol}}{\\text{cc}}$. Importantly, though, we can write out these units a tad more informatively:\n\n\n\n\n\n\n\n$\\displaystyle\\frac{\\text{mol of N2O in brain tissue}}{\\text{g of brain tissue}}$\n\n\n\n\n\n\n\n\n\n$\\displaystyle\\frac{\\text{mol of N2O in brain vasculature}}{\\text{cc of brain vasculature}}$\n\n\n\n\n\n\n\n\nNext, note that $S$, by definition, has units that can be represented as:\n\n\n\n\n$$\\frac{\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}}{\\frac{ \\text{mol of N2O in brain vasculature}}{ \\text{cc of brain vasculature}}}$$\n\n\n\n\nNow, returning to $(\\dagger_1)$, if we write out our more descriptive units we have:\n\n\n\n\n\\begin{align}\\frac{Q_B(\\tau^*)}{W}\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{g brain tissue}}&=V_{\\tau^*}S \\frac{\\text{mol of N2O in brain vasculature}}{\\text{cc of brain vasculature}} \\cdot \\frac{\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}}{\\frac{ \\text{mol of N2O in brain vasculature}}{ \\text{cc of brain vasculature}}}\\\\&=V_{\\tau^*}S\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}\\end{align}\n\n\n\n\nNotice that we still have this issue of physical dimension mismatch...however, if we approximate the density of the brain tissue as being largely similarly to water, then we know that water has the density of $~1.0 \\frac{\\text{g}}{\\text{cc}}$...so we assert:\n\n\n\n\n$$\\text{density of brain tissue is approximately } 1.0 \\frac{\\text{g of brain tissue}}{\\text{cc of brain tissue}}$$\n\n\n\n\nAccordingly, if we multiply $V_{\\tau^*}S\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}$ by the inverse of the brain density, we have:\n\n\n\n\n$$V_{\\tau^*}S\\cdot 1\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}} \\cdot \\frac{\\text{cc of brain tissue}}{\\text{g of brain tissue}}=V_{\\tau^*}S \\frac{\\text{mol of N2O in brain tissue}}{\\text{g of brain tissue}}$$\n\n\n\n\nTherefore, the more correct way of writing $(\\dagger_1)$ is:\n\n\n\n\n$\\frac{Q_B(\\tau^*)}{W}=V_{\\tau^*}S \\cdot \\rho^{-1}_{\\text{brain}} \\quad \\color{green}{(\\dagger_2)}$\n\n\n\n\nAt this point, if we substitute the $\\color{green}{(\\dagger_2)}$ expression in for the CBF formula, we have:\n\n\n\n\n$$\\text{CBF}(\\tau^*)=\\frac{V_{\\tau^*}S \\cdot \\rho^{-1}_{\\text{brain}}}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}\\right)$$\n\n\n\n\nI suppose as long as you remember what the units are, given that the magnitude of $\\rho^{-1}_{\\text{brain}}$ is approximately $1.0$, we can drop it from the equation and write:\n\n\n\n\n$$\\text{CBF}(\\tau^*)=\\frac{V_{\\tau^*}S}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}\\right) \\quad (\\dagger_3)$$\n\n\n\n\nNOW, to answer the question of where does the $\\frac{1}{100 \\text{g}}$ come from...honestly, I feel like it is completely arbitrary and have no sense as to why this choice was made. As far as I can tell, Kety & Schmidt could have just as easily left the equation in its $(\\dagger_3)$ form. However, for some reason that hopefully someone out there can figure out, they decided to multiply $(\\dagger_3)$ by unity in the form of $\\frac{100}{100}$, which then allowed them to rewrite $(\\dagger_3)$ as:\n\n\n\n\n\\begin{align}\\text{CBF}(\\tau^*)&=\\frac{100}{100}\\times\\frac{V_{\\tau^*}S}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}\\right)\\\\&=\\frac{100V_{\\tau^*}S}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{100 g}}\\right)\\end{align}","answer_url":"https://biology.stackexchange.com/a/115117","author":"S.C.","author_url":"https://biology.stackexchange.com/users/50049/s-c","content_license":"CC BY-SA 4.0","created_at":"2024-08-04T16:36:41+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:25.304620+00:00","license":"CC BY-SA 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4.0","contributor":{"display_name":"S.C.","profile_url":"https://biology.stackexchange.com/users/50049/s-c","user_type":"registered"},"created_at":"2024-08-04T19:06:47+00:00","raw_file":"raw/codex_api_v1/d27b3e16c09e1430a099a72b8b6dd2aeca3c9f4116d2c57936f72acccbad600e_1790824094070868300_0.json","raw_sha256":"75ae5a3acd2d5ed1aadac056a0d6e41f6b40d63445afc68b8af4b71a0282b5d9","revision_guid":"36847CEC-F86F-4E47-89EF-3B6D4174AA48","revision_number":6,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/36847CEC-F86F-4E47-89EF-3B6D4174AA48/view-source"}],"url":"https://biology.stackexchange.com/a/115117"}],"contexts":[{"context_id":"question","html":"<p>The title of this post pretty much says it all. I've looked around quite a bit for the original paper that invoked the decision to normalize a fluid volume to <span class=\"math-container\">$\\frac{1}{100 \\text{ gram}}$</span>. I thought that some early infrared spectrophotometry studies (which I believe are the first quantifications of CBV) would explain this...but they do not. Perhaps this is related to a more general (and older) approach to perfusion quantification methods, but I really do not know.</p>\n","text":"The title of this post pretty much says it all. I've looked around quite a bit for the original paper that invoked the decision to normalize a fluid volume to $\\frac{1}{100 \\text{ gram}}$. I thought that some early infrared spectrophotometry studies (which I believe are the first quantifications of CBV) would explain this...but they do not. Perhaps this is related to a more general (and older) approach to perfusion quantification methods, but I really do not know."},{"context_id":"115117","html":"<p>The below is speculative, but I believe it to be approximately, if not entirely, correct.</p>\n<p>The origin of this 'unit of reporting' appears to stem from the original attempts of Kety &amp; Schmidt to provide the first quantitative measurement of cerebral blood flow (CBF). There are a few papers spanning several years...with the first one coming out in 1945...but the most relevant one that provides some insight is here: <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC439518/\" rel=\"nofollow noreferrer\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC439518/</a>.</p>\n<p>They provide a logical derivation that uses some basic calculus and laws of incompressible fluid flow to produce the following equation:</p>\n<p><span class=\"math-container\">$$\\text{CBF}(\\tau)=\\frac{\\frac{Q_B(\\tau)}{W}}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}$$</span></p>\n<p>, where <span class=\"math-container\">$Q_B(\\tau)$</span> denotes the number of N2O atoms in the brain (we will use the SI unit <span class=\"math-container\">$\\text{mol}$</span> to report this value), <span class=\"math-container\">$W$</span> denotes the whole weight of the brain, and <span class=\"math-container\">$A$</span> and <span class=\"math-container\">$V$</span> represent the arterial and venous concentrations of N2O, respectively. The authors' derivation to <em>this point</em> in the paper is well explained, and the corresponding physical dimensions of CBF are easily tracked as being: <span class=\"math-container\">$\\displaystyle \\frac{\\text{volume}}{\\text{time}\\cdot\\text{mass}}$</span>.  If we choose centimeters cubed (<span class=\"math-container\">$\\text{cc}$</span>) as our unit of volume, minutes (<span class=\"math-container\">$\\text{min}$</span>) as our unit of time, and grams (<span class=\"math-container\">$\\text{g}$</span>) as our unit of mass, then the dimension are more specifically written as: <span class=\"math-container\">$\\displaystyle \\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}$</span>. So far, so good...but where does the <span class=\"math-container\">$\\frac{1}{\\text{100 g}}$</span> come from?</p>\n<p>Their derivation continues with the following claim:</p>\n<blockquote>\n<p>For long enough <span class=\"math-container\">$\\tau^*$</span>, <span class=\"math-container\">$\\frac{Q_B(\\tau^*)}{W}=V_{\\tau^*}S$</span>, where <span class=\"math-container\">$S$</span> is the partitioning coefficient of N2O between the brain tissue and brain vasculature.</p>\n</blockquote>\n<p>With no additional explanation, they then write:</p>\n<blockquote>\n<p>By substituting appropriately and multiplying through by 100, one obtains a value for cerebral blood flow in convenient units: <span class=\"math-container\">\\begin{align} \\text{CBF}(\\tau^*)=\\frac{100 V_{\\tau^*}S}{\\int_0^{\\tau^*}[A(t)-V(t)]dt}\\end{align}</span> where CBF is expressed as cc. of blood flow per <span class=\"math-container\">$100$</span> g. of brain per minute</p>\n</blockquote>\n<p>These final steps are missing quite a bit of explanation...so here is my attempt at justifying the steps. Firstly, returning to the claim that:</p>\n<p><span class=\"math-container\">$$\\frac{Q_B(\\tau^*)}{W}=V_{\\tau^*}S \\quad (\\dagger_1)$$</span>, you should immediately see that the physical dimensions do not match up (and therefore, the equality is invalid). On the left side we have <span class=\"math-container\">$\\displaystyle\\frac{\\text{mol}}{\\text{g}}$</span>, and on the right side, we have <span class=\"math-container\">$\\displaystyle\\frac{\\text{mol}}{\\text{cc}}$</span>. Importantly, though, we can write out these units a tad more informatively:</p>\n<ol>\n<li><p><span class=\"math-container\">$\\displaystyle\\frac{\\text{mol of N2O in brain tissue}}{\\text{g of brain tissue}}$</span></p>\n</li>\n<li><p><span class=\"math-container\">$\\displaystyle\\frac{\\text{mol of N2O in brain vasculature}}{\\text{cc of brain vasculature}}$</span></p>\n</li>\n</ol>\n<p>Next, note that <span class=\"math-container\">$S$</span>, by definition, has units that can be represented as:</p>\n<p><span class=\"math-container\">$$\\frac{\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}}{\\frac{ \\text{mol of N2O in brain vasculature}}{ \\text{cc of brain vasculature}}}$$</span></p>\n<p>Now, returning to <span class=\"math-container\">$(\\dagger_1)$</span>, if we write out our more descriptive units we have:</p>\n<p><span class=\"math-container\">\\begin{align}\\frac{Q_B(\\tau^*)}{W}\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{g brain tissue}}&amp;=V_{\\tau^*}S \\frac{\\text{mol of N2O in brain vasculature}}{\\text{cc of brain vasculature}} \\cdot \\frac{\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}}{\\frac{ \\text{mol of N2O in brain vasculature}}{ \\text{cc of brain vasculature}}}\\\\&amp;=V_{\\tau^*}S\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}\\end{align}</span></p>\n<p>Notice that we still have this issue of physical dimension mismatch...<strong>however</strong>, if we <strong>approximate the density of the brain tissue</strong> as being largely similarly to <strong>water</strong>, then we know that water has the density of <span class=\"math-container\">$~1.0 \\frac{\\text{g}}{\\text{cc}}$</span>...so we assert:</p>\n<p><span class=\"math-container\">$$\\text{density of brain tissue is approximately } 1.0 \\frac{\\text{g of brain tissue}}{\\text{cc of brain tissue}}$$</span></p>\n<p>Accordingly, if we multiply <span class=\"math-container\">$V_{\\tau^*}S\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}$</span> by the inverse of the brain density, we have:</p>\n<p><span class=\"math-container\">$$V_{\\tau^*}S\\cdot 1\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}} \\cdot \\frac{\\text{cc of brain tissue}}{\\text{g of brain tissue}}=V_{\\tau^*}S \\frac{\\text{mol of N2O in brain tissue}}{\\text{g of brain tissue}}$$</span></p>\n<p><strong>Therefore</strong>, the more correct way of writing <span class=\"math-container\">$(\\dagger_1)$</span> is:</p>\n<p><span class=\"math-container\">$\\frac{Q_B(\\tau^*)}{W}=V_{\\tau^*}S \\cdot \\rho^{-1}_{\\text{brain}} \\quad \\color{green}{(\\dagger_2)}$</span></p>\n<p>At this point, if we substitute the <span class=\"math-container\">$\\color{green}{(\\dagger_2)}$</span> expression in for the CBF formula, we have:</p>\n<p><span class=\"math-container\">$$\\text{CBF}(\\tau^*)=\\frac{V_{\\tau^*}S \\cdot \\rho^{-1}_{\\text{brain}}}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}\\right)$$</span></p>\n<p>I suppose as long as you remember what the units are, given that the magnitude of <span class=\"math-container\">$\\rho^{-1}_{\\text{brain}}$</span> is approximately <span class=\"math-container\">$1.0$</span>, we can drop it from the equation and write:</p>\n<p><span class=\"math-container\">$$\\text{CBF}(\\tau^*)=\\frac{V_{\\tau^*}S}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}\\right) \\quad (\\dagger_3)$$</span></p>\n<p><strong>NOW</strong>, to answer the question of where does the <span class=\"math-container\">$\\frac{1}{100 \\text{g}}$</span> come from...honestly, I feel like it is completely arbitrary and have no sense as to why this choice was made. As far as I can tell, Kety &amp; Schmidt could have just as easily left the equation in its <span class=\"math-container\">$(\\dagger_3)$</span> form. However, for some reason that hopefully someone out there can figure out, they decided to multiply <span class=\"math-container\">$(\\dagger_3)$</span> by unity in the form of <span class=\"math-container\">$\\frac{100}{100}$</span>, which then allowed them to rewrite <span class=\"math-container\">$(\\dagger_3)$</span> as:</p>\n<p><span class=\"math-container\">\\begin{align}\\text{CBF}(\\tau^*)&amp;=\\frac{100}{100}\\times\\frac{V_{\\tau^*}S}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}\\right)\\\\&amp;=\\frac{100V_{\\tau^*}S}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{100 g}}\\right)\\end{align}</span></p>\n","text":"The below is speculative, but I believe it to be approximately, if not entirely, correct.\n\n\n\n\nThe origin of this 'unit of reporting' appears to stem from the original attempts of Kety & Schmidt to provide the first quantitative measurement of cerebral blood flow (CBF). There are a few papers spanning several years...with the first one coming out in 1945...but the most relevant one that provides some insight is here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC439518/ (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC439518/).\n\n\n\n\nThey provide a logical derivation that uses some basic calculus and laws of incompressible fluid flow to produce the following equation:\n\n\n\n\n$$\\text{CBF}(\\tau)=\\frac{\\frac{Q_B(\\tau)}{W}}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}$$\n\n\n\n\n, where $Q_B(\\tau)$ denotes the number of N2O atoms in the brain (we will use the SI unit $\\text{mol}$ to report this value), $W$ denotes the whole weight of the brain, and $A$ and $V$ represent the arterial and venous concentrations of N2O, respectively. The authors' derivation to this point in the paper is well explained, and the corresponding physical dimensions of CBF are easily tracked as being: $\\displaystyle \\frac{\\text{volume}}{\\text{time}\\cdot\\text{mass}}$.  If we choose centimeters cubed ($\\text{cc}$) as our unit of volume, minutes ($\\text{min}$) as our unit of time, and grams ($\\text{g}$) as our unit of mass, then the dimension are more specifically written as: $\\displaystyle \\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}$. So far, so good...but where does the $\\frac{1}{\\text{100 g}}$ come from?\n\n\n\n\nTheir derivation continues with the following claim:\n\n\n\n\n\n\n\nFor long enough $\\tau^*$, $\\frac{Q_B(\\tau^*)}{W}=V_{\\tau^*}S$, where $S$ is the partitioning coefficient of N2O between the brain tissue and brain vasculature.\n\n\n\n\n\n\n\nWith no additional explanation, they then write:\n\n\n\n\n\n\n\nBy substituting appropriately and multiplying through by 100, one obtains a value for cerebral blood flow in convenient units: \\begin{align} \\text{CBF}(\\tau^*)=\\frac{100 V_{\\tau^*}S}{\\int_0^{\\tau^*}[A(t)-V(t)]dt}\\end{align} where CBF is expressed as cc. of blood flow per $100$ g. of brain per minute\n\n\n\n\n\n\n\nThese final steps are missing quite a bit of explanation...so here is my attempt at justifying the steps. Firstly, returning to the claim that:\n\n\n\n\n$$\\frac{Q_B(\\tau^*)}{W}=V_{\\tau^*}S \\quad (\\dagger_1)$$, you should immediately see that the physical dimensions do not match up (and therefore, the equality is invalid). On the left side we have $\\displaystyle\\frac{\\text{mol}}{\\text{g}}$, and on the right side, we have $\\displaystyle\\frac{\\text{mol}}{\\text{cc}}$. Importantly, though, we can write out these units a tad more informatively:\n\n\n\n\n\n\n\n$\\displaystyle\\frac{\\text{mol of N2O in brain tissue}}{\\text{g of brain tissue}}$\n\n\n\n\n\n\n\n\n\n$\\displaystyle\\frac{\\text{mol of N2O in brain vasculature}}{\\text{cc of brain vasculature}}$\n\n\n\n\n\n\n\n\nNext, note that $S$, by definition, has units that can be represented as:\n\n\n\n\n$$\\frac{\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}}{\\frac{ \\text{mol of N2O in brain vasculature}}{ \\text{cc of brain vasculature}}}$$\n\n\n\n\nNow, returning to $(\\dagger_1)$, if we write out our more descriptive units we have:\n\n\n\n\n\\begin{align}\\frac{Q_B(\\tau^*)}{W}\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{g brain tissue}}&=V_{\\tau^*}S \\frac{\\text{mol of N2O in brain vasculature}}{\\text{cc of brain vasculature}} \\cdot \\frac{\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}}{\\frac{ \\text{mol of N2O in brain vasculature}}{ \\text{cc of brain vasculature}}}\\\\&=V_{\\tau^*}S\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}\\end{align}\n\n\n\n\nNotice that we still have this issue of physical dimension mismatch...however, if we approximate the density of the brain tissue as being largely similarly to water, then we know that water has the density of $~1.0 \\frac{\\text{g}}{\\text{cc}}$...so we assert:\n\n\n\n\n$$\\text{density of brain tissue is approximately } 1.0 \\frac{\\text{g of brain tissue}}{\\text{cc of brain tissue}}$$\n\n\n\n\nAccordingly, if we multiply $V_{\\tau^*}S\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}}$ by the inverse of the brain density, we have:\n\n\n\n\n$$V_{\\tau^*}S\\cdot 1\\frac{ \\text{mol of N2O in brain tissue}}{ \\text{cc brain tissue}} \\cdot \\frac{\\text{cc of brain tissue}}{\\text{g of brain tissue}}=V_{\\tau^*}S \\frac{\\text{mol of N2O in brain tissue}}{\\text{g of brain tissue}}$$\n\n\n\n\nTherefore, the more correct way of writing $(\\dagger_1)$ is:\n\n\n\n\n$\\frac{Q_B(\\tau^*)}{W}=V_{\\tau^*}S \\cdot \\rho^{-1}_{\\text{brain}} \\quad \\color{green}{(\\dagger_2)}$\n\n\n\n\nAt this point, if we substitute the $\\color{green}{(\\dagger_2)}$ expression in for the CBF formula, we have:\n\n\n\n\n$$\\text{CBF}(\\tau^*)=\\frac{V_{\\tau^*}S \\cdot \\rho^{-1}_{\\text{brain}}}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}\\right)$$\n\n\n\n\nI suppose as long as you remember what the units are, given that the magnitude of $\\rho^{-1}_{\\text{brain}}$ is approximately $1.0$, we can drop it from the equation and write:\n\n\n\n\n$$\\text{CBF}(\\tau^*)=\\frac{V_{\\tau^*}S}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}\\right) \\quad (\\dagger_3)$$\n\n\n\n\nNOW, to answer the question of where does the $\\frac{1}{100 \\text{g}}$ come from...honestly, I feel like it is completely arbitrary and have no sense as to why this choice was made. As far as I can tell, Kety & Schmidt could have just as easily left the equation in its $(\\dagger_3)$ form. However, for some reason that hopefully someone out there can figure out, they decided to multiply $(\\dagger_3)$ by unity in the form of $\\frac{100}{100}$, which then allowed them to rewrite $(\\dagger_3)$ as:\n\n\n\n\n\\begin{align}\\text{CBF}(\\tau^*)&=\\frac{100}{100}\\times\\frac{V_{\\tau^*}S}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{g}}\\right)\\\\&=\\frac{100V_{\\tau^*}S}{\\int_0^{\\tau}\\left[A(t)-V(t)\\right]dt}\\left(\\frac{\\text{cc}}{\\text{min}\\cdot\\text{100 g}}\\right)\\end{align}"}],"domain":"biology","external_citations":["https://www.ncbi.nlm.nih.gov/pmc/articles/PMC439518/"],"ground_truth_type":"metadata_grounded","group_id":"428764ad25fa6d00416051bd4fd4716052644c2ce78eacd237a3c4cdfb99cb7f","hard_case_family":["no_accepted_answer"],"id":"RHM-ed59bc9af000735da4165839","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:05.762873+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/04ed2aa314c5d877c5d79e42620d1f80988a21de8d429a22d8c6af5280cfd6e8_0.json","raw_sha256":"6dd355b99094bb9ba2c965ee7dd7b0e95f92a8078d3b2b85b64196fcb6cf717c","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=5&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"S.C.","profile_url":"https://biology.stackexchange.com/users/50049/s-c","user_type":"registered"},"created_at":"2024-08-02T20:49:00+00:00","raw_file":"raw/codex_api_v1/d27b3e16c09e1430a099a72b8b6dd2aeca3c9f4116d2c57936f72acccbad600e_1790824094070868300_0.json","raw_sha256":"75ae5a3acd2d5ed1aadac056a0d6e41f6b40d63445afc68b8af4b71a0282b5d9","revision_guid":"2507F4B3-E4C2-4884-8F48-743EC73C072F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2507F4B3-E4C2-4884-8F48-743EC73C072F/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115099","source_record_sha256":"8ee3e2ba572669343459163e2eb582a489777ef47e6073d06fe19a8717b3a773","source_url":"https://biology.stackexchange.com/questions/115099/what-is-the-historical-justification-for-the-per-100-gram-of-tissue-term-in-th","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What is the historical justification for the 'per 100 gram of tissue' term in the units of cerebral blood volume?\nThe title of this post pretty much says it all. I've looked around quite a bit for the original paper that invoked the decision to normalize a fluid volume to $\\frac{1}{100 \\text{ gram}}$. I thought that some early infrared spectrophotometry studies (which I believe are the first quantifications of CBV) would explain this...but they do not. Perhaps this is related to a more general (and older) approach to perfusion quantification methods, but I really do not know.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115117,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":115130,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>There are two implicit parts to the question:</p>\n<ul>\n<li>what animals are as a taxon and</li>\n<li>why we call this taxon &quot;animals&quot; (= Animalia = Metazoa).</li>\n</ul>\n<p>Organisms are classified mostly based on the understanding of the <a href=\"https://en.wikipedia.org/wiki/Phylogenetic_tree\" rel=\"nofollow noreferrer\">evolutionary relationships</a> between them. Nowadays, evolutionary relationships for extant organisms are resolved using molecular data, in particular <a href=\"https://en.wikipedia.org/wiki/Phylogenomics\" rel=\"nofollow noreferrer\">multiple gene sequences</a> which provide many simple characters for phylogenetic reconstructions.</p>\n<p>There are many branches on the tree of life (clades), each one has the potential to be treated as a taxon. To understand what clade deserves a name and corresponds to a particular rank, taxonomists search for well-supported clades with easily recognizable derived traits associated with them.</p>\n<p>So, animals can be defined as the organisms belonging to the clade that <a href=\"https://en.wikipedia.org/wiki/Circumscription_(taxonomy)\" rel=\"nofollow noreferrer\">includes</a> organisms from <a href=\"https://en.wikipedia.org/wiki/Trichoplax\" rel=\"nofollow noreferrer\"><em>Trichoplax</em></a> and sponges to humans, or in other words: which includes the last common ancestor of these organisms and all its descendants. It is a well-supported deep clade and we call it Animalia = Metazoa based on the fact that most organisms that have been included in the typological definitions (i.e. definitions based on formal morphological inclusion criteria) of the traditional taxon &quot;Animalia&quot; starting from Linnaeus belong here. The typological taxon &quot;Animalia&quot; in turn is an improvement upon the earlier typological definitions of the word &quot;animals/ζῷα/animalia&quot; starting from Aristotle and both are attempts at formalizing the intuition languages originally have for the word &quot;animals&quot;.</p>\n<p>Thanks to shared ancestry, animals have a number of <a href=\"https://en.wikipedia.org/wiki/Apomorphy_and_synapomorphy\" rel=\"nofollow noreferrer\">synapomorphies</a> (features evolved in their last common ancestor) which include multicellularity, anisogamy, specific developmental signalling pathways, reduced mitochondrial genome and others. Synapomorphies are not inclusion criteria as in typology. Even if some other group developed a similar trait (e.g. multicellularity evolved several times among eukaryotes independently) or even if some animals lose some of these traits (although outside of zoological taxonomy, one extreme case might be transmissible cancers, such as <a href=\"https://en.wikipedia.org/wiki/Canine_transmissible_venereal_tumor\" rel=\"nofollow noreferrer\">canine transmissible venereal tumour</a> which are essentially unicellular parasites recently derived from multicellular animals) those organisms do not become/stop being animals.</p>\n<p>Oxford Dictionary in your citation does not define what an animal is. From the perspective of modern biology, it only mentions some traits found in some animals — not all animals have nervous system and not all rapidly respond to stimuli. Analogously, organisms that independently evolved fast responses do not become animals: they do not share ancestry with them and they lack their synapomorphies. Whatever similarities they might have with animals would be due to plesiomorphies (traits inherited from a more distant ancestors) or convergences/homoplasies (traits evolved independently).</p>\n","answer_id":115130,"answer_text":"There are two implicit parts to the question:\n\n\n\n\n\nwhat animals are as a taxon and\n\n\n\n\nwhy we call this taxon \"animals\" (= Animalia = Metazoa).\n\n\n\n\n\nOrganisms are classified mostly based on the understanding of the evolutionary relationships (https://en.wikipedia.org/wiki/Phylogenetic_tree) between them. Nowadays, evolutionary relationships for extant organisms are resolved using molecular data, in particular multiple gene sequences (https://en.wikipedia.org/wiki/Phylogenomics) which provide many simple characters for phylogenetic reconstructions.\n\n\n\n\nThere are many branches on the tree of life (clades), each one has the potential to be treated as a taxon. To understand what clade deserves a name and corresponds to a particular rank, taxonomists search for well-supported clades with easily recognizable derived traits associated with them.\n\n\n\n\nSo, animals can be defined as the organisms belonging to the clade that includes (https://en.wikipedia.org/wiki/Circumscription_(taxonomy)) organisms from Trichoplax (https://en.wikipedia.org/wiki/Trichoplax) and sponges to humans, or in other words: which includes the last common ancestor of these organisms and all its descendants. It is a well-supported deep clade and we call it Animalia = Metazoa based on the fact that most organisms that have been included in the typological definitions (i.e. definitions based on formal morphological inclusion criteria) of the traditional taxon \"Animalia\" starting from Linnaeus belong here. The typological taxon \"Animalia\" in turn is an improvement upon the earlier typological definitions of the word \"animals/ζῷα/animalia\" starting from Aristotle and both are attempts at formalizing the intuition languages originally have for the word \"animals\".\n\n\n\n\nThanks to shared ancestry, animals have a number of synapomorphies (https://en.wikipedia.org/wiki/Apomorphy_and_synapomorphy) (features evolved in their last common ancestor) which include multicellularity, anisogamy, specific developmental signalling pathways, reduced mitochondrial genome and others. Synapomorphies are not inclusion criteria as in typology. Even if some other group developed a similar trait (e.g. multicellularity evolved several times among eukaryotes independently) or even if some animals lose some of these traits (although outside of zoological taxonomy, one extreme case might be transmissible cancers, such as canine transmissible venereal tumour (https://en.wikipedia.org/wiki/Canine_transmissible_venereal_tumor) which are essentially unicellular parasites recently derived from multicellular animals) those organisms do not become/stop being animals.\n\n\n\n\nOxford Dictionary in your citation does not define what an animal is. From the perspective of modern biology, it only mentions some traits found in some animals — not all animals have nervous system and not all rapidly respond to stimuli. Analogously, organisms that independently evolved fast responses do not become animals: they do not share ancestry with them and they lack their synapomorphies. Whatever similarities they might have with animals would be due to plesiomorphies (traits inherited from a more distant ancestors) or convergences/homoplasies (traits evolved independently).","answer_url":"https://biology.stackexchange.com/a/115130","author":"alephreish","author_url":"https://biology.stackexchange.com/users/4579/alephreish","content_license":"CC BY-SA 4.0","created_at":"2024-08-07T09:36:34+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:25.304620+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/7fe0b66593eb4c0f175024453138b8bd50811f1580a079ffb990af38e09cd1cf_0.json","raw_sha256":"b0a655f3b4c9626cf981180b3ac018a4a26330c5ab9b925b3df78bedd8169a84","source_api":"Stack Exchange API 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I do not find this definition very clear. In particular, it seems almost circular, as if an animal is anything we define to be an animal.</p>\n<p>I tried finding a different definition, but the Oxford dictionary definition doesn’t seem to me to be any more satisfactory:</p>\n<blockquote>\n<p>“a living organism that feeds on organic matter, typically having specialized sense organs and nervous system and able to respond rapidly to stimuli”</p>\n</blockquote>\n<p>Certain plants such as Venus fly trap would seem to me to fall under this definition.</p>\n<p>So, is there a formally accepted definition of an animal in biology? If it is the definition given by Wikipedia, how do we decide which organisms fall into this kingdom? Or is it just that whatever <em>morally</em> feels like an animal (e.g. human, cat, dog, horse, fish, etc.) gets put into this kingdom?</p>\n","text":"The Wikipedia entry for animal (https://en.wikipedia.org/wiki/Animal) defines it as a “multicellular eukaryotic organism in the biological kingdom, Animalia”. I do not find this definition very clear. In particular, it seems almost circular, as if an animal is anything we define to be an animal.\n\n\n\n\nI tried finding a different definition, but the Oxford dictionary definition doesn’t seem to me to be any more satisfactory:\n\n\n\n\n\n\n\n“a living organism that feeds on organic matter, typically having specialized sense organs and nervous system and able to respond rapidly to stimuli”\n\n\n\n\n\n\n\nCertain plants such as Venus fly trap would seem to me to fall under this definition.\n\n\n\n\nSo, is there a formally accepted definition of an animal in biology? If it is the definition given by Wikipedia, how do we decide which organisms fall into this kingdom? Or is it just that whatever morally feels like an animal (e.g. human, cat, dog, horse, fish, etc.) gets put into this kingdom?"},{"context_id":"115130","html":"<p>There are two implicit parts to the question:</p>\n<ul>\n<li>what animals are as a taxon and</li>\n<li>why we call this taxon &quot;animals&quot; (= Animalia = Metazoa).</li>\n</ul>\n<p>Organisms are classified mostly based on the understanding of the <a href=\"https://en.wikipedia.org/wiki/Phylogenetic_tree\" rel=\"nofollow noreferrer\">evolutionary relationships</a> between them. Nowadays, evolutionary relationships for extant organisms are resolved using molecular data, in particular <a href=\"https://en.wikipedia.org/wiki/Phylogenomics\" rel=\"nofollow noreferrer\">multiple gene sequences</a> which provide many simple characters for phylogenetic reconstructions.</p>\n<p>There are many branches on the tree of life (clades), each one has the potential to be treated as a taxon. To understand what clade deserves a name and corresponds to a particular rank, taxonomists search for well-supported clades with easily recognizable derived traits associated with them.</p>\n<p>So, animals can be defined as the organisms belonging to the clade that <a href=\"https://en.wikipedia.org/wiki/Circumscription_(taxonomy)\" rel=\"nofollow noreferrer\">includes</a> organisms from <a href=\"https://en.wikipedia.org/wiki/Trichoplax\" rel=\"nofollow noreferrer\"><em>Trichoplax</em></a> and sponges to humans, or in other words: which includes the last common ancestor of these organisms and all its descendants. It is a well-supported deep clade and we call it Animalia = Metazoa based on the fact that most organisms that have been included in the typological definitions (i.e. definitions based on formal morphological inclusion criteria) of the traditional taxon &quot;Animalia&quot; starting from Linnaeus belong here. The typological taxon &quot;Animalia&quot; in turn is an improvement upon the earlier typological definitions of the word &quot;animals/ζῷα/animalia&quot; starting from Aristotle and both are attempts at formalizing the intuition languages originally have for the word &quot;animals&quot;.</p>\n<p>Thanks to shared ancestry, animals have a number of <a href=\"https://en.wikipedia.org/wiki/Apomorphy_and_synapomorphy\" rel=\"nofollow noreferrer\">synapomorphies</a> (features evolved in their last common ancestor) which include multicellularity, anisogamy, specific developmental signalling pathways, reduced mitochondrial genome and others. Synapomorphies are not inclusion criteria as in typology. Even if some other group developed a similar trait (e.g. multicellularity evolved several times among eukaryotes independently) or even if some animals lose some of these traits (although outside of zoological taxonomy, one extreme case might be transmissible cancers, such as <a href=\"https://en.wikipedia.org/wiki/Canine_transmissible_venereal_tumor\" rel=\"nofollow noreferrer\">canine transmissible venereal tumour</a> which are essentially unicellular parasites recently derived from multicellular animals) those organisms do not become/stop being animals.</p>\n<p>Oxford Dictionary in your citation does not define what an animal is. From the perspective of modern biology, it only mentions some traits found in some animals — not all animals have nervous system and not all rapidly respond to stimuli. Analogously, organisms that independently evolved fast responses do not become animals: they do not share ancestry with them and they lack their synapomorphies. Whatever similarities they might have with animals would be due to plesiomorphies (traits inherited from a more distant ancestors) or convergences/homoplasies (traits evolved independently).</p>\n","text":"There are two implicit parts to the question:\n\n\n\n\n\nwhat animals are as a taxon and\n\n\n\n\nwhy we call this taxon \"animals\" (= Animalia = Metazoa).\n\n\n\n\n\nOrganisms are classified mostly based on the understanding of the evolutionary relationships (https://en.wikipedia.org/wiki/Phylogenetic_tree) between them. Nowadays, evolutionary relationships for extant organisms are resolved using molecular data, in particular multiple gene sequences (https://en.wikipedia.org/wiki/Phylogenomics) which provide many simple characters for phylogenetic reconstructions.\n\n\n\n\nThere are many branches on the tree of life (clades), each one has the potential to be treated as a taxon. To understand what clade deserves a name and corresponds to a particular rank, taxonomists search for well-supported clades with easily recognizable derived traits associated with them.\n\n\n\n\nSo, animals can be defined as the organisms belonging to the clade that includes (https://en.wikipedia.org/wiki/Circumscription_(taxonomy)) organisms from Trichoplax (https://en.wikipedia.org/wiki/Trichoplax) and sponges to humans, or in other words: which includes the last common ancestor of these organisms and all its descendants. It is a well-supported deep clade and we call it Animalia = Metazoa based on the fact that most organisms that have been included in the typological definitions (i.e. definitions based on formal morphological inclusion criteria) of the traditional taxon \"Animalia\" starting from Linnaeus belong here. The typological taxon \"Animalia\" in turn is an improvement upon the earlier typological definitions of the word \"animals/ζῷα/animalia\" starting from Aristotle and both are attempts at formalizing the intuition languages originally have for the word \"animals\".\n\n\n\n\nThanks to shared ancestry, animals have a number of synapomorphies (https://en.wikipedia.org/wiki/Apomorphy_and_synapomorphy) (features evolved in their last common ancestor) which include multicellularity, anisogamy, specific developmental signalling pathways, reduced mitochondrial genome and others. Synapomorphies are not inclusion criteria as in typology. Even if some other group developed a similar trait (e.g. multicellularity evolved several times among eukaryotes independently) or even if some animals lose some of these traits (although outside of zoological taxonomy, one extreme case might be transmissible cancers, such as canine transmissible venereal tumour (https://en.wikipedia.org/wiki/Canine_transmissible_venereal_tumor) which are essentially unicellular parasites recently derived from multicellular animals) those organisms do not become/stop being animals.\n\n\n\n\nOxford Dictionary in your citation does not define what an animal is. From the perspective of modern biology, it only mentions some traits found in some animals — not all animals have nervous system and not all rapidly respond to stimuli. Analogously, organisms that independently evolved fast responses do not become animals: they do not share ancestry with them and they lack their synapomorphies. Whatever similarities they might have with animals would be due to plesiomorphies (traits inherited from a more distant ancestors) or convergences/homoplasies (traits evolved independently)."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Animal","https://en.wikipedia.org/wiki/Apomorphy_and_synapomorphy","https://en.wikipedia.org/wiki/Canine_transmissible_venereal_tumor","https://en.wikipedia.org/wiki/Circumscription_(taxonomy)","https://en.wikipedia.org/wiki/Phylogenetic_tree","https://en.wikipedia.org/wiki/Phylogenomics","https://en.wikipedia.org/wiki/Trichoplax"],"ground_truth_type":"metadata_grounded","group_id":"611c485d82a01866c73516901e8293c9171cc0caf6cee36c3dbbcec407d6621d","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-86f78b6df36867f31830bed4","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:05.762873+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/04ed2aa314c5d877c5d79e42620d1f80988a21de8d429a22d8c6af5280cfd6e8_0.json","raw_sha256":"6dd355b99094bb9ba2c965ee7dd7b0e95f92a8078d3b2b85b64196fcb6cf717c","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=5&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Chris","profile_url":"https://biology.stackexchange.com/users/85239/chris","user_type":"registered"},"created_at":"2024-08-07T04:53:28+00:00","raw_file":"raw/codex_api_v1/d27b3e16c09e1430a099a72b8b6dd2aeca3c9f4116d2c57936f72acccbad600e_1790824094070868300_0.json","raw_sha256":"75ae5a3acd2d5ed1aadac056a0d6e41f6b40d63445afc68b8af4b71a0282b5d9","revision_guid":"AEB4924E-86CB-4EED-801C-7C65DE43C272","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AEB4924E-86CB-4EED-801C-7C65DE43C272/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-08-07T12:59:37+00:00","raw_file":"raw/codex_api_v1/d27b3e16c09e1430a099a72b8b6dd2aeca3c9f4116d2c57936f72acccbad600e_1790824094070868300_0.json","raw_sha256":"75ae5a3acd2d5ed1aadac056a0d6e41f6b40d63445afc68b8af4b71a0282b5d9","revision_guid":"E36B1678-FE66-416E-B57E-0C5244142CE0","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/E36B1678-FE66-416E-B57E-0C5244142CE0/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Doug Deden","profile_url":"https://biology.stackexchange.com/users/63098/doug-deden","user_type":"registered"},"created_at":"2024-08-14T22:16:35+00:00","raw_file":"raw/codex_api_v1/920b7e5633cbad837bacc37f0887fd883044a5fce63b6e0fa3cc1504390bec54_1790824091899465600_0.json","raw_sha256":"bac2cc1988c9b300f258cae319a9302dc73ac2617e76f7491908df2a0b939d11","revision_guid":"0CCA1742-9B48-449F-931E-AC27F5CAE4D3","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0CCA1742-9B48-449F-931E-AC27F5CAE4D3/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2024-08-14T22:16:35+00:00","raw_file":"raw/codex_api_v1/920b7e5633cbad837bacc37f0887fd883044a5fce63b6e0fa3cc1504390bec54_1790824091899465600_0.json","raw_sha256":"bac2cc1988c9b300f258cae319a9302dc73ac2617e76f7491908df2a0b939d11","revision_guid":"4D024967-3C40-4C1E-AB3E-536E1AC0BD29","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4D024967-3C40-4C1E-AB3E-536E1AC0BD29/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115129","source_record_sha256":"b337e5e95a21f8569dacb99abd35c1324c55b946e436cb3b641e07757108ff18","source_url":"https://biology.stackexchange.com/questions/115129/formal-definition-of-an-animal","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Formal definition of an animal\nThe Wikipedia entry for animal (https://en.wikipedia.org/wiki/Animal) defines it as a “multicellular eukaryotic organism in the biological kingdom, Animalia”. I do not find this definition very clear. In particular, it seems almost circular, as if an animal is anything we define to be an animal.\n\n\n\n\nI tried finding a different definition, but the Oxford dictionary definition doesn’t seem to me to be any more satisfactory:\n\n\n\n\n\n\n\n“a living organism that feeds on organic matter, typically having specialized sense organs and nervous system and able to respond rapidly to stimuli”\n\n\n\n\n\n\n\nCertain plants such as Venus fly trap would seem to me to fall under this definition.\n\n\n\n\nSo, is there a formally accepted definition of an animal in biology? If it is the definition given by Wikipedia, how do we decide which organisms fall into this kingdom? Or is it just that whatever morally feels like an animal (e.g. human, cat, dog, horse, fish, etc.) gets put into this kingdom?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115130,"score":17}],"split":"test"}
{"accepted_status":{"accepted_answer_id":115307,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>My comments disappeared, so I'll explain here:</p>\n<p>There are two forms of the exponential growth model, in discrete time or continuous time.</p>\n<p>A discrete-time model is most appropriate for a population that grows at discrete times in regular intervals, such as an animal that reproduces during a specific breeding season. We only consider t = 0, 1, 2, etc., and not the times in-between. The discrete-time exponential growth model is derived from N(t + 1) = λ N(t), where N(t + 1) is the population 1 time step after N(t) - that is, the population at any one time step is λ times the population at the previous time step. From this, we get N(t) = N(0) λ^t.</p>\n<p>A continuous-time model is appropriate when growth happens continuously, without seasonality, etc. - perhaps a human population - or when time steps are negligible relative to the time period of interest. The continuous-time exponential growth model is dN(t)/dt = r N(t) - that is, the population grows at a rate of r times the population. By solving the differential equation, we get N(t) = N(0) e^(rt). Euler's constant comes up because of its unique property, d[e^x]/dx = e^x, so dN(t)/dt = d[N(0) e^(rt)]/dx = r N(0) e^(rt) = r N(t)</p>\n<p>These two models are equivalent when r = ln(λ). (Note that the symbols r and  λ are commonly, but far from always used for these values.) So whether we choose to express the model in as N(t) = N(0) λ^t or N(t) = N(0) e^(rt) comes down to whether it is more intuitive to think about the growth rate in discrete time (λ) or continuous time (r).</p>\n","answer_id":115307,"answer_text":"My comments disappeared, so I'll explain here:\n\n\n\n\nThere are two forms of the exponential growth model, in discrete time or continuous time.\n\n\n\n\nA discrete-time model is most appropriate for a population that grows at discrete times in regular intervals, such as an animal that reproduces during a specific breeding season. We only consider t = 0, 1, 2, etc., and not the times in-between. The discrete-time exponential growth model is derived from N(t + 1) = λ N(t), where N(t + 1) is the population 1 time step after N(t) - that is, the population at any one time step is λ times the population at the previous time step. From this, we get N(t) = N(0) λ^t.\n\n\n\n\nA continuous-time model is appropriate when growth happens continuously, without seasonality, etc. - perhaps a human population - or when time steps are negligible relative to the time period of interest. The continuous-time exponential growth model is dN(t)/dt = r N(t) - that is, the population grows at a rate of r times the population. By solving the differential equation, we get N(t) = N(0) e^(rt). Euler's constant comes up because of its unique property, d[e^x]/dx = e^x, so dN(t)/dt = d[N(0) e^(rt)]/dx = r N(0) e^(rt) = r N(t)\n\n\n\n\nThese two models are equivalent when r = ln(λ). (Note that the symbols r and  λ are commonly, but far from always used for these values.) So whether we choose to express the model in as N(t) = N(0) λ^t or N(t) = N(0) e^(rt) comes down to whether it is more intuitive to think about the growth rate in discrete time (λ) or continuous time (r).","answer_url":"https://biology.stackexchange.com/a/115307","author":"Eonema","author_url":"https://biology.stackexchange.com/users/61325/eonema","content_license":"CC BY-SA 4.0","created_at":"2024-09-05T22:24:57+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:25.304620+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/7fe0b66593eb4c0f175024453138b8bd50811f1580a079ffb990af38e09cd1cf_0.json","raw_sha256":"b0a655f3b4c9626cf981180b3ac018a4a26330c5ab9b925b3df78bedd8169a84","source_api":"Stack Exchange API 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tD.</p>\n","answer_id":115313,"answer_text":"Generally you can rearrange the exponential growth equation to get\n\n\n\n\nr = ln(W'/W) / t.\n\n\n\n\nSo indeed if time t = 1 and W'/W = 1.1, then your growth rate would be\n\n\n\n\nr = ln(1.1).\n\n\n\n\nFor example in microbiology frequently also the doubling time tD is used, thereby W'/W = 2 and growth rate r = ln(2) / tD.","answer_url":"https://biology.stackexchange.com/a/115313","author":"silvado","author_url":"https://biology.stackexchange.com/users/2931/silvado","content_license":"CC BY-SA 4.0","created_at":"2024-09-06T11:46:51+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:25.304620+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/7fe0b66593eb4c0f175024453138b8bd50811f1580a079ffb990af38e09cd1cf_0.json","raw_sha256":"b0a655f3b4c9626cf981180b3ac018a4a26330c5ab9b925b3df78bedd8169a84","source_api":"Stack 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growth rate and <span class=\"math-container\">$t$</span> time.</p>\n<p>I wanted to have a clear mathematical understanding. So far according to what I understand, if the size is growing by 10% per unit of time, then the growth rate in the above function should be</p>\n<p><span class=\"math-container\">$$r=\\ln(1.1).$$</span></p>\n<p>Am I right? Considering infinite resources.</p>\n","text":"In my textbook the exponential growth rate is described as\n\n\n\n\n$$W'= W e^{rt}.$$\n\n\n\n\nHere $W'$ is the final size, $W$ initial size, $r$ growth rate and $t$ time.\n\n\n\n\nI wanted to have a clear mathematical understanding. So far according to what I understand, if the size is growing by 10% per unit of time, then the growth rate in the above function should be\n\n\n\n\n$$r=\\ln(1.1).$$\n\n\n\n\nAm I right? Considering infinite resources."},{"context_id":"115307","html":"<p>My comments disappeared, so I'll explain here:</p>\n<p>There are two forms of the exponential growth model, in discrete time or continuous time.</p>\n<p>A discrete-time model is most appropriate for a population that grows at discrete times in regular intervals, such as an animal that reproduces during a specific breeding season. We only consider t = 0, 1, 2, etc., and not the times in-between. The discrete-time exponential growth model is derived from N(t + 1) = λ N(t), where N(t + 1) is the population 1 time step after N(t) - that is, the population at any one time step is λ times the population at the previous time step. From this, we get N(t) = N(0) λ^t.</p>\n<p>A continuous-time model is appropriate when growth happens continuously, without seasonality, etc. - perhaps a human population - or when time steps are negligible relative to the time period of interest. The continuous-time exponential growth model is dN(t)/dt = r N(t) - that is, the population grows at a rate of r times the population. By solving the differential equation, we get N(t) = N(0) e^(rt). Euler's constant comes up because of its unique property, d[e^x]/dx = e^x, so dN(t)/dt = d[N(0) e^(rt)]/dx = r N(0) e^(rt) = r N(t)</p>\n<p>These two models are equivalent when r = ln(λ). (Note that the symbols r and  λ are commonly, but far from always used for these values.) So whether we choose to express the model in as N(t) = N(0) λ^t or N(t) = N(0) e^(rt) comes down to whether it is more intuitive to think about the growth rate in discrete time (λ) or continuous time (r).</p>\n","text":"My comments disappeared, so I'll explain here:\n\n\n\n\nThere are two forms of the exponential growth model, in discrete time or continuous time.\n\n\n\n\nA discrete-time model is most appropriate for a population that grows at discrete times in regular intervals, such as an animal that reproduces during a specific breeding season. We only consider t = 0, 1, 2, etc., and not the times in-between. The discrete-time exponential growth model is derived from N(t + 1) = λ N(t), where N(t + 1) is the population 1 time step after N(t) - that is, the population at any one time step is λ times the population at the previous time step. From this, we get N(t) = N(0) λ^t.\n\n\n\n\nA continuous-time model is appropriate when growth happens continuously, without seasonality, etc. - perhaps a human population - or when time steps are negligible relative to the time period of interest. The continuous-time exponential growth model is dN(t)/dt = r N(t) - that is, the population grows at a rate of r times the population. By solving the differential equation, we get N(t) = N(0) e^(rt). Euler's constant comes up because of its unique property, d[e^x]/dx = e^x, so dN(t)/dt = d[N(0) e^(rt)]/dx = r N(0) e^(rt) = r N(t)\n\n\n\n\nThese two models are equivalent when r = ln(λ). (Note that the symbols r and  λ are commonly, but far from always used for these values.) So whether we choose to express the model in as N(t) = N(0) λ^t or N(t) = N(0) e^(rt) comes down to whether it is more intuitive to think about the growth rate in discrete time (λ) or continuous time (r)."},{"context_id":"115313","html":"<p>Generally you can rearrange the exponential growth equation to get</p>\n<p>r = ln(W'/W) / t.</p>\n<p>So indeed if time t = 1 and W'/W = 1.1, then your growth rate would be</p>\n<p>r = ln(1.1).</p>\n<p>For example in microbiology frequently also the doubling time tD is used, thereby W'/W = 2 and growth rate r = ln(2) / tD.</p>\n","text":"Generally you can rearrange the exponential growth equation to get\n\n\n\n\nr = ln(W'/W) / t.\n\n\n\n\nSo indeed if time t = 1 and W'/W = 1.1, then your growth rate would be\n\n\n\n\nr = ln(1.1).\n\n\n\n\nFor example in microbiology frequently also the doubling time tD is used, thereby W'/W = 2 and growth rate r = ln(2) / tD."}],"domain":"biology","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"a3cec4b5967888c579000a0b4431a8858f59e8673696c078a8502aadf31cc458","hard_case_family":["multiple_answer_candidates"],"id":"RHM-bdf9cb0138e54b3d096d0b89","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:05.762873+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/04ed2aa314c5d877c5d79e42620d1f80988a21de8d429a22d8c6af5280cfd6e8_0.json","raw_sha256":"6dd355b99094bb9ba2c965ee7dd7b0e95f92a8078d3b2b85b64196fcb6cf717c","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=5&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user145522","profile_url":"https://biology.stackexchange.com/users/87194/user145522","user_type":"registered"},"created_at":"2024-09-04T21:30:03+00:00","raw_file":"raw/codex_api_v1/cedb71cd945e8f995b79cadd8e6718011c2863cc935a3a1410ded32d454feeef_1790824099288070500_0.json","raw_sha256":"6569d2607abeaad3ebe6e725128dec16202338bf9cbd6c8013a07c01af6e0905","revision_guid":"2FABE5B1-3F0E-4B19-99C2-CB7787F48740","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2FABE5B1-3F0E-4B19-99C2-CB7787F48740/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user145522","profile_url":"https://biology.stackexchange.com/users/87194/user145522","user_type":"registered"},"created_at":"2024-09-04T21:33:40+00:00","raw_file":"raw/codex_api_v1/cedb71cd945e8f995b79cadd8e6718011c2863cc935a3a1410ded32d454feeef_1790824099288070500_0.json","raw_sha256":"6569d2607abeaad3ebe6e725128dec16202338bf9cbd6c8013a07c01af6e0905","revision_guid":"77FB0FC6-3622-414D-9F8A-D7F36EF09FFC","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/77FB0FC6-3622-414D-9F8A-D7F36EF09FFC/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user145522","profile_url":"https://biology.stackexchange.com/users/87194/user145522","user_type":"registered"},"created_at":"2024-09-04T21:37:10+00:00","raw_file":"raw/codex_api_v1/cedb71cd945e8f995b79cadd8e6718011c2863cc935a3a1410ded32d454feeef_1790824099288070500_0.json","raw_sha256":"6569d2607abeaad3ebe6e725128dec16202338bf9cbd6c8013a07c01af6e0905","revision_guid":"0FC6188A-6DFE-439F-B8DF-9193FBB391F9","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0FC6188A-6DFE-439F-B8DF-9193FBB391F9/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Domen","profile_url":"https://biology.stackexchange.com/users/39423/domen","user_type":"registered"},"created_at":"2024-09-13T09:00:45+00:00","raw_file":"raw/codex_api_v1/cedb71cd945e8f995b79cadd8e6718011c2863cc935a3a1410ded32d454feeef_1790824099288070500_0.json","raw_sha256":"6569d2607abeaad3ebe6e725128dec16202338bf9cbd6c8013a07c01af6e0905","revision_guid":"8B7428DE-9CBB-4968-B703-311970260B49","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8B7428DE-9CBB-4968-B703-311970260B49/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115304","source_record_sha256":"b1c564618f96066baaf364e8fc385d505f93cd6009a392359cbd8f6580579318","source_url":"https://biology.stackexchange.com/questions/115304/what-would-be-the-growth-rate-in-the-following-scenario","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What would be the growth rate in the following scenario?\nIn my textbook the exponential growth rate is described as\n\n\n\n\n$$W'= W e^{rt}.$$\n\n\n\n\nHere $W'$ is the final size, $W$ initial size, $r$ growth rate and $t$ time.\n\n\n\n\nI wanted to have a clear mathematical understanding. So far according to what I understand, if the size is growing by 10% per unit of time, then the growth rate in the above function should be\n\n\n\n\n$$r=\\ln(1.1).$$\n\n\n\n\nAm I right? Considering infinite resources.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115307,"score":0},{"answer_id":115313,"score":0}],"split":"test"}
{"accepted_status":{"accepted_answer_id":115406,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<blockquote>\n<p><strong>Clarification 1:</strong> Is it correct to use the genome size instead of the amplicon size? Should I also use the genome size for my calculations?</p>\n</blockquote>\n<p>The ng concentration of DNA in your sample includes all of the DNA, not just your amplicon, so it depends on which sample type you're converting from. Are you measuring a genomic DNA extraction from bacterial cells or a purified PCR product? Either can technically be used for making a standard curve, but amplicons can be a little problematic. It's more common to use either the whole genome, or a plasmid with the target sequence cloned into it. <a href=\"https://assets.thermofisher.com/TFS-Assets/LSG/Application-Notes/cms_042486.pdf\" rel=\"nofollow noreferrer\">Here's a guide on that</a>. I sometimes purchase synthetic templates from IDT for my standards, but I always include about 30-40 flanking bases on either side of the target, so I have to include those bases in my copy number calculations.</p>\n<blockquote>\n<p><strong>Clarification 2:</strong> When I used the DNA amount and the amplicon size in the formula, the gene copy numbers were extremely high—eleven orders of magnitude higher than the reference, whereas many articles state that it should be closer to eight orders of magnitude. Is this number acceptable?</p>\n</blockquote>\n<p>You're converting from weight to copy number. If you only use the amplicon sequence, you're assuming that 100% of the DNA sample consists of full-length copies of your amplicon (as in a purified PCR product). If it's genomic DNA, then you're actually converting to genome copies, of which only a tiny fraction contains your amplicon sequence. A Pseudomonas genome is at least 4 orders of magnitude larger than your amplicon, so around 99.99% of a gDNA sample is NOT your amplicon sequence (depending on whether or not there are multiple copies on the genome). That alone accounts for the differences your getting between the two calculation methods.</p>\n","answer_id":115406,"answer_text":"Clarification 1: Is it correct to use the genome size instead of the amplicon size? Should I also use the genome size for my calculations?\n\n\n\n\n\n\n\nThe ng concentration of DNA in your sample includes all of the DNA, not just your amplicon, so it depends on which sample type you're converting from. Are you measuring a genomic DNA extraction from bacterial cells or a purified PCR product? Either can technically be used for making a standard curve, but amplicons can be a little problematic. It's more common to use either the whole genome, or a plasmid with the target sequence cloned into it. Here's a guide on that (https://assets.thermofisher.com/TFS-Assets/LSG/Application-Notes/cms_042486.pdf). I sometimes purchase synthetic templates from IDT for my standards, but I always include about 30-40 flanking bases on either side of the target, so I have to include those bases in my copy number calculations.\n\n\n\n\n\n\n\nClarification 2: When I used the DNA amount and the amplicon size in the formula, the gene copy numbers were extremely high—eleven orders of magnitude higher than the reference, whereas many articles state that it should be closer to eight orders of magnitude. Is this number acceptable?\n\n\n\n\n\n\n\nYou're converting from weight to copy number. If you only use the amplicon sequence, you're assuming that 100% of the DNA sample consists of full-length copies of your amplicon (as in a purified PCR product). If it's genomic DNA, then you're actually converting to genome copies, of which only a tiny fraction contains your amplicon sequence. A Pseudomonas genome is at least 4 orders of magnitude larger than your amplicon, so around 99.99% of a gDNA sample is NOT your amplicon sequence (depending on whether or not there are multiple copies on the genome). That alone accounts for the differences your getting between the two calculation methods.","answer_url":"https://biology.stackexchange.com/a/115406","author":"MikeyC","author_url":"https://biology.stackexchange.com/users/56688/mikeyc","content_license":"CC BY-SA 4.0","created_at":"2024-09-24T23:06:16+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:25.304620+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/7fe0b66593eb4c0f175024453138b8bd50811f1580a079ffb990af38e09cd1cf_0.json","raw_sha256":"b0a655f3b4c9626cf981180b3ac018a4a26330c5ab9b925b3df78bedd8169a84","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/115493;115490;115488;115483;115479;115477;115456;115453;115452;115447;115445;115444;115436;115431;115427;115413;115404;115403;115396;115391;115389;115388;115386;115383;115382;115379;115367;115365;115355;115340;115334;115328;115321;115314;115309;115304;115296;115295;115292;115283;115272;115270;115269;115265;115264;115260;115255;115252;115243;115235;115233;115225;115218;115215;115214;115213;115207;115204;115179;115177;115170;115167;115165;115164;115154;115149;115137;115131;115129;115115;115107;115099;115095;115094;115093;115085;115082;115081;115077;115076;115075;115074;115073;115072;115063;115044;115039;115035;115030;115025;115022;115019;115016;115012;115003;115002;114997;114993;114991;114987/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":115403,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"MikeyC","profile_url":"https://biology.stackexchange.com/users/56688/mikeyc","user_type":"registered"},"created_at":"2024-09-24T23:06:16+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"668AEB70-9544-46B6-981C-1CDB2AAAFF46","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/668AEB70-9544-46B6-981C-1CDB2AAAFF46/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"KGee","author_url":"https://biology.stackexchange.com/users/68289/kgee","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"KGee","profile_url":"https://biology.stackexchange.com/users/68289/kgee","user_type":"registered"},"created_at":"2024-09-24T17:05:45+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"9157EFDE-CBCF-4ACD-8878-DB446A1B625A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9157EFDE-CBCF-4ACD-8878-DB446A1B625A/view-source"}],"url":"https://biology.stackexchange.com/questions/115403/clarification-on-gene-copy-number-calculation-amplicon-vs-genome-size"},{"author":"MikeyC","author_url":"https://biology.stackexchange.com/users/56688/mikeyc","content_license":"CC BY-SA 4.0","context_id":"115406","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"MikeyC","profile_url":"https://biology.stackexchange.com/users/56688/mikeyc","user_type":"registered"},"created_at":"2024-09-24T23:06:16+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"668AEB70-9544-46B6-981C-1CDB2AAAFF46","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/668AEB70-9544-46B6-981C-1CDB2AAAFF46/view-source"}],"url":"https://biology.stackexchange.com/a/115406"}],"contexts":[{"context_id":"question","html":"<p>I need clarification regarding gene copy number calculation. I used the <strong>amount of DNA extracted (90 ng/ml)</strong> to calculate the copy number of <em>Pseudomonas sp</em>. <strong>The amplicon size was 164 bp</strong>. I'm using the below formula for my calculations.\n<a href=\"https://www.idtdna.com/pages/education/decoded/article/calculations-converting-from-nanograms-to-copy-number\" rel=\"nofollow noreferrer\">https://www.idtdna.com/pages/education/decoded/article/calculations-converting-from-nanograms-to-copy-number</a>\nwhich uses the length of dsDNA amplicon.</p>\n<p>I addition, I found a webpage where they calculated the copy number using the whole genome as a template.\n<a href=\"https://www.technologynetworks.com/tn/tools/copynumbercalculator\" rel=\"nofollow noreferrer\">https://www.technologynetworks.com/tn/tools/copynumbercalculator</a> --&gt; In definition session there is an example.</p>\n<p><strong>Clarification 1:</strong> Is it correct to use the genome size instead of the amplicon size? Should I also use the genome size for my calculations?</p>\n<p><strong>Clarification 2:</strong> When I used the DNA amount and the amplicon size in the formula, the gene copy numbers were extremely high—eleven orders of magnitude higher than the reference, whereas many articles state that it should be closer to eight orders of magnitude. Is this number acceptable?</p>\n","text":"I need clarification regarding gene copy number calculation. I used the amount of DNA extracted (90 ng/ml) to calculate the copy number of Pseudomonas sp. The amplicon size was 164 bp. I'm using the below formula for my calculations.\nhttps://www.idtdna.com/pages/education/decoded/article/calculations-converting-from-nanograms-to-copy-number (https://www.idtdna.com/pages/education/decoded/article/calculations-converting-from-nanograms-to-copy-number)\nwhich uses the length of dsDNA amplicon.\n\n\n\n\nI addition, I found a webpage where they calculated the copy number using the whole genome as a template.\nhttps://www.technologynetworks.com/tn/tools/copynumbercalculator (https://www.technologynetworks.com/tn/tools/copynumbercalculator) --> In definition session there is an example.\n\n\n\n\nClarification 1: Is it correct to use the genome size instead of the amplicon size? Should I also use the genome size for my calculations?\n\n\n\n\nClarification 2: When I used the DNA amount and the amplicon size in the formula, the gene copy numbers were extremely high—eleven orders of magnitude higher than the reference, whereas many articles state that it should be closer to eight orders of magnitude. Is this number acceptable?"},{"context_id":"115406","html":"<blockquote>\n<p><strong>Clarification 1:</strong> Is it correct to use the genome size instead of the amplicon size? Should I also use the genome size for my calculations?</p>\n</blockquote>\n<p>The ng concentration of DNA in your sample includes all of the DNA, not just your amplicon, so it depends on which sample type you're converting from. Are you measuring a genomic DNA extraction from bacterial cells or a purified PCR product? Either can technically be used for making a standard curve, but amplicons can be a little problematic. It's more common to use either the whole genome, or a plasmid with the target sequence cloned into it. <a href=\"https://assets.thermofisher.com/TFS-Assets/LSG/Application-Notes/cms_042486.pdf\" rel=\"nofollow noreferrer\">Here's a guide on that</a>. I sometimes purchase synthetic templates from IDT for my standards, but I always include about 30-40 flanking bases on either side of the target, so I have to include those bases in my copy number calculations.</p>\n<blockquote>\n<p><strong>Clarification 2:</strong> When I used the DNA amount and the amplicon size in the formula, the gene copy numbers were extremely high—eleven orders of magnitude higher than the reference, whereas many articles state that it should be closer to eight orders of magnitude. Is this number acceptable?</p>\n</blockquote>\n<p>You're converting from weight to copy number. If you only use the amplicon sequence, you're assuming that 100% of the DNA sample consists of full-length copies of your amplicon (as in a purified PCR product). If it's genomic DNA, then you're actually converting to genome copies, of which only a tiny fraction contains your amplicon sequence. A Pseudomonas genome is at least 4 orders of magnitude larger than your amplicon, so around 99.99% of a gDNA sample is NOT your amplicon sequence (depending on whether or not there are multiple copies on the genome). That alone accounts for the differences your getting between the two calculation methods.</p>\n","text":"Clarification 1: Is it correct to use the genome size instead of the amplicon size? Should I also use the genome size for my calculations?\n\n\n\n\n\n\n\nThe ng concentration of DNA in your sample includes all of the DNA, not just your amplicon, so it depends on which sample type you're converting from. Are you measuring a genomic DNA extraction from bacterial cells or a purified PCR product? Either can technically be used for making a standard curve, but amplicons can be a little problematic. It's more common to use either the whole genome, or a plasmid with the target sequence cloned into it. Here's a guide on that (https://assets.thermofisher.com/TFS-Assets/LSG/Application-Notes/cms_042486.pdf). I sometimes purchase synthetic templates from IDT for my standards, but I always include about 30-40 flanking bases on either side of the target, so I have to include those bases in my copy number calculations.\n\n\n\n\n\n\n\nClarification 2: When I used the DNA amount and the amplicon size in the formula, the gene copy numbers were extremely high—eleven orders of magnitude higher than the reference, whereas many articles state that it should be closer to eight orders of magnitude. Is this number acceptable?\n\n\n\n\n\n\n\nYou're converting from weight to copy number. If you only use the amplicon sequence, you're assuming that 100% of the DNA sample consists of full-length copies of your amplicon (as in a purified PCR product). If it's genomic DNA, then you're actually converting to genome copies, of which only a tiny fraction contains your amplicon sequence. A Pseudomonas genome is at least 4 orders of magnitude larger than your amplicon, so around 99.99% of a gDNA sample is NOT your amplicon sequence (depending on whether or not there are multiple copies on the genome). That alone accounts for the differences your getting between the two calculation methods."}],"domain":"biology","external_citations":["https://assets.thermofisher.com/TFS-Assets/LSG/Application-Notes/cms_042486.pdf","https://www.idtdna.com/pages/education/decoded/article/calculations-converting-from-nanograms-to-copy-number","https://www.technologynetworks.com/tn/tools/copynumbercalculator"],"ground_truth_type":"metadata_grounded","group_id":"d9a6fb4e50cd6da4c4e9713b9c86d748ea32ed382a4a71d89303ec1e7ca7775c","hard_case_family":["multiple_sources"],"id":"RHM-b137567652cbd9ed856344de","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:05.762873+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/04ed2aa314c5d877c5d79e42620d1f80988a21de8d429a22d8c6af5280cfd6e8_0.json","raw_sha256":"6dd355b99094bb9ba2c965ee7dd7b0e95f92a8078d3b2b85b64196fcb6cf717c","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=5&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"KGee","profile_url":"https://biology.stackexchange.com/users/68289/kgee","user_type":"registered"},"created_at":"2024-09-24T17:05:45+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"9157EFDE-CBCF-4ACD-8878-DB446A1B625A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9157EFDE-CBCF-4ACD-8878-DB446A1B625A/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115403","source_record_sha256":"50832d8b8801a2d8bd9f483f571ff178fbda5aeb8b3119109b05c468657cc91e","source_url":"https://biology.stackexchange.com/questions/115403/clarification-on-gene-copy-number-calculation-amplicon-vs-genome-size","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Clarification on Gene Copy Number Calculation: Amplicon vs. Genome Size\nI need clarification regarding gene copy number calculation. I used the amount of DNA extracted (90 ng/ml) to calculate the copy number of Pseudomonas sp. The amplicon size was 164 bp. I'm using the below formula for my calculations.\nhttps://www.idtdna.com/pages/education/decoded/article/calculations-converting-from-nanograms-to-copy-number (https://www.idtdna.com/pages/education/decoded/article/calculations-converting-from-nanograms-to-copy-number)\nwhich uses the length of dsDNA amplicon.\n\n\n\n\nI addition, I found a webpage where they calculated the copy number using the whole genome as a template.\nhttps://www.technologynetworks.com/tn/tools/copynumbercalculator (https://www.technologynetworks.com/tn/tools/copynumbercalculator) --> In definition session there is an example.\n\n\n\n\nClarification 1: Is it correct to use the genome size instead of the amplicon size? Should I also use the genome size for my calculations?\n\n\n\n\nClarification 2: When I used the DNA amount and the amplicon size in the formula, the gene copy numbers were extremely high—eleven orders of magnitude higher than the reference, whereas many articles state that it should be closer to eight orders of magnitude. Is this number acceptable?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115406,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":115489,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>That's actually a great question, and it makes a lot of sense to wonder why we don't see histones, methyl groups, or transcription factors in Rosalind Franklin's famous Photo 51. The key to understanding this lies in the context of the experiment and the type of DNA Franklin was studying.\n<a href=\"https://i.sstatic.net/QeubiDnZ.webp\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/QeubiDnZ.webp\" alt=\"enter image description here\" /></a></p>\n<p><a href=\"https://i.sstatic.net/0D34i7CY.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/0D34i7CY.png\" alt=\"enter image description here\" /></a></p>\n<p>When Franklin took the X-ray diffraction image that became Photo 51, she was working with highly purified DNA fibers, not DNA from inside a living cell. This purified DNA had been isolated by the Swiss scientist Rudolf Signer and was stripped of any proteins, histones, or other cellular components like transcription factors. The DNA was essentially &quot;naked&quot; and free from the structures it normally associates with inside the nucleus.</p>\n<p>Another important point is that X-ray diffraction only reveals the overall repeating structure of molecules, especially those that form highly ordered, crystalline or <a href=\"https://en.wikipedia.org/wiki/Paracrystallinity\" rel=\"nofollow noreferrer\">paracrystalline</a> patterns. In Franklin's case, she hydrated the DNA just enough to form a paracrystalline structure, where the molecules were aligned in a regular, repeating pattern. The repeating nature of DNA's helical structure is what generated the characteristic &quot;X&quot; shape in Photo 51, which provided critical information about the double helix.</p>\n<p>Histones, transcription factors, or even methyl groups would not form such regular, repeating patterns. They are more varied in size and shape, and they don't contribute to a uniform diffraction pattern like the helical backbone of DNA does. Furthermore, their presence would have been too sparse or irregular to significantly affect the X-ray diffraction image. In the purified conditions Franklin was working with, these additional elements weren't present to interfere with the image, which is why they didn't show up.</p>\n<p>So, the reason why you don't see those other components in Photo 51 is simply because Franklin was working with DNA in a highly purified, idealized form, and the X-ray diffraction method specifically highlighted the repeating, regular structure of the DNA itself.</p>\n","answer_id":115489,"answer_text":"That's actually a great question, and it makes a lot of sense to wonder why we don't see histones, methyl groups, or transcription factors in Rosalind Franklin's famous Photo 51. The key to understanding this lies in the context of the experiment and the type of DNA Franklin was studying.\n[image: enter image description here; source: https://i.sstatic.net/QeubiDnZ.webp] (https://i.sstatic.net/QeubiDnZ.webp)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/0D34i7CY.png] (https://i.sstatic.net/0D34i7CY.png)\n\n\n\n\nWhen Franklin took the X-ray diffraction image that became Photo 51, she was working with highly purified DNA fibers, not DNA from inside a living cell. This purified DNA had been isolated by the Swiss scientist Rudolf Signer and was stripped of any proteins, histones, or other cellular components like transcription factors. The DNA was essentially \"naked\" and free from the structures it normally associates with inside the nucleus.\n\n\n\n\nAnother important point is that X-ray diffraction only reveals the overall repeating structure of molecules, especially those that form highly ordered, crystalline or paracrystalline (https://en.wikipedia.org/wiki/Paracrystallinity) patterns. In Franklin's case, she hydrated the DNA just enough to form a paracrystalline structure, where the molecules were aligned in a regular, repeating pattern. The repeating nature of DNA's helical structure is what generated the characteristic \"X\" shape in Photo 51, which provided critical information about the double helix.\n\n\n\n\nHistones, transcription factors, or even methyl groups would not form such regular, repeating patterns. They are more varied in size and shape, and they don't contribute to a uniform diffraction pattern like the helical backbone of DNA does. Furthermore, their presence would have been too sparse or irregular to significantly affect the X-ray diffraction image. In the purified conditions Franklin was working with, these additional elements weren't present to interfere with the image, which is why they didn't show up.\n\n\n\n\nSo, the reason why you don't see those other components in Photo 51 is simply because Franklin was working with DNA in a highly purified, idealized form, and the X-ray diffraction method specifically highlighted the repeating, regular structure of the DNA itself.","answer_url":"https://biology.stackexchange.com/a/115489","author":"Circuit Sage","author_url":"https://biology.stackexchange.com/users/90746/circuit-sage","content_license":"CC BY-SA 4.0","created_at":"2024-10-16T06:23:36+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:25.304620+00:00","license":"CC BY-SA 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Sage","profile_url":"https://biology.stackexchange.com/users/90746/circuit-sage","user_type":"registered"},"created_at":"2024-10-16T06:29:32+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"5ACFCCBF-2D86-4440-8153-515E0AC2CABC","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5ACFCCBF-2D86-4440-8153-515E0AC2CABC/view-source"},{"content_license":null,"contributor":{"display_name":"AliceD","profile_url":"https://biology.stackexchange.com/users/9943/aliced","user_type":"registered"},"created_at":"2024-10-17T09:15:54+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"442564BD-DB2A-45FE-93C7-CC8B8831A707","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/442564BD-DB2A-45FE-93C7-CC8B8831A707/view-source"},{"content_license":"CC 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Sage","profile_url":"https://biology.stackexchange.com/users/90746/circuit-sage","user_type":"registered"},"created_at":"2024-10-16T06:23:36+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"58A8848C-E746-40DB-A9D1-5743E24E4D0A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/58A8848C-E746-40DB-A9D1-5743E24E4D0A/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Circuit 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BY-SA 4.0","contributor":{"display_name":"uhoh","profile_url":"https://biology.stackexchange.com/users/27918/uhoh","user_type":"registered"},"created_at":"2024-10-19T01:31:31+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"482A8FEE-69AF-4A96-AF96-B57AADE3E988","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/482A8FEE-69AF-4A96-AF96-B57AADE3E988/view-source"}],"url":"https://biology.stackexchange.com/a/115489"}],"contexts":[{"context_id":"question","html":"<p>When DNA is condensing, it wraps around histones, where it can also be methylated with the addition of a methyl group. On top of this, DNA has transcription factors which determine what can be transcribed into RNA.</p>\n<p>I understand that Rosalind Franklin had pure DNA from <a href=\"https://www.nature.com/articles/d41586-023-01313-5\" rel=\"nofollow noreferrer\">Signer which she converted to a paracrystalline form by raising the humidity of the specimen.</a> How was it that none of these structures that we know DNA attaches to or are attached to DNA didn't show up in photo 51?</p>\n","text":"When DNA is condensing, it wraps around histones, where it can also be methylated with the addition of a methyl group. On top of this, DNA has transcription factors which determine what can be transcribed into RNA.\n\n\n\n\nI understand that Rosalind Franklin had pure DNA from Signer which she converted to a paracrystalline form by raising the humidity of the specimen. (https://www.nature.com/articles/d41586-023-01313-5) How was it that none of these structures that we know DNA attaches to or are attached to DNA didn't show up in photo 51?"},{"context_id":"115489","html":"<p>That's actually a great question, and it makes a lot of sense to wonder why we don't see histones, methyl groups, or transcription factors in Rosalind Franklin's famous Photo 51. The key to understanding this lies in the context of the experiment and the type of DNA Franklin was studying.\n<a href=\"https://i.sstatic.net/QeubiDnZ.webp\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/QeubiDnZ.webp\" alt=\"enter image description here\" /></a></p>\n<p><a href=\"https://i.sstatic.net/0D34i7CY.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/0D34i7CY.png\" alt=\"enter image description here\" /></a></p>\n<p>When Franklin took the X-ray diffraction image that became Photo 51, she was working with highly purified DNA fibers, not DNA from inside a living cell. This purified DNA had been isolated by the Swiss scientist Rudolf Signer and was stripped of any proteins, histones, or other cellular components like transcription factors. The DNA was essentially &quot;naked&quot; and free from the structures it normally associates with inside the nucleus.</p>\n<p>Another important point is that X-ray diffraction only reveals the overall repeating structure of molecules, especially those that form highly ordered, crystalline or <a href=\"https://en.wikipedia.org/wiki/Paracrystallinity\" rel=\"nofollow noreferrer\">paracrystalline</a> patterns. In Franklin's case, she hydrated the DNA just enough to form a paracrystalline structure, where the molecules were aligned in a regular, repeating pattern. The repeating nature of DNA's helical structure is what generated the characteristic &quot;X&quot; shape in Photo 51, which provided critical information about the double helix.</p>\n<p>Histones, transcription factors, or even methyl groups would not form such regular, repeating patterns. They are more varied in size and shape, and they don't contribute to a uniform diffraction pattern like the helical backbone of DNA does. Furthermore, their presence would have been too sparse or irregular to significantly affect the X-ray diffraction image. In the purified conditions Franklin was working with, these additional elements weren't present to interfere with the image, which is why they didn't show up.</p>\n<p>So, the reason why you don't see those other components in Photo 51 is simply because Franklin was working with DNA in a highly purified, idealized form, and the X-ray diffraction method specifically highlighted the repeating, regular structure of the DNA itself.</p>\n","text":"That's actually a great question, and it makes a lot of sense to wonder why we don't see histones, methyl groups, or transcription factors in Rosalind Franklin's famous Photo 51. The key to understanding this lies in the context of the experiment and the type of DNA Franklin was studying.\n[image: enter image description here; source: https://i.sstatic.net/QeubiDnZ.webp] (https://i.sstatic.net/QeubiDnZ.webp)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/0D34i7CY.png] (https://i.sstatic.net/0D34i7CY.png)\n\n\n\n\nWhen Franklin took the X-ray diffraction image that became Photo 51, she was working with highly purified DNA fibers, not DNA from inside a living cell. This purified DNA had been isolated by the Swiss scientist Rudolf Signer and was stripped of any proteins, histones, or other cellular components like transcription factors. The DNA was essentially \"naked\" and free from the structures it normally associates with inside the nucleus.\n\n\n\n\nAnother important point is that X-ray diffraction only reveals the overall repeating structure of molecules, especially those that form highly ordered, crystalline or paracrystalline (https://en.wikipedia.org/wiki/Paracrystallinity) patterns. In Franklin's case, she hydrated the DNA just enough to form a paracrystalline structure, where the molecules were aligned in a regular, repeating pattern. The repeating nature of DNA's helical structure is what generated the characteristic \"X\" shape in Photo 51, which provided critical information about the double helix.\n\n\n\n\nHistones, transcription factors, or even methyl groups would not form such regular, repeating patterns. They are more varied in size and shape, and they don't contribute to a uniform diffraction pattern like the helical backbone of DNA does. Furthermore, their presence would have been too sparse or irregular to significantly affect the X-ray diffraction image. In the purified conditions Franklin was working with, these additional elements weren't present to interfere with the image, which is why they didn't show up.\n\n\n\n\nSo, the reason why you don't see those other components in Photo 51 is simply because Franklin was working with DNA in a highly purified, idealized form, and the X-ray diffraction method specifically highlighted the repeating, regular structure of the DNA itself."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Paracrystallinity","https://i.sstatic.net/0D34i7CY.png","https://i.sstatic.net/QeubiDnZ.webp","https://www.nature.com/articles/d41586-023-01313-5"],"ground_truth_type":"metadata_grounded","group_id":"91369b8f249dec6e767a0ad24ebba607398a05d232a2e46d35cf44e5aeaa8a79","hard_case_family":["multiple_sources"],"id":"RHM-cef5ad1c7c1e698af21cd0c2","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:05.762873+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/04ed2aa314c5d877c5d79e42620d1f80988a21de8d429a22d8c6af5280cfd6e8_0.json","raw_sha256":"6dd355b99094bb9ba2c965ee7dd7b0e95f92a8078d3b2b85b64196fcb6cf717c","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=5&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"andy","profile_url":"https://biology.stackexchange.com/users/65288/andy","user_type":"registered"},"created_at":"2024-10-16T04:34:34+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"FC9A413A-8EFC-4D08-9D67-EF174BD8D9C6","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FC9A413A-8EFC-4D08-9D67-EF174BD8D9C6/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-10-16T12:34:48+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"7FEE7B3E-7FD1-4827-AE4A-F5459FA50A69","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/7FEE7B3E-7FD1-4827-AE4A-F5459FA50A69/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"terdon","profile_url":"https://biology.stackexchange.com/users/1306/terdon","user_type":"moderator"},"created_at":"2024-10-16T14:01:50+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"8DE5DCF6-7ADC-4143-BBC5-6B713A1800D1","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8DE5DCF6-7ADC-4143-BBC5-6B713A1800D1/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2024-10-20T15:40:04+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"AF039BEC-C95E-4E6C-8353-D4383BA5186B","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AF039BEC-C95E-4E6C-8353-D4383BA5186B/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115488","source_record_sha256":"8c8392d511c7a804ab7a3e6df48cb9195d2ddbe1be8591fc88834dbdb3cf4505","source_url":"https://biology.stackexchange.com/questions/115488/why-didnt-rosalind-franklins-x-ray-crystallography-photograph-contain-any-hist","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Why didn't Rosalind Franklin's X-Ray crystallography photograph contain any histones, methyl groups, or transcription factors?\nWhen DNA is condensing, it wraps around histones, where it can also be methylated with the addition of a methyl group. On top of this, DNA has transcription factors which determine what can be transcribed into RNA.\n\n\n\n\nI understand that Rosalind Franklin had pure DNA from Signer which she converted to a paracrystalline form by raising the humidity of the specimen. (https://www.nature.com/articles/d41586-023-01313-5) How was it that none of these structures that we know DNA attaches to or are attached to DNA didn't show up in photo 51?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115489,"score":21}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Well, a cell requires nucleus for growth, modification and maturation. Once the cell has attained its size and functionality, nucleus is not a necessity. As you know RBCs carry oxygen (also carbon dioxide in a different form, about 20 -25 percent), space is required for it. So, to increase the capacity of the RBCs to carry more oxygen, by increasing the space to accommodate more haemoglobin, nucleus is destroyed in an RBC. The avg. lifespan of an RBC is 120 days. so, for 120 days, it can function without the nucleus.<br><br> You may think of other examples of cells that don't contain nucleus like Sieve cells of phloem etc.</p>\n","answer_id":115492,"answer_text":"Well, a cell requires nucleus for growth, modification and maturation. Once the cell has attained its size and functionality, nucleus is not a necessity. As you know RBCs carry oxygen (also carbon dioxide in a different form, about 20 -25 percent), space is required for it. So, to increase the capacity of the RBCs to carry more oxygen, by increasing the space to accommodate more haemoglobin, nucleus is destroyed in an RBC. The avg. lifespan of an RBC is 120 days. so, for 120 days, it can function without the nucleus.\n\n You may think of other examples of cells that don't contain nucleus like Sieve cells of phloem etc.","answer_url":"https://biology.stackexchange.com/a/115492","author":"Hrishikesh","author_url":"https://biology.stackexchange.com/users/90874/hrishikesh","content_license":"CC BY-SA 4.0","created_at":"2024-10-16T15:20:03+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:26.693224+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/202c0322d4dfac9d4b1c407daba4209579e5cfe73de17e5d578734e1f3315727_0.json","raw_sha256":"63f5bd02e37151da0b36b32c57da219bbcfbb084387a964a28411ca327805827","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/115493;115490;115488;115483;115479;115477;115456;115453;115452;115447;115445;115444;115436;115431;115427;115413;115404;115403;115396;115391;115389;115388;115386;115383;115382;115379;115367;115365;115355;115340;115334;115328;115321;115314;115309;115304;115296;115295;115292;115283;115272;115270;115269;115265;115264;115260;115255;115252;115243;115235;115233;115225;115218;115215;115214;115213;115207;115204;115179;115177;115170;115167;115165;115164;115154;115149;115137;115131;115129;115115;115107;115099;115095;115094;115093;115085;115082;115081;115077;115076;115075;115074;115073;115072;115063;115044;115039;115035;115030;115025;115022;115019;115016;115012;115003;115002;114997;114993;114991;114987/answers?filter=withbody&order=asc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":115490,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Hrishikesh","profile_url":"https://biology.stackexchange.com/users/90874/hrishikesh","user_type":"registered"},"created_at":"2024-10-16T15:20:03+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"885CF551-4ECE-4236-82DC-43B45C41EABA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/885CF551-4ECE-4236-82DC-43B45C41EABA/view-source"},{"content_license":null,"contributor":{"display_name":"AliceD","profile_url":"https://biology.stackexchange.com/users/9943/aliced","user_type":"registered"},"created_at":"2024-10-22T13:12:18+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"E4AF0735-F46A-481B-BA49-13D93E969DFB","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/E4AF0735-F46A-481B-BA49-13D93E969DFB/view-source"}],"score":-1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Iris","author_url":"https://biology.stackexchange.com/users/90855/iris","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Iris","profile_url":"https://biology.stackexchange.com/users/90855/iris","user_type":"registered"},"created_at":"2024-10-16T11:16:45+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"1D85ED80-72C7-412D-A7D1-AF12F404E19F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/1D85ED80-72C7-412D-A7D1-AF12F404E19F/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user394522","profile_url":"https://biology.stackexchange.com/users/78594/user394522","user_type":"registered"},"created_at":"2024-10-18T11:21:09+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"61C2861E-5F98-4425-9E37-A1B4342352D1","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/61C2861E-5F98-4425-9E37-A1B4342352D1/view-source"}],"url":"https://biology.stackexchange.com/questions/115490/why-does-the-nucleus-not-exist-in-mature-red-blood-cells"},{"author":"Hrishikesh","author_url":"https://biology.stackexchange.com/users/90874/hrishikesh","content_license":"CC BY-SA 4.0","context_id":"115492","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Hrishikesh","profile_url":"https://biology.stackexchange.com/users/90874/hrishikesh","user_type":"registered"},"created_at":"2024-10-16T15:20:03+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"885CF551-4ECE-4236-82DC-43B45C41EABA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/885CF551-4ECE-4236-82DC-43B45C41EABA/view-source"},{"content_license":null,"contributor":{"display_name":"AliceD","profile_url":"https://biology.stackexchange.com/users/9943/aliced","user_type":"registered"},"created_at":"2024-10-22T13:12:18+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"E4AF0735-F46A-481B-BA49-13D93E969DFB","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/E4AF0735-F46A-481B-BA49-13D93E969DFB/view-source"}],"url":"https://biology.stackexchange.com/a/115492"}],"contexts":[{"context_id":"question","html":"<p>I'm currently a high schooler learning biology. I just wanted to know why does the nucleus not exist in mature red blood cells. It would be great if someone answered my question in a basic way as I have not learnt it in depth yet, just wanted to understand the basics first. Thanks in advance for your help. :)</p>\n","text":"I'm currently a high schooler learning biology. I just wanted to know why does the nucleus not exist in mature red blood cells. It would be great if someone answered my question in a basic way as I have not learnt it in depth yet, just wanted to understand the basics first. Thanks in advance for your help. :)"},{"context_id":"115492","html":"<p>Well, a cell requires nucleus for growth, modification and maturation. Once the cell has attained its size and functionality, nucleus is not a necessity. As you know RBCs carry oxygen (also carbon dioxide in a different form, about 20 -25 percent), space is required for it. So, to increase the capacity of the RBCs to carry more oxygen, by increasing the space to accommodate more haemoglobin, nucleus is destroyed in an RBC. The avg. lifespan of an RBC is 120 days. so, for 120 days, it can function without the nucleus.<br><br> You may think of other examples of cells that don't contain nucleus like Sieve cells of phloem etc.</p>\n","text":"Well, a cell requires nucleus for growth, modification and maturation. Once the cell has attained its size and functionality, nucleus is not a necessity. As you know RBCs carry oxygen (also carbon dioxide in a different form, about 20 -25 percent), space is required for it. So, to increase the capacity of the RBCs to carry more oxygen, by increasing the space to accommodate more haemoglobin, nucleus is destroyed in an RBC. The avg. lifespan of an RBC is 120 days. so, for 120 days, it can function without the nucleus.\n\n You may think of other examples of cells that don't contain nucleus like Sieve cells of phloem etc."}],"domain":"biology","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"ef07f042094a9b15ecf450ededf89adefb742d679ceb67818a4ef425a9a4e4b0","hard_case_family":["no_accepted_answer"],"id":"RHM-f6ea8a22d7cbe8179a929b98","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:05.762873+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/04ed2aa314c5d877c5d79e42620d1f80988a21de8d429a22d8c6af5280cfd6e8_0.json","raw_sha256":"6dd355b99094bb9ba2c965ee7dd7b0e95f92a8078d3b2b85b64196fcb6cf717c","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=5&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Iris","profile_url":"https://biology.stackexchange.com/users/90855/iris","user_type":"registered"},"created_at":"2024-10-16T11:16:45+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"1D85ED80-72C7-412D-A7D1-AF12F404E19F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/1D85ED80-72C7-412D-A7D1-AF12F404E19F/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user394522","profile_url":"https://biology.stackexchange.com/users/78594/user394522","user_type":"registered"},"created_at":"2024-10-18T11:21:09+00:00","raw_file":"raw/codex_api_v1/43e0404e391fda3d45541a0db7438bd3a1c2df66d07b9f1a745a1d6a3713c815_1790824097103199200_0.json","raw_sha256":"e55dfe05ee755247d42e0fe87b0ef88822dd9b82f6af36ed5017c907e0ff3823","revision_guid":"61C2861E-5F98-4425-9E37-A1B4342352D1","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/61C2861E-5F98-4425-9E37-A1B4342352D1/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115490","source_record_sha256":"0e5797195bf8d6eddabdaf808f2151737e06617553dc85af4673fbad18a270e7","source_url":"https://biology.stackexchange.com/questions/115490/why-does-the-nucleus-not-exist-in-mature-red-blood-cells","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Why does the nucleus not exist in mature red blood cells?\nI'm currently a high schooler learning biology. I just wanted to know why does the nucleus not exist in mature red blood cells. It would be great if someone answered my question in a basic way as I have not learnt it in depth yet, just wanted to understand the basics first. Thanks in advance for your help. :)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115492,"score":-1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":115697,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>In an answer to <a href=\"https://biology.stackexchange.com/questions/10737/why-do-organisms-excrete-nitrogenous-wastes/92410#92410\">a previous evolutionary ”why“ question</a> I devoted a paragraph to the general problem with questions of the type “Why has such and such not evolved, it would obviously be advantageous?”. Two points I made were:</p>\n<ul>\n<li>“It would be too difficult, costly or would have disadvantageous consequences”</li>\n</ul>\n<p><em>and/or</em></p>\n<ul>\n<li>“The assumption that it would convey a selective advantage… is incorrect.”</li>\n</ul>\n<p>In the present case both apply. A mechanism that evolved for elimination of ammonia in a particular species would be fixed if it did just that. <em>Not</em> if it also <em>might</em> do something else for which the organism already has highly evolved and sophisticated machinery†. And it is worth my repeating that the idea that energy costs are a limiting factory in the evolution of multicellular organisms is false. We are not bacteria competing for a limited supply of nutrients so we can procreate more rapidly. We have energy to “waste” (and long gestation periods).</p>\n<p>Second, the fact that so few organisms can oxidize ammonia to nitrogen implies that this is a multistep conversion with chemical difficulties that can only be overcome in certain environmental niches. In contrast, the urea cycle is built up largely from pre-existing part reactions that had already evolved in a wide range of bacteria (see, e.g. this <a href=\"https://onlinelibrary.wiley.com/doi/10.1002/bies.950100506\" rel=\"noreferrer\">Bioessay review</a>). The key reaction that produces carbamoyl phosphate from ammonia and bicarbonate has a counterpart in pyrimidine synthesis, and although there are separate enzymes for these processes in eukaryotes (pyrimidine synthesis uses glutamine, rather than ammonia) a single bifunctional enzyme is found in bacteria (<em>see</em> the Wikipedia entry for <a href=\"https://en.wikipedia.org/wiki/Carbamoyl_phosphate_synthetase\" rel=\"noreferrer\">carbamoyl phosphate synthetase</a>).</p>\n<p>† I have not dealt with possible problems mentioned by the poster regarding the generation of nitrogen gas in the blood as these are only secondary to my main points, which would exclude the idea from the start.</p>\n","answer_id":115697,"answer_text":"In an answer to a previous evolutionary ”why“ question (https://biology.stackexchange.com/questions/10737/why-do-organisms-excrete-nitrogenous-wastes/92410#92410) I devoted a paragraph to the general problem with questions of the type “Why has such and such not evolved, it would obviously be advantageous?”. Two points I made were:\n\n\n\n\n\n“It would be too difficult, costly or would have disadvantageous consequences”\n\n\n\n\n\nand/or\n\n\n\n\n\n“The assumption that it would convey a selective advantage… is incorrect.”\n\n\n\n\n\nIn the present case both apply. A mechanism that evolved for elimination of ammonia in a particular species would be fixed if it did just that. Not if it also might do something else for which the organism already has highly evolved and sophisticated machinery†. And it is worth my repeating that the idea that energy costs are a limiting factory in the evolution of multicellular organisms is false. We are not bacteria competing for a limited supply of nutrients so we can procreate more rapidly. We have energy to “waste” (and long gestation periods).\n\n\n\n\nSecond, the fact that so few organisms can oxidize ammonia to nitrogen implies that this is a multistep conversion with chemical difficulties that can only be overcome in certain environmental niches. In contrast, the urea cycle is built up largely from pre-existing part reactions that had already evolved in a wide range of bacteria (see, e.g. this Bioessay review (https://onlinelibrary.wiley.com/doi/10.1002/bies.950100506)). The key reaction that produces carbamoyl phosphate from ammonia and bicarbonate has a counterpart in pyrimidine synthesis, and although there are separate enzymes for these processes in eukaryotes (pyrimidine synthesis uses glutamine, rather than ammonia) a single bifunctional enzyme is found in bacteria (see the Wikipedia entry for carbamoyl phosphate synthetase (https://en.wikipedia.org/wiki/Carbamoyl_phosphate_synthetase)).\n\n\n\n\n† I have not dealt with possible problems mentioned by the poster regarding the generation of nitrogen gas in the blood as these are only secondary to my main points, which would exclude the idea from the start.","answer_url":"https://biology.stackexchange.com/a/115697","author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","created_at":"2024-11-26T11:50:17+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:22.614155+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2c8799380b8f5d7bf0fd42e594fd78a1835b27e1da9f481cc00f096bab9c01ca_0.json","raw_sha256":"348375a094fdfd6d9ca55d0bddc65d8dc7a7f0757e1e5a44c25e22a66b1a4892","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/116119;116113;116097;116096;116091;116087;116076;116067;116063;116059;116055;116037;116034;116028;116022;116012;116005;115997;115989;115988;115987;115979;115978;115976;115974;115973;115970;115966;115965;115957;115952;115939;115933;115932;115927;115921;115915;115903;115897;115894;115886;115885;115884;115881;115880;115868;115867;115857;115852;115840;115830;115825;115819;115815;115791;115780;115773;115764;115759;115756;115743;115736;115726;115723;115713;115699;115691;115689;115685;115678;115668;115664;115657;115650;115642;115639;115632;115627;115626;115609;115602;115598;115592;115588;115587;115580;115578;115570;115566;115562;115549;115537;115536;115531;115530;115528;115525;115521;115513;115510/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":115689,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2024-11-26T11:50:17+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"AAE08A83-E66D-41D5-9571-4F1B97454D69","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AAE08A83-E66D-41D5-9571-4F1B97454D69/view-source"}],"score":7},{"answer_html":"<p>Since animals get most of their nitrogen intake through protein / amino acids, breaking that down to molecular nitrogen is a multi-step process. Indeed that breakdown process can provide energy all the way down to the molecular components.</p>\n<p>However, in a multi-step process, if you have limited resources, it is generally speaking an advantage to focus all your resources on the <strong>most efficient step</strong>. This way you can convert more energy than if say you'd put only half of your resources on the most efficient step and the other half in a less efficient step.</p>\n<p>If we are just looking at one of the most basic amino acids, Glutamic acid, we have a Gibbs free energy of formation of -476 kJ/mol (<a href=\"https://chemeo.com\" rel=\"nofollow noreferrer\">chemeo.com</a>). Glutamate can be broken down in a single biochemical reaction to ammonia and a carbohydrate. Ammonia has a Gibbs free energy of formation of -16 kJ/mol, which indicates that the first degradation step provides much more energy than the subsequent steps. Because of this, organisms that get nitrogen in the form of amino acids have an energy-efficiency advantage if they only do the breakdown until ammonia and not all the way to molecular nitrogen.</p>\n<p>Of course that leaves an ecological niche for other organisms to make use of the wasted ammonia and convert the remaining energy there. Actually this is also a multi-step process, which is mostly done by different microbial species (ammonia oxidizer, nitrifyers, and denitrifyers). This has been studied from the perspective of microbial division of labor.</p>\n","answer_id":115708,"answer_text":"Since animals get most of their nitrogen intake through protein / amino acids, breaking that down to molecular nitrogen is a multi-step process. Indeed that breakdown process can provide energy all the way down to the molecular components.\n\n\n\n\nHowever, in a multi-step process, if you have limited resources, it is generally speaking an advantage to focus all your resources on the most efficient step. This way you can convert more energy than if say you'd put only half of your resources on the most efficient step and the other half in a less efficient step.\n\n\n\n\nIf we are just looking at one of the most basic amino acids, Glutamic acid, we have a Gibbs free energy of formation of -476 kJ/mol (chemeo.com (https://chemeo.com)). Glutamate can be broken down in a single biochemical reaction to ammonia and a carbohydrate. Ammonia has a Gibbs free energy of formation of -16 kJ/mol, which indicates that the first degradation step provides much more energy than the subsequent steps. Because of this, organisms that get nitrogen in the form of amino acids have an energy-efficiency advantage if they only do the breakdown until ammonia and not all the way to molecular nitrogen.\n\n\n\n\nOf course that leaves an ecological niche for other organisms to make use of the wasted ammonia and convert the remaining energy there. Actually this is also a multi-step process, which is mostly done by different microbial species (ammonia oxidizer, nitrifyers, and denitrifyers). This has been studied from the perspective of microbial division of labor.","answer_url":"https://biology.stackexchange.com/a/115708","author":"silvado","author_url":"https://biology.stackexchange.com/users/2931/silvado","content_license":"CC BY-SA 4.0","created_at":"2024-11-29T10:51:33+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:22.614155+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2c8799380b8f5d7bf0fd42e594fd78a1835b27e1da9f481cc00f096bab9c01ca_0.json","raw_sha256":"348375a094fdfd6d9ca55d0bddc65d8dc7a7f0757e1e5a44c25e22a66b1a4892","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/116119;116113;116097;116096;116091;116087;116076;116067;116063;116059;116055;116037;116034;116028;116022;116012;116005;115997;115989;115988;115987;115979;115978;115976;115974;115973;115970;115966;115965;115957;115952;115939;115933;115932;115927;115921;115915;115903;115897;115894;115886;115885;115884;115881;115880;115868;115867;115857;115852;115840;115830;115825;115819;115815;115791;115780;115773;115764;115759;115756;115743;115736;115726;115723;115713;115699;115691;115689;115685;115678;115668;115664;115657;115650;115642;115639;115632;115627;115626;115609;115602;115598;115592;115588;115587;115580;115578;115570;115566;115562;115549;115537;115536;115531;115530;115528;115525;115521;115513;115510/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":115689,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"silvado","profile_url":"https://biology.stackexchange.com/users/2931/silvado","user_type":"registered"},"created_at":"2024-11-29T10:51:33+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"37BB19F5-F1E4-41E0-9674-224553478EF1","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/37BB19F5-F1E4-41E0-9674-224553478EF1/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Logan R. Kearsley","author_url":"https://biology.stackexchange.com/users/25805/logan-r-kearsley","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Logan R. Kearsley","profile_url":"https://biology.stackexchange.com/users/25805/logan-r-kearsley","user_type":"registered"},"created_at":"2024-11-24T22:31:12+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"E415493A-48C5-442E-BD74-C794CF3BE75B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E415493A-48C5-442E-BD74-C794CF3BE75B/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Logan R. Kearsley","profile_url":"https://biology.stackexchange.com/users/25805/logan-r-kearsley","user_type":"registered"},"created_at":"2024-11-25T14:23:30+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"4225163C-EF69-4ED7-AC4F-6FFB234B15BC","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4225163C-EF69-4ED7-AC4F-6FFB234B15BC/view-source"}],"url":"https://biology.stackexchange.com/questions/115689/why-do-animals-excrete-organic-nitrogen-compounds-instead-of-n2-gas"},{"author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","context_id":"115697","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2024-11-26T11:50:17+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"AAE08A83-E66D-41D5-9571-4F1B97454D69","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AAE08A83-E66D-41D5-9571-4F1B97454D69/view-source"}],"url":"https://biology.stackexchange.com/a/115697"},{"author":"silvado","author_url":"https://biology.stackexchange.com/users/2931/silvado","content_license":"CC BY-SA 4.0","context_id":"115708","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"silvado","profile_url":"https://biology.stackexchange.com/users/2931/silvado","user_type":"registered"},"created_at":"2024-11-29T10:51:33+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"37BB19F5-F1E4-41E0-9674-224553478EF1","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/37BB19F5-F1E4-41E0-9674-224553478EF1/view-source"}],"url":"https://biology.stackexchange.com/a/115708"}],"contexts":[{"context_id":"question","html":"<p>Protein metabolism produces ammonia, which needs to be disposed of; but oxidation of ammonia into water and dinitrogen produces energy, while creating urea or uric acid consumes energy, and excreting it expands water. So, it seems like there would be some small advantage to animals exhaling N2 instead of excreting nitrogen in liquid or solid form. Nevertheless, no animal does so, and as far as I know, the only organisms that <em>do</em> are denitrifying bacteria and archaea.</p>\n<p>So, is there a good reason why animals <em>shouldn't</em> produce nitrogen gas? bother with that, rather than just exhaling nitrogen gas? Or is it just a matter of &quot;<a href=\"https://biology.stackexchange.com/q/35532/5198\">evolution isn't directed</a>&quot;--a random quirk that the ancestors of animals didn't happen to develop ammonia-oxidizing pathways?</p>\n<p>There are a few reasons I can think of, or that have been suggested to me, that nitrogen production might actually be deleterious, but I can't find references to back up any of them:</p>\n<ol>\n<li>Nitrogen has low solubility, and bubbles in blood or tissues are bad. Would this actually be a limiting factor?</li>\n<li>The pathways that oxidize ammonia in microbes might interfere with other parts of animalian metabolism. I have absolutely no idea how plausible this is.</li>\n<li>The energy gain from oxidizing ammonia may be too small to justify the cost of maintaining metabolic machinery for it.</li>\n</ol>\n<p>So, is there any actual science on this?</p>\n","text":"Protein metabolism produces ammonia, which needs to be disposed of; but oxidation of ammonia into water and dinitrogen produces energy, while creating urea or uric acid consumes energy, and excreting it expands water. So, it seems like there would be some small advantage to animals exhaling N2 instead of excreting nitrogen in liquid or solid form. Nevertheless, no animal does so, and as far as I know, the only organisms that do are denitrifying bacteria and archaea.\n\n\n\n\nSo, is there a good reason why animals shouldn't produce nitrogen gas? bother with that, rather than just exhaling nitrogen gas? Or is it just a matter of \"evolution isn't directed (https://biology.stackexchange.com/q/35532/5198)\"--a random quirk that the ancestors of animals didn't happen to develop ammonia-oxidizing pathways?\n\n\n\n\nThere are a few reasons I can think of, or that have been suggested to me, that nitrogen production might actually be deleterious, but I can't find references to back up any of them:\n\n\n\n\n\nNitrogen has low solubility, and bubbles in blood or tissues are bad. Would this actually be a limiting factor?\n\n\n\n\nThe pathways that oxidize ammonia in microbes might interfere with other parts of animalian metabolism. I have absolutely no idea how plausible this is.\n\n\n\n\nThe energy gain from oxidizing ammonia may be too small to justify the cost of maintaining metabolic machinery for it.\n\n\n\n\n\nSo, is there any actual science on this?"},{"context_id":"115697","html":"<p>In an answer to <a href=\"https://biology.stackexchange.com/questions/10737/why-do-organisms-excrete-nitrogenous-wastes/92410#92410\">a previous evolutionary ”why“ question</a> I devoted a paragraph to the general problem with questions of the type “Why has such and such not evolved, it would obviously be advantageous?”. Two points I made were:</p>\n<ul>\n<li>“It would be too difficult, costly or would have disadvantageous consequences”</li>\n</ul>\n<p><em>and/or</em></p>\n<ul>\n<li>“The assumption that it would convey a selective advantage… is incorrect.”</li>\n</ul>\n<p>In the present case both apply. A mechanism that evolved for elimination of ammonia in a particular species would be fixed if it did just that. <em>Not</em> if it also <em>might</em> do something else for which the organism already has highly evolved and sophisticated machinery†. And it is worth my repeating that the idea that energy costs are a limiting factory in the evolution of multicellular organisms is false. We are not bacteria competing for a limited supply of nutrients so we can procreate more rapidly. We have energy to “waste” (and long gestation periods).</p>\n<p>Second, the fact that so few organisms can oxidize ammonia to nitrogen implies that this is a multistep conversion with chemical difficulties that can only be overcome in certain environmental niches. In contrast, the urea cycle is built up largely from pre-existing part reactions that had already evolved in a wide range of bacteria (see, e.g. this <a href=\"https://onlinelibrary.wiley.com/doi/10.1002/bies.950100506\" rel=\"noreferrer\">Bioessay review</a>). The key reaction that produces carbamoyl phosphate from ammonia and bicarbonate has a counterpart in pyrimidine synthesis, and although there are separate enzymes for these processes in eukaryotes (pyrimidine synthesis uses glutamine, rather than ammonia) a single bifunctional enzyme is found in bacteria (<em>see</em> the Wikipedia entry for <a href=\"https://en.wikipedia.org/wiki/Carbamoyl_phosphate_synthetase\" rel=\"noreferrer\">carbamoyl phosphate synthetase</a>).</p>\n<p>† I have not dealt with possible problems mentioned by the poster regarding the generation of nitrogen gas in the blood as these are only secondary to my main points, which would exclude the idea from the start.</p>\n","text":"In an answer to a previous evolutionary ”why“ question (https://biology.stackexchange.com/questions/10737/why-do-organisms-excrete-nitrogenous-wastes/92410#92410) I devoted a paragraph to the general problem with questions of the type “Why has such and such not evolved, it would obviously be advantageous?”. Two points I made were:\n\n\n\n\n\n“It would be too difficult, costly or would have disadvantageous consequences”\n\n\n\n\n\nand/or\n\n\n\n\n\n“The assumption that it would convey a selective advantage… is incorrect.”\n\n\n\n\n\nIn the present case both apply. A mechanism that evolved for elimination of ammonia in a particular species would be fixed if it did just that. Not if it also might do something else for which the organism already has highly evolved and sophisticated machinery†. And it is worth my repeating that the idea that energy costs are a limiting factory in the evolution of multicellular organisms is false. We are not bacteria competing for a limited supply of nutrients so we can procreate more rapidly. We have energy to “waste” (and long gestation periods).\n\n\n\n\nSecond, the fact that so few organisms can oxidize ammonia to nitrogen implies that this is a multistep conversion with chemical difficulties that can only be overcome in certain environmental niches. In contrast, the urea cycle is built up largely from pre-existing part reactions that had already evolved in a wide range of bacteria (see, e.g. this Bioessay review (https://onlinelibrary.wiley.com/doi/10.1002/bies.950100506)). The key reaction that produces carbamoyl phosphate from ammonia and bicarbonate has a counterpart in pyrimidine synthesis, and although there are separate enzymes for these processes in eukaryotes (pyrimidine synthesis uses glutamine, rather than ammonia) a single bifunctional enzyme is found in bacteria (see the Wikipedia entry for carbamoyl phosphate synthetase (https://en.wikipedia.org/wiki/Carbamoyl_phosphate_synthetase)).\n\n\n\n\n† I have not dealt with possible problems mentioned by the poster regarding the generation of nitrogen gas in the blood as these are only secondary to my main points, which would exclude the idea from the start."},{"context_id":"115708","html":"<p>Since animals get most of their nitrogen intake through protein / amino acids, breaking that down to molecular nitrogen is a multi-step process. Indeed that breakdown process can provide energy all the way down to the molecular components.</p>\n<p>However, in a multi-step process, if you have limited resources, it is generally speaking an advantage to focus all your resources on the <strong>most efficient step</strong>. This way you can convert more energy than if say you'd put only half of your resources on the most efficient step and the other half in a less efficient step.</p>\n<p>If we are just looking at one of the most basic amino acids, Glutamic acid, we have a Gibbs free energy of formation of -476 kJ/mol (<a href=\"https://chemeo.com\" rel=\"nofollow noreferrer\">chemeo.com</a>). Glutamate can be broken down in a single biochemical reaction to ammonia and a carbohydrate. Ammonia has a Gibbs free energy of formation of -16 kJ/mol, which indicates that the first degradation step provides much more energy than the subsequent steps. Because of this, organisms that get nitrogen in the form of amino acids have an energy-efficiency advantage if they only do the breakdown until ammonia and not all the way to molecular nitrogen.</p>\n<p>Of course that leaves an ecological niche for other organisms to make use of the wasted ammonia and convert the remaining energy there. Actually this is also a multi-step process, which is mostly done by different microbial species (ammonia oxidizer, nitrifyers, and denitrifyers). This has been studied from the perspective of microbial division of labor.</p>\n","text":"Since animals get most of their nitrogen intake through protein / amino acids, breaking that down to molecular nitrogen is a multi-step process. Indeed that breakdown process can provide energy all the way down to the molecular components.\n\n\n\n\nHowever, in a multi-step process, if you have limited resources, it is generally speaking an advantage to focus all your resources on the most efficient step. This way you can convert more energy than if say you'd put only half of your resources on the most efficient step and the other half in a less efficient step.\n\n\n\n\nIf we are just looking at one of the most basic amino acids, Glutamic acid, we have a Gibbs free energy of formation of -476 kJ/mol (chemeo.com (https://chemeo.com)). Glutamate can be broken down in a single biochemical reaction to ammonia and a carbohydrate. Ammonia has a Gibbs free energy of formation of -16 kJ/mol, which indicates that the first degradation step provides much more energy than the subsequent steps. Because of this, organisms that get nitrogen in the form of amino acids have an energy-efficiency advantage if they only do the breakdown until ammonia and not all the way to molecular nitrogen.\n\n\n\n\nOf course that leaves an ecological niche for other organisms to make use of the wasted ammonia and convert the remaining energy there. Actually this is also a multi-step process, which is mostly done by different microbial species (ammonia oxidizer, nitrifyers, and denitrifyers). This has been studied from the perspective of microbial division of labor."}],"domain":"biology","external_citations":["https://biology.stackexchange.com/q/35532/5198","https://biology.stackexchange.com/questions/10737/why-do-organisms-excrete-nitrogenous-wastes/92410#92410","https://chemeo.com","https://en.wikipedia.org/wiki/Carbamoyl_phosphate_synthetase","https://onlinelibrary.wiley.com/doi/10.1002/bies.950100506"],"ground_truth_type":"metadata_grounded","group_id":"70f3c0c017a29e701e1d961e0850c55210b735106f7647ea74b83fde4868cc79","hard_case_family":["multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-6ad387839ea47ce46bcfa3d6","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:04.377249+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/54ece81cba3a5a552bb15d6d3feedc4324a2ba2706d33480080ece9537efd4b1_0.json","raw_sha256":"f1eb8f7eda9336b81701b663029f9411e040c0bcf262148b7ede9a103ae73e69","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=4&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Logan R. Kearsley","profile_url":"https://biology.stackexchange.com/users/25805/logan-r-kearsley","user_type":"registered"},"created_at":"2024-11-24T22:31:12+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"E415493A-48C5-442E-BD74-C794CF3BE75B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E415493A-48C5-442E-BD74-C794CF3BE75B/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Logan R. Kearsley","profile_url":"https://biology.stackexchange.com/users/25805/logan-r-kearsley","user_type":"registered"},"created_at":"2024-11-25T14:23:30+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"4225163C-EF69-4ED7-AC4F-6FFB234B15BC","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4225163C-EF69-4ED7-AC4F-6FFB234B15BC/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115689","source_record_sha256":"d0b6b8cbb060c50c66eb3a8aacdfd7348b79c9b4e16907f66f40a2ddfca94090","source_url":"https://biology.stackexchange.com/questions/115689/why-do-animals-excrete-organic-nitrogen-compounds-instead-of-n2-gas","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Why do animals excrete organic nitrogen compounds instead of N2 gas?\nProtein metabolism produces ammonia, which needs to be disposed of; but oxidation of ammonia into water and dinitrogen produces energy, while creating urea or uric acid consumes energy, and excreting it expands water. So, it seems like there would be some small advantage to animals exhaling N2 instead of excreting nitrogen in liquid or solid form. Nevertheless, no animal does so, and as far as I know, the only organisms that do are denitrifying bacteria and archaea.\n\n\n\n\nSo, is there a good reason why animals shouldn't produce nitrogen gas? bother with that, rather than just exhaling nitrogen gas? Or is it just a matter of \"evolution isn't directed (https://biology.stackexchange.com/q/35532/5198)\"--a random quirk that the ancestors of animals didn't happen to develop ammonia-oxidizing pathways?\n\n\n\n\nThere are a few reasons I can think of, or that have been suggested to me, that nitrogen production might actually be deleterious, but I can't find references to back up any of them:\n\n\n\n\n\nNitrogen has low solubility, and bubbles in blood or tissues are bad. Would this actually be a limiting factor?\n\n\n\n\nThe pathways that oxidize ammonia in microbes might interfere with other parts of animalian metabolism. I have absolutely no idea how plausible this is.\n\n\n\n\nThe energy gain from oxidizing ammonia may be too small to justify the cost of maintaining metabolic machinery for it.\n\n\n\n\n\nSo, is there any actual science on this?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115697,"score":7},{"answer_id":115708,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":115720,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Bilateria are most likely not nested in Cnidaria. Peterson and Davidson, 2000<sup>1</sup> and Medina <em>et al</em>, 2001<sup>2</sup> discuss the developmental history of the Bilateria with respect to other groups within Animalia.</p>\n<p>It seems most likely that Cnidaria and Bilateria share a common ancestor, which explains the common gene groupings. As such, Cnidaria is a branch of the Eumetazoan tree, as is Bilateria. This ancestor would also have been an ancestor of Ctenophora, but seemingly not of Porifera, which may have diverged before the divergence of Cilateria and Cnidaria, though this is hotly debated. The following image from Peterson and Davidson, 2000<sup>1</sup> shows their relationships based on <a href=\"https://en.wikipedia.org/wiki/Hox_gene\" rel=\"nofollow noreferrer\">Homeobox gene</a> evolution:</p>\n<p><a href=\"https://i.sstatic.net/oTOnLZbA.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/oTOnLZbA.png\" alt=\"Evolutionary tree of bilateria\" /></a></p>\n<p><sup> Image attribution: From reference 1. Note the following text from image caption: This view of Hox cluster evolution devolves from studies of de Rosa et al. (33), Finnerty and Martindale (30), and others (see text). The adult enteropneust, the larval enteropneust, and the larval sea urchin photographs are from the authors' collections; the rest of the animal pictures are from ref. 40 [reproduced with permission from ref. 40 (Copyright 1980, Stanford University Press)]</sup></p>\n<p>Medina <em>et al</em>, 2001<sup>2</sup> reached a similar conclusion using ribosomal RNA sequencing, as you can see in the following image. Note the difference between the two maximum likelihood trees; on the left is the small subunit tree and the right has the large subunit tree.</p>\n<p><a href=\"https://i.sstatic.net/zO8meEg5.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/zO8meEg5.png\" alt=\"relationships of the bilateria and other metazoa\" /></a></p>\n<p><sup> image attribution: from reference 2.</sup></p>\n<p>As you can see there is some rearrangement of the order of relatedness between the Cnidaria, Ctenophora and Porifera between the two RNA types. This sort of information has led to some controversy in the literature, with some studies supporting the Porifera-first tree and some disagreeing with this, based on ever larger data-sets including more genes and more organisms, as noted in the introduction of this review by <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC11105162/\" rel=\"nofollow noreferrer\">Steenwyk and King, 2024</a><sup>3</sup> (see  section titled <em>The Tangled Branches in the Tree of Life</em>).</p>\n<p>Refs:</p>\n<ol>\n<li><p>Peterson KJ, Davidson EH. Regulatory evolution and the origin of the bilaterians. Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4430-3. doi: 10.1073/pnas.97.9.4430. PMID: 10781037; PMCID: PMC34315.</p>\n</li>\n<li><p>Medina M, Collins AG, Silberman JD, Sogin ML. Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9707-12. doi: 10.1073/pnas.171316998. PMID: 11504944; PMCID: PMC55517.</p>\n</li>\n<li><p>Steenwyk JL, King N. The promise and pitfalls of synteny in phylogenomics. PLoS Biol. 2024 May 20;22(5):e3002632. doi: 10.1371/journal.pbio.3002632. PMID: 38768403; PMCID: PMC11105162.</p>\n</li>\n</ol>\n","answer_id":115720,"answer_text":"Bilateria are most likely not nested in Cnidaria. Peterson and Davidson, 20001 and Medina et al, 20012 discuss the developmental history of the Bilateria with respect to other groups within Animalia.\n\n\n\n\nIt seems most likely that Cnidaria and Bilateria share a common ancestor, which explains the common gene groupings. As such, Cnidaria is a branch of the Eumetazoan tree, as is Bilateria. This ancestor would also have been an ancestor of Ctenophora, but seemingly not of Porifera, which may have diverged before the divergence of Cilateria and Cnidaria, though this is hotly debated. The following image from Peterson and Davidson, 20001 shows their relationships based on Homeobox gene (https://en.wikipedia.org/wiki/Hox_gene) evolution:\n\n\n\n\n[image: Evolutionary tree of bilateria; source: https://i.sstatic.net/oTOnLZbA.png] (https://i.sstatic.net/oTOnLZbA.png)\n\n\n\n\n Image attribution: From reference 1. Note the following text from image caption: This view of Hox cluster evolution devolves from studies of de Rosa et al. (33), Finnerty and Martindale (30), and others (see text). The adult enteropneust, the larval enteropneust, and the larval sea urchin photographs are from the authors' collections; the rest of the animal pictures are from ref. 40 [reproduced with permission from ref. 40 (Copyright 1980, Stanford University Press)]\n\n\n\n\nMedina et al, 20012 reached a similar conclusion using ribosomal RNA sequencing, as you can see in the following image. Note the difference between the two maximum likelihood trees; on the left is the small subunit tree and the right has the large subunit tree.\n\n\n\n\n[image: relationships of the bilateria and other metazoa; source: https://i.sstatic.net/zO8meEg5.png] (https://i.sstatic.net/zO8meEg5.png)\n\n\n\n\n image attribution: from reference 2.\n\n\n\n\nAs you can see there is some rearrangement of the order of relatedness between the Cnidaria, Ctenophora and Porifera between the two RNA types. This sort of information has led to some controversy in the literature, with some studies supporting the Porifera-first tree and some disagreeing with this, based on ever larger data-sets including more genes and more organisms, as noted in the introduction of this review by Steenwyk and King, 2024 (https://pmc.ncbi.nlm.nih.gov/articles/PMC11105162/)3 (see  section titled The Tangled Branches in the Tree of Life).\n\n\n\n\nRefs:\n\n\n\n\n\n\n\nPeterson KJ, Davidson EH. Regulatory evolution and the origin of the bilaterians. Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4430-3. doi: 10.1073/pnas.97.9.4430. PMID: 10781037; PMCID: PMC34315.\n\n\n\n\n\n\n\n\n\nMedina M, Collins AG, Silberman JD, Sogin ML. Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9707-12. doi: 10.1073/pnas.171316998. PMID: 11504944; PMCID: PMC55517.\n\n\n\n\n\n\n\n\n\nSteenwyk JL, King N. The promise and pitfalls of synteny in phylogenomics. PLoS Biol. 2024 May 20;22(5):e3002632. doi: 10.1371/journal.pbio.3002632. PMID: 38768403; PMCID: PMC11105162.","answer_url":"https://biology.stackexchange.com/a/115720","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2024-12-02T00:23:48+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:22.614155+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2c8799380b8f5d7bf0fd42e594fd78a1835b27e1da9f481cc00f096bab9c01ca_0.json","raw_sha256":"348375a094fdfd6d9ca55d0bddc65d8dc7a7f0757e1e5a44c25e22a66b1a4892","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/116119;116113;116097;116096;116091;116087;116076;116067;116063;116059;116055;116037;116034;116028;116022;116012;116005;115997;115989;115988;115987;115979;115978;115976;115974;115973;115970;115966;115965;115957;115952;115939;115933;115932;115927;115921;115915;115903;115897;115894;115886;115885;115884;115881;115880;115868;115867;115857;115852;115840;115830;115825;115819;115815;115791;115780;115773;115764;115759;115756;115743;115736;115726;115723;115713;115699;115691;115689;115685;115678;115668;115664;115657;115650;115642;115639;115632;115627;115626;115609;115602;115598;115592;115588;115587;115580;115578;115570;115566;115562;115549;115537;115536;115531;115530;115528;115525;115521;115513;115510/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":115713,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2024-12-02T00:23:48+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"188997A1-6B75-4AD6-B9C0-724C0F5BB1FA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/188997A1-6B75-4AD6-B9C0-724C0F5BB1FA/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"sashoalm","author_url":"https://biology.stackexchange.com/users/23100/sashoalm","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"sashoalm","profile_url":"https://biology.stackexchange.com/users/23100/sashoalm","user_type":"registered"},"created_at":"2024-11-30T10:01:05+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"72ED3BB4-2EF2-4CE5-ACF5-FF1EEEBBEF72","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/72ED3BB4-2EF2-4CE5-ACF5-FF1EEEBBEF72/view-source"}],"url":"https://biology.stackexchange.com/questions/115713/are-bilaterians-well-nested-in-cnidaria"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"115720","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2024-12-02T00:23:48+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"188997A1-6B75-4AD6-B9C0-724C0F5BB1FA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/188997A1-6B75-4AD6-B9C0-724C0F5BB1FA/view-source"}],"url":"https://biology.stackexchange.com/a/115720"}],"contexts":[{"context_id":"question","html":"<p>From looking at articles, it seems that all the major neurotransmitters - serotonin, dopamine and noradrenaline - are present in Cnidaria. This, in addition to the fact that Cnidaria have a nervous system which uses the same neurotransmitters, would raise the question of whether Bilateria arose from within Cnidaria.</p>\n<p>My questions are:</p>\n<ul>\n<li>Does Bilateria arise from within Cnidaria in the same way that birds are dinosaurs?</li>\n<li>If so, would cnydocytes have been ancestral in Bilateria but lost?</li>\n<li>Do Bilateria and Cnidaria share a common ancestor that is not shared with Placozoa, Porifera and Ctenophora?</li>\n<li>If so, was this common ancestor similar to an Anthosoa, but lacking in cnydocytes?</li>\n</ul>\n","text":"From looking at articles, it seems that all the major neurotransmitters - serotonin, dopamine and noradrenaline - are present in Cnidaria. This, in addition to the fact that Cnidaria have a nervous system which uses the same neurotransmitters, would raise the question of whether Bilateria arose from within Cnidaria.\n\n\n\n\nMy questions are:\n\n\n\n\n\nDoes Bilateria arise from within Cnidaria in the same way that birds are dinosaurs?\n\n\n\n\nIf so, would cnydocytes have been ancestral in Bilateria but lost?\n\n\n\n\nDo Bilateria and Cnidaria share a common ancestor that is not shared with Placozoa, Porifera and Ctenophora?\n\n\n\n\nIf so, was this common ancestor similar to an Anthosoa, but lacking in cnydocytes?"},{"context_id":"115720","html":"<p>Bilateria are most likely not nested in Cnidaria. Peterson and Davidson, 2000<sup>1</sup> and Medina <em>et al</em>, 2001<sup>2</sup> discuss the developmental history of the Bilateria with respect to other groups within Animalia.</p>\n<p>It seems most likely that Cnidaria and Bilateria share a common ancestor, which explains the common gene groupings. As such, Cnidaria is a branch of the Eumetazoan tree, as is Bilateria. This ancestor would also have been an ancestor of Ctenophora, but seemingly not of Porifera, which may have diverged before the divergence of Cilateria and Cnidaria, though this is hotly debated. The following image from Peterson and Davidson, 2000<sup>1</sup> shows their relationships based on <a href=\"https://en.wikipedia.org/wiki/Hox_gene\" rel=\"nofollow noreferrer\">Homeobox gene</a> evolution:</p>\n<p><a href=\"https://i.sstatic.net/oTOnLZbA.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/oTOnLZbA.png\" alt=\"Evolutionary tree of bilateria\" /></a></p>\n<p><sup> Image attribution: From reference 1. Note the following text from image caption: This view of Hox cluster evolution devolves from studies of de Rosa et al. (33), Finnerty and Martindale (30), and others (see text). The adult enteropneust, the larval enteropneust, and the larval sea urchin photographs are from the authors' collections; the rest of the animal pictures are from ref. 40 [reproduced with permission from ref. 40 (Copyright 1980, Stanford University Press)]</sup></p>\n<p>Medina <em>et al</em>, 2001<sup>2</sup> reached a similar conclusion using ribosomal RNA sequencing, as you can see in the following image. Note the difference between the two maximum likelihood trees; on the left is the small subunit tree and the right has the large subunit tree.</p>\n<p><a href=\"https://i.sstatic.net/zO8meEg5.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/zO8meEg5.png\" alt=\"relationships of the bilateria and other metazoa\" /></a></p>\n<p><sup> image attribution: from reference 2.</sup></p>\n<p>As you can see there is some rearrangement of the order of relatedness between the Cnidaria, Ctenophora and Porifera between the two RNA types. This sort of information has led to some controversy in the literature, with some studies supporting the Porifera-first tree and some disagreeing with this, based on ever larger data-sets including more genes and more organisms, as noted in the introduction of this review by <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC11105162/\" rel=\"nofollow noreferrer\">Steenwyk and King, 2024</a><sup>3</sup> (see  section titled <em>The Tangled Branches in the Tree of Life</em>).</p>\n<p>Refs:</p>\n<ol>\n<li><p>Peterson KJ, Davidson EH. Regulatory evolution and the origin of the bilaterians. Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4430-3. doi: 10.1073/pnas.97.9.4430. PMID: 10781037; PMCID: PMC34315.</p>\n</li>\n<li><p>Medina M, Collins AG, Silberman JD, Sogin ML. Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9707-12. doi: 10.1073/pnas.171316998. PMID: 11504944; PMCID: PMC55517.</p>\n</li>\n<li><p>Steenwyk JL, King N. The promise and pitfalls of synteny in phylogenomics. PLoS Biol. 2024 May 20;22(5):e3002632. doi: 10.1371/journal.pbio.3002632. PMID: 38768403; PMCID: PMC11105162.</p>\n</li>\n</ol>\n","text":"Bilateria are most likely not nested in Cnidaria. Peterson and Davidson, 20001 and Medina et al, 20012 discuss the developmental history of the Bilateria with respect to other groups within Animalia.\n\n\n\n\nIt seems most likely that Cnidaria and Bilateria share a common ancestor, which explains the common gene groupings. As such, Cnidaria is a branch of the Eumetazoan tree, as is Bilateria. This ancestor would also have been an ancestor of Ctenophora, but seemingly not of Porifera, which may have diverged before the divergence of Cilateria and Cnidaria, though this is hotly debated. The following image from Peterson and Davidson, 20001 shows their relationships based on Homeobox gene (https://en.wikipedia.org/wiki/Hox_gene) evolution:\n\n\n\n\n[image: Evolutionary tree of bilateria; source: https://i.sstatic.net/oTOnLZbA.png] (https://i.sstatic.net/oTOnLZbA.png)\n\n\n\n\n Image attribution: From reference 1. Note the following text from image caption: This view of Hox cluster evolution devolves from studies of de Rosa et al. (33), Finnerty and Martindale (30), and others (see text). The adult enteropneust, the larval enteropneust, and the larval sea urchin photographs are from the authors' collections; the rest of the animal pictures are from ref. 40 [reproduced with permission from ref. 40 (Copyright 1980, Stanford University Press)]\n\n\n\n\nMedina et al, 20012 reached a similar conclusion using ribosomal RNA sequencing, as you can see in the following image. Note the difference between the two maximum likelihood trees; on the left is the small subunit tree and the right has the large subunit tree.\n\n\n\n\n[image: relationships of the bilateria and other metazoa; source: https://i.sstatic.net/zO8meEg5.png] (https://i.sstatic.net/zO8meEg5.png)\n\n\n\n\n image attribution: from reference 2.\n\n\n\n\nAs you can see there is some rearrangement of the order of relatedness between the Cnidaria, Ctenophora and Porifera between the two RNA types. This sort of information has led to some controversy in the literature, with some studies supporting the Porifera-first tree and some disagreeing with this, based on ever larger data-sets including more genes and more organisms, as noted in the introduction of this review by Steenwyk and King, 2024 (https://pmc.ncbi.nlm.nih.gov/articles/PMC11105162/)3 (see  section titled The Tangled Branches in the Tree of Life).\n\n\n\n\nRefs:\n\n\n\n\n\n\n\nPeterson KJ, Davidson EH. Regulatory evolution and the origin of the bilaterians. Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4430-3. doi: 10.1073/pnas.97.9.4430. PMID: 10781037; PMCID: PMC34315.\n\n\n\n\n\n\n\n\n\nMedina M, Collins AG, Silberman JD, Sogin ML. Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9707-12. doi: 10.1073/pnas.171316998. PMID: 11504944; PMCID: PMC55517.\n\n\n\n\n\n\n\n\n\nSteenwyk JL, King N. The promise and pitfalls of synteny in phylogenomics. PLoS Biol. 2024 May 20;22(5):e3002632. doi: 10.1371/journal.pbio.3002632. PMID: 38768403; PMCID: PMC11105162."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Hox_gene","https://i.sstatic.net/oTOnLZbA.png","https://i.sstatic.net/zO8meEg5.png","https://pmc.ncbi.nlm.nih.gov/articles/PMC11105162/"],"ground_truth_type":"metadata_grounded","group_id":"f9035fadf25ee7332bba7472418369f932530ed1ca7a0387e2d2d31ea818a576","hard_case_family":["multiple_sources"],"id":"RHM-4503e4d9d82533ef53516739","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:04.377249+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/54ece81cba3a5a552bb15d6d3feedc4324a2ba2706d33480080ece9537efd4b1_0.json","raw_sha256":"f1eb8f7eda9336b81701b663029f9411e040c0bcf262148b7ede9a103ae73e69","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=4&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"sashoalm","profile_url":"https://biology.stackexchange.com/users/23100/sashoalm","user_type":"registered"},"created_at":"2024-11-30T10:01:05+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"72ED3BB4-2EF2-4CE5-ACF5-FF1EEEBBEF72","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/72ED3BB4-2EF2-4CE5-ACF5-FF1EEEBBEF72/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115713","source_record_sha256":"9c3bfa3340e9a796a3fa78a5770a8aed9aa5c8ca86aeba97141215facebb9338","source_url":"https://biology.stackexchange.com/questions/115713/are-bilaterians-well-nested-in-cnidaria","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Are bilaterians well-nested in Cnidaria?\nFrom looking at articles, it seems that all the major neurotransmitters - serotonin, dopamine and noradrenaline - are present in Cnidaria. This, in addition to the fact that Cnidaria have a nervous system which uses the same neurotransmitters, would raise the question of whether Bilateria arose from within Cnidaria.\n\n\n\n\nMy questions are:\n\n\n\n\n\nDoes Bilateria arise from within Cnidaria in the same way that birds are dinosaurs?\n\n\n\n\nIf so, would cnydocytes have been ancestral in Bilateria but lost?\n\n\n\n\nDo Bilateria and Cnidaria share a common ancestor that is not shared with Placozoa, Porifera and Ctenophora?\n\n\n\n\nIf so, was this common ancestor similar to an Anthosoa, but lacking in cnydocytes?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115720,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>There seems little evidence that it does, for if it did it would hardly enhance the growth of the livestock. It’s the <a href=\"https://en.wikipedia.org/wiki/Methanogens_in_digestive_tract_of_ruminants\" rel=\"nofollow noreferrer\">methanogenic bacteria</a> that enable ruminant digestion in the first place!</p>\n<p><em>Biochemistry</em><br>\nThe biochemistry of methane production in ruminant digestion is well described in a freely accessible <a href=\"https://doi.org/10.5713/ab.23.0294\" rel=\"nofollow noreferrer\">review by Mackie <em>et al.</em> (2024)</a>. Although there are many different bacteria involved and a variety of pathways and intermediates, the important point is that methane production results from two separate processes, conducted by different bacteria. The first is the anaerobic fermentation of organic foodstuffs, which produces hydrogen gas. The second is the reaction of the hydrogen gas with carbon dioxide to form methane. This is summarized in this figure from the review:\n<a href=\"https://i.sstatic.net/MskVblpB.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/MskVblpB.png\" alt=\"Degradation of organic matter by ruminants\" /></a>\nThe biochemical rationale for this is that the second step (methanogenesis) reoxidizes that NADH produced in fermentation to NAD+, allowing the first step to continue. The hydrogen is a necessary reducing agent in processes by which the methanogenic bacteria generate energy as ATP, methane being an unneeded byproduct.\n<a href=\"https://i.sstatic.net/YB8361x7.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/YB8361x7.png\" alt=\"Coupling of fermentation and methanogenesis in ruminants\" /></a></p>\n","answer_id":115727,"answer_text":"There seems little evidence that it does, for if it did it would hardly enhance the growth of the livestock. It’s the methanogenic bacteria (https://en.wikipedia.org/wiki/Methanogens_in_digestive_tract_of_ruminants) that enable ruminant digestion in the first place!\n\n\n\n\nBiochemistry\n\nThe biochemistry of methane production in ruminant digestion is well described in a freely accessible review by Mackie et al. (2024) (https://doi.org/10.5713/ab.23.0294). Although there are many different bacteria involved and a variety of pathways and intermediates, the important point is that methane production results from two separate processes, conducted by different bacteria. The first is the anaerobic fermentation of organic foodstuffs, which produces hydrogen gas. The second is the reaction of the hydrogen gas with carbon dioxide to form methane. This is summarized in this figure from the review:\n[image: Degradation of organic matter by ruminants; source: https://i.sstatic.net/MskVblpB.png] (https://i.sstatic.net/MskVblpB.png)\nThe biochemical rationale for this is that the second step (methanogenesis) reoxidizes that NADH produced in fermentation to NAD+, allowing the first step to continue. The hydrogen is a necessary reducing agent in processes by which the methanogenic bacteria generate energy as ATP, methane being an unneeded byproduct.\n[image: Coupling of fermentation and methanogenesis in ruminants; source: https://i.sstatic.net/YB8361x7.png] (https://i.sstatic.net/YB8361x7.png)","answer_url":"https://biology.stackexchange.com/a/115727","author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","created_at":"2024-12-03T18:51:49+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:22.614155+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2c8799380b8f5d7bf0fd42e594fd78a1835b27e1da9f481cc00f096bab9c01ca_0.json","raw_sha256":"348375a094fdfd6d9ca55d0bddc65d8dc7a7f0757e1e5a44c25e22a66b1a4892","source_api":"Stack Exchange API 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Hikes","profile_url":"https://biology.stackexchange.com/users/39747/kurt-hikes","user_type":"registered"},"created_at":"2024-12-03T08:29:52+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"3B65F12F-6EB4-49C9-A384-C01D32D002E3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3B65F12F-6EB4-49C9-A384-C01D32D002E3/view-source"}],"url":"https://biology.stackexchange.com/questions/115726/does-feeding-livestock-antibiotics-reduce-their-methane-output"},{"author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","context_id":"115727","revision_attribution":[{"content_license":"CC BY-SA 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methane?</p>\n","text":"Feeding antimicrobial to livestock willy-nilly to enhance growth and feeding 'efficiency' (or 'conversion') is controversial, of course, but....\n\n\n\n\nDoes this have the positive side effect of reducing the microbe-produced gases that the livestock expel via flatulence and education, such as methane?"},{"context_id":"115727","html":"<p>There seems little evidence that it does, for if it did it would hardly enhance the growth of the livestock. It’s the <a href=\"https://en.wikipedia.org/wiki/Methanogens_in_digestive_tract_of_ruminants\" rel=\"nofollow noreferrer\">methanogenic bacteria</a> that enable ruminant digestion in the first place!</p>\n<p><em>Biochemistry</em><br>\nThe biochemistry of methane production in ruminant digestion is well described in a freely accessible <a href=\"https://doi.org/10.5713/ab.23.0294\" rel=\"nofollow noreferrer\">review by Mackie <em>et al.</em> (2024)</a>. Although there are many different bacteria involved and a variety of pathways and intermediates, the important point is that methane production results from two separate processes, conducted by different bacteria. The first is the anaerobic fermentation of organic foodstuffs, which produces hydrogen gas. The second is the reaction of the hydrogen gas with carbon dioxide to form methane. This is summarized in this figure from the review:\n<a href=\"https://i.sstatic.net/MskVblpB.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/MskVblpB.png\" alt=\"Degradation of organic matter by ruminants\" /></a>\nThe biochemical rationale for this is that the second step (methanogenesis) reoxidizes that NADH produced in fermentation to NAD+, allowing the first step to continue. The hydrogen is a necessary reducing agent in processes by which the methanogenic bacteria generate energy as ATP, methane being an unneeded byproduct.\n<a href=\"https://i.sstatic.net/YB8361x7.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/YB8361x7.png\" alt=\"Coupling of fermentation and methanogenesis in ruminants\" /></a></p>\n","text":"There seems little evidence that it does, for if it did it would hardly enhance the growth of the livestock. It’s the methanogenic bacteria (https://en.wikipedia.org/wiki/Methanogens_in_digestive_tract_of_ruminants) that enable ruminant digestion in the first place!\n\n\n\n\nBiochemistry\n\nThe biochemistry of methane production in ruminant digestion is well described in a freely accessible review by Mackie et al. (2024) (https://doi.org/10.5713/ab.23.0294). Although there are many different bacteria involved and a variety of pathways and intermediates, the important point is that methane production results from two separate processes, conducted by different bacteria. The first is the anaerobic fermentation of organic foodstuffs, which produces hydrogen gas. The second is the reaction of the hydrogen gas with carbon dioxide to form methane. This is summarized in this figure from the review:\n[image: Degradation of organic matter by ruminants; source: https://i.sstatic.net/MskVblpB.png] (https://i.sstatic.net/MskVblpB.png)\nThe biochemical rationale for this is that the second step (methanogenesis) reoxidizes that NADH produced in fermentation to NAD+, allowing the first step to continue. The hydrogen is a necessary reducing agent in processes by which the methanogenic bacteria generate energy as ATP, methane being an unneeded byproduct.\n[image: Coupling of fermentation and methanogenesis in ruminants; source: https://i.sstatic.net/YB8361x7.png] (https://i.sstatic.net/YB8361x7.png)"}],"domain":"biology","external_citations":["https://doi.org/10.5713/ab.23.0294","https://en.wikipedia.org/wiki/Methanogens_in_digestive_tract_of_ruminants","https://i.sstatic.net/MskVblpB.png","https://i.sstatic.net/YB8361x7.png"],"ground_truth_type":"metadata_grounded","group_id":"53e62baa1828ef893404c3ab1fd16a942ecef2bb9619e05441fbc631db16c298","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-cd28ed4862130a5e58c87e2e","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:04.377249+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/54ece81cba3a5a552bb15d6d3feedc4324a2ba2706d33480080ece9537efd4b1_0.json","raw_sha256":"f1eb8f7eda9336b81701b663029f9411e040c0bcf262148b7ede9a103ae73e69","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=4&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Kurt Hikes","profile_url":"https://biology.stackexchange.com/users/39747/kurt-hikes","user_type":"registered"},"created_at":"2024-12-03T08:29:52+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"3B65F12F-6EB4-49C9-A384-C01D32D002E3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3B65F12F-6EB4-49C9-A384-C01D32D002E3/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115726","source_record_sha256":"b714fc5ffbf0f56aa458b5fab1a7dbf4f4bfad2e030be453f4b9f1f18725de98","source_url":"https://biology.stackexchange.com/questions/115726/does-feeding-livestock-antibiotics-reduce-their-methane-output","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Does feeding livestock antibiotics reduce their methane output?\nFeeding antimicrobial to livestock willy-nilly to enhance growth and feeding 'efficiency' (or 'conversion') is controversial, of course, but....\n\n\n\n\nDoes this have the positive side effect of reducing the microbe-produced gases that the livestock expel via flatulence and education, such as methane?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115727,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The most noteworthy way to differentiate is by size. Wolves are bigger:</p>\n<p><a href=\"https://i.sstatic.net/9QwB9TyK.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/9QwB9TyK.png\" alt=\"CANINE FOOTPRINTS\" /></a>\n<sup> Image source: <a href=\"https://wdfw.wa.gov/species-habitats/at-risk/species-recovery/gray-wolf/identification\" rel=\"noreferrer\">WDFW</a> </sup></p>\n<p>Regarding the size of young wolves (from <a href=\"https://westernwildlife.org/signs-of-wolves/\" rel=\"noreferrer\">here</a>):</p>\n<blockquote>\n<p>Young wolves’ feet grow large very quickly, and by the time they are about three months old (around July) even young wolves’ tracks are larger than most coyote tracks</p>\n</blockquote>\n<p>Some additional characteristics from the <a href=\"https://wdfw.wa.gov/species-habitats/at-risk/species-recovery/gray-wolf/identification\" rel=\"noreferrer\">Washington Department of Fish and Wildlife</a> :</p>\n<blockquote>\n<p>Wolf tracks are about 5 inches long by 4 inches wide, with four symmetrical toes and evident claws, and a single lobe on the front of the foot pad. Coyote tracks are similar, but about half that size, and even the largest domestic dog breeds usually have smaller tracks. The paths of wolves usually show a direct, energy efficient or purposeful route, whereas those of dogs often meander.</p>\n</blockquote>\n","answer_id":115841,"answer_text":"The most noteworthy way to differentiate is by size. Wolves are bigger:\n\n\n\n\n[image: CANINE FOOTPRINTS; source: https://i.sstatic.net/9QwB9TyK.png] (https://i.sstatic.net/9QwB9TyK.png)\n Image source: WDFW (https://wdfw.wa.gov/species-habitats/at-risk/species-recovery/gray-wolf/identification) \n\n\n\n\nRegarding the size of young wolves (from here (https://westernwildlife.org/signs-of-wolves/)):\n\n\n\n\n\n\n\nYoung wolves’ feet grow large very quickly, and by the time they are about three months old (around July) even young wolves’ tracks are larger than most coyote tracks\n\n\n\n\n\n\n\nSome additional characteristics from the Washington Department of Fish and Wildlife (https://wdfw.wa.gov/species-habitats/at-risk/species-recovery/gray-wolf/identification) :\n\n\n\n\n\n\n\nWolf tracks are about 5 inches long by 4 inches wide, with four symmetrical toes and evident claws, and a single lobe on the front of the foot pad. Coyote tracks are similar, but about half that size, and even the largest domestic dog breeds usually have smaller tracks. The paths of wolves usually show a direct, energy efficient or purposeful route, whereas those of dogs often meander.","answer_url":"https://biology.stackexchange.com/a/115841","author":"theforestecologist","author_url":"https://biology.stackexchange.com/users/16866/theforestecologist","content_license":"CC BY-SA 4.0","created_at":"2024-12-22T17:41:26+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:22.614155+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2c8799380b8f5d7bf0fd42e594fd78a1835b27e1da9f481cc00f096bab9c01ca_0.json","raw_sha256":"348375a094fdfd6d9ca55d0bddc65d8dc7a7f0757e1e5a44c25e22a66b1a4892","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/116119;116113;116097;116096;116091;116087;116076;116067;116063;116059;116055;116037;116034;116028;116022;116012;116005;115997;115989;115988;115987;115979;115978;115976;115974;115973;115970;115966;115965;115957;115952;115939;115933;115932;115927;115921;115915;115903;115897;115894;115886;115885;115884;115881;115880;115868;115867;115857;115852;115840;115830;115825;115819;115815;115791;115780;115773;115764;115759;115756;115743;115736;115726;115723;115713;115699;115691;115689;115685;115678;115668;115664;115657;115650;115642;115639;115632;115627;115626;115609;115602;115598;115592;115588;115587;115580;115578;115570;115566;115562;115549;115537;115536;115531;115530;115528;115525;115521;115513;115510/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":115840,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"theforestecologist","profile_url":"https://biology.stackexchange.com/users/16866/theforestecologist","user_type":"registered"},"created_at":"2024-12-22T17:41:26+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"A29F37F1-ED55-4D42-A53A-D87BB92DDA47","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A29F37F1-ED55-4D42-A53A-D87BB92DDA47/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"theforestecologist","profile_url":"https://biology.stackexchange.com/users/16866/theforestecologist","user_type":"registered"},"created_at":"2024-12-22T17:49:00+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"C53F95B9-1A52-40A5-8D7E-B02062A30731","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C53F95B9-1A52-40A5-8D7E-B02062A30731/view-source"}],"score":12},{"answer_html":"<p><a href=\"https://biology.stackexchange.com/a/115841/38754\">The answer by theforestecologist</a> covers the basics of differentiating the tracks, so I won’t repeat that in detail here.</p>\n<p>As for the actual tracks pictured, they are too large for a coyote, which suggests either a wolf or a dog, but they’re a bit on the small side for a wolf, which would suggest either a young wolf or a large dog. The stride length isn’t a huge help in differentiating, as there are plenty of dog breeds that have that short of a stride relative to the size of their paws.</p>\n<p>Beyond that it would require seeing both the overall path taken, and the area in general. For example, if the path the tracks take is meandering significantly it’s probably a dog (wolves generally don’t wander aimlessly or get constantly distracted like many dogs do), while a lack of accompanying human tracks nearby would make it all but certain that these are wolf tracks (if it were a dog in such a remote area, it would almost certainly be accompanied by a human).</p>\n","answer_id":115854,"answer_text":"The answer by theforestecologist (https://biology.stackexchange.com/a/115841/38754) covers the basics of differentiating the tracks, so I won’t repeat that in detail here.\n\n\n\n\nAs for the actual tracks pictured, they are too large for a coyote, which suggests either a wolf or a dog, but they’re a bit on the small side for a wolf, which would suggest either a young wolf or a large dog. The stride length isn’t a huge help in differentiating, as there are plenty of dog breeds that have that short of a stride relative to the size of their paws.\n\n\n\n\nBeyond that it would require seeing both the overall path taken, and the area in general. For example, if the path the tracks take is meandering significantly it’s probably a dog (wolves generally don’t wander aimlessly or get constantly distracted like many dogs do), while a lack of accompanying human tracks nearby would make it all but certain that these are wolf tracks (if it were a dog in such a remote area, it would almost certainly be accompanied by a human).","answer_url":"https://biology.stackexchange.com/a/115854","author":"Austin Hemmelgarn","author_url":"https://biology.stackexchange.com/users/38754/austin-hemmelgarn","content_license":"CC BY-SA 4.0","created_at":"2024-12-23T19:29:29+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:22.614155+00:00","license":"CC BY-SA 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Darkness","profile_url":"https://biology.stackexchange.com/users/15368/amazon-dies-in-darkness","user_type":"registered"},"created_at":"2024-12-24T13:58:58+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"C79A0B04-936C-486E-8304-65C0529BC6CE","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C79A0B04-936C-486E-8304-65C0529BC6CE/view-source"}],"url":"https://biology.stackexchange.com/questions/115840/how-to-differentiate-coyote-vs-wolf-tracks"},{"author":"theforestecologist","author_url":"https://biology.stackexchange.com/users/16866/theforestecologist","content_license":"CC BY-SA 4.0","context_id":"115841","revision_attribution":[{"content_license":"CC BY-SA 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spotted these canine paw prints in the snow on <a href=\"https://www.thecanadianencyclopedia.ca/en/article/crown-land\" rel=\"nofollow noreferrer\">crown (public) land</a> in Eastern Ontario, Canada. They're not dog prints; the location is too remote for that.</p>\n<p>I figure the only options are coyote or wolf. How can I differentiate between the two?</p>\n<p><a href=\"https://i.sstatic.net/0qfw9HCY.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/0qfw9HCY.jpg\" alt=\"enter image description here\" /></a></p>\n","text":"I spotted these canine paw prints in the snow on crown (public) land (https://www.thecanadianencyclopedia.ca/en/article/crown-land) in Eastern Ontario, Canada. They're not dog prints; the location is too remote for that.\n\n\n\n\nI figure the only options are coyote or wolf. How can I differentiate between the two?\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/0qfw9HCY.jpg] (https://i.sstatic.net/0qfw9HCY.jpg)"},{"context_id":"115841","html":"<p>The most noteworthy way to differentiate is by size. Wolves are bigger:</p>\n<p><a href=\"https://i.sstatic.net/9QwB9TyK.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/9QwB9TyK.png\" alt=\"CANINE FOOTPRINTS\" /></a>\n<sup> Image source: <a href=\"https://wdfw.wa.gov/species-habitats/at-risk/species-recovery/gray-wolf/identification\" rel=\"noreferrer\">WDFW</a> </sup></p>\n<p>Regarding the size of young wolves (from <a href=\"https://westernwildlife.org/signs-of-wolves/\" rel=\"noreferrer\">here</a>):</p>\n<blockquote>\n<p>Young wolves’ feet grow large very quickly, and by the time they are about three months old (around July) even young wolves’ tracks are larger than most coyote tracks</p>\n</blockquote>\n<p>Some additional characteristics from the <a href=\"https://wdfw.wa.gov/species-habitats/at-risk/species-recovery/gray-wolf/identification\" rel=\"noreferrer\">Washington Department of Fish and Wildlife</a> :</p>\n<blockquote>\n<p>Wolf tracks are about 5 inches long by 4 inches wide, with four symmetrical toes and evident claws, and a single lobe on the front of the foot pad. Coyote tracks are similar, but about half that size, and even the largest domestic dog breeds usually have smaller tracks. The paths of wolves usually show a direct, energy efficient or purposeful route, whereas those of dogs often meander.</p>\n</blockquote>\n","text":"The most noteworthy way to differentiate is by size. Wolves are bigger:\n\n\n\n\n[image: CANINE FOOTPRINTS; source: https://i.sstatic.net/9QwB9TyK.png] (https://i.sstatic.net/9QwB9TyK.png)\n Image source: WDFW (https://wdfw.wa.gov/species-habitats/at-risk/species-recovery/gray-wolf/identification) \n\n\n\n\nRegarding the size of young wolves (from here (https://westernwildlife.org/signs-of-wolves/)):\n\n\n\n\n\n\n\nYoung wolves’ feet grow large very quickly, and by the time they are about three months old (around July) even young wolves’ tracks are larger than most coyote tracks\n\n\n\n\n\n\n\nSome additional characteristics from the Washington Department of Fish and Wildlife (https://wdfw.wa.gov/species-habitats/at-risk/species-recovery/gray-wolf/identification) :\n\n\n\n\n\n\n\nWolf tracks are about 5 inches long by 4 inches wide, with four symmetrical toes and evident claws, and a single lobe on the front of the foot pad. Coyote tracks are similar, but about half that size, and even the largest domestic dog breeds usually have smaller tracks. The paths of wolves usually show a direct, energy efficient or purposeful route, whereas those of dogs often meander."},{"context_id":"115854","html":"<p><a href=\"https://biology.stackexchange.com/a/115841/38754\">The answer by theforestecologist</a> covers the basics of differentiating the tracks, so I won’t repeat that in detail here.</p>\n<p>As for the actual tracks pictured, they are too large for a coyote, which suggests either a wolf or a dog, but they’re a bit on the small side for a wolf, which would suggest either a young wolf or a large dog. The stride length isn’t a huge help in differentiating, as there are plenty of dog breeds that have that short of a stride relative to the size of their paws.</p>\n<p>Beyond that it would require seeing both the overall path taken, and the area in general. For example, if the path the tracks take is meandering significantly it’s probably a dog (wolves generally don’t wander aimlessly or get constantly distracted like many dogs do), while a lack of accompanying human tracks nearby would make it all but certain that these are wolf tracks (if it were a dog in such a remote area, it would almost certainly be accompanied by a human).</p>\n","text":"The answer by theforestecologist (https://biology.stackexchange.com/a/115841/38754) covers the basics of differentiating the tracks, so I won’t repeat that in detail here.\n\n\n\n\nAs for the actual tracks pictured, they are too large for a coyote, which suggests either a wolf or a dog, but they’re a bit on the small side for a wolf, which would suggest either a young wolf or a large dog. The stride length isn’t a huge help in differentiating, as there are plenty of dog breeds that have that short of a stride relative to the size of their paws.\n\n\n\n\nBeyond that it would require seeing both the overall path taken, and the area in general. For example, if the path the tracks take is meandering significantly it’s probably a dog (wolves generally don’t wander aimlessly or get constantly distracted like many dogs do), while a lack of accompanying human tracks nearby would make it all but certain that these are wolf tracks (if it were a dog in such a remote area, it would almost certainly be accompanied by a human)."}],"domain":"biology","external_citations":["https://biology.stackexchange.com/a/115841/38754","https://i.sstatic.net/0qfw9HCY.jpg","https://i.sstatic.net/9QwB9TyK.png","https://wdfw.wa.gov/species-habitats/at-risk/species-recovery/gray-wolf/identification","https://westernwildlife.org/signs-of-wolves/","https://www.thecanadianencyclopedia.ca/en/article/crown-land"],"ground_truth_type":"metadata_grounded","group_id":"0fb1a7161b6b128cbb010f0106d8741102c8e629346debfefdf75b135704aaca","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-cbfe399b09d9b729430e75c1","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:04.377249+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/54ece81cba3a5a552bb15d6d3feedc4324a2ba2706d33480080ece9537efd4b1_0.json","raw_sha256":"f1eb8f7eda9336b81701b663029f9411e040c0bcf262148b7ede9a103ae73e69","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=4&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"User1974","profile_url":"https://biology.stackexchange.com/users/31741/user1974","user_type":"registered"},"created_at":"2024-12-22T17:02:28+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"3370474C-0777-48C5-87AC-FB75D9E6D89E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3370474C-0777-48C5-87AC-FB75D9E6D89E/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"theforestecologist","profile_url":"https://biology.stackexchange.com/users/16866/theforestecologist","user_type":"registered"},"created_at":"2024-12-22T18:10:35+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"C968CDF9-DAB4-4E7A-8302-AD169042B820","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C968CDF9-DAB4-4E7A-8302-AD169042B820/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-12-23T01:03:22+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"9A52C79B-B85D-4324-BC6A-D509AEAB037B","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/9A52C79B-B85D-4324-BC6A-D509AEAB037B/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Amazon Dies In Darkness","profile_url":"https://biology.stackexchange.com/users/15368/amazon-dies-in-darkness","user_type":"registered"},"created_at":"2024-12-24T13:58:58+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"C79A0B04-936C-486E-8304-65C0529BC6CE","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C79A0B04-936C-486E-8304-65C0529BC6CE/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115840","source_record_sha256":"d19e549b8906c82e19d1c8661c992c956d3b70d0dac584fa8316ab64a3b2952c","source_url":"https://biology.stackexchange.com/questions/115840/how-to-differentiate-coyote-vs-wolf-tracks","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How to differentiate coyote vs wolf tracks\nI spotted these canine paw prints in the snow on crown (public) land (https://www.thecanadianencyclopedia.ca/en/article/crown-land) in Eastern Ontario, Canada. They're not dog prints; the location is too remote for that.\n\n\n\n\nI figure the only options are coyote or wolf. How can I differentiate between the two?\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/0qfw9HCY.jpg] (https://i.sstatic.net/0qfw9HCY.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115841,"score":12},{"answer_id":115854,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":115920,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p><strong>“Primary Function”: A Disclaimer</strong></p>\n<p>Asking for the primary function of a biochemical process is akin to asking why it evolved. Such questions, by their very nature are impossible to answer. What may be answerable, and what I think is of interest in this case, is <em>what positive effects the process elicits</em>. Only then can one discuss which could have justified the emergence of the process.</p>\n<p>This answer address the first point — <em>which of the positive functions ascribed to the phosphorylation of glucose to glucose 6-phosphate is true</em>.</p>\n<p><strong>Possibility 1: Trapping Glucose in the cell</strong></p>\n<p>There is no doubt that the phosphorylation of glucose to glucose 6-phosphate (G6P) ‘traps’ glucose in the cell. The cell membrane is impermeable to this charged compound and the glucose transporters do not recognize the phosphorylated forms of glucose.</p>\n<p>In addition, the conversion of intracellular glucose to G6P lowers the concentration of the former, maintaining an extracellular: intracellular glucose concentration gradient which facilitates further uptake of glucose.</p>\n<p><strong>Possibility 2: Glucose ‘Activation’</strong></p>\n<p>In my opinion this is incorrect. As exemplified in <a href=\"https://biology.stackexchange.com/questions/115773/why-is-the-transfer-of-a-phosphoryl-group-used-by-atp-to-drive-reactions-rather/115858#115858\">another answer</a>, the activation of a molecule by phosphoryl group transfer from ATP facilitates bond formation, both by transfer of energy and provision of a suitable catalytic pathway. However the 6-phosphate group of G6P does not take part in any such reaction, and all it is ‘activated’ for is the phosphorylation of ADP to regenerate the ATP used in its formation.</p>\n<p>I can find no source for the claim of activation other than a single assertion on a discussion site: <em>“Phosphorylation occurs in the first step of glycolysis to activate the glucose molecule and make it more reactive.”</em> However the poster does not expand on this or develop his argument further. I shall consider the phrase “make it more reactive” under Possibility 3.</p>\n<p>It should be emphasized that a phosphoryl group at the 1-hydroxyl position in glucose 1-phosphate (G1P) is involved in reaction with UTP to form UDP-glucose, which is an activated form of glucose. It is activated to form a glycosidic linkage to the terminal glucosyl residue in a glycogen chain. (G1P is formed from G6P in a reaction catalysed by phosphoglucomutase.)</p>\n<p><strong>Possibility 3: Facilitating the subsequent reactions of glycolysis</strong></p>\n<p>The 5th edition of the respected text <em>Biochemistry</em> by Berg <em>et al.</em> (originally Streyer) has the following comment on the phosphorylation of glucose to G6P:</p>\n<blockquote>\n<p>“This step is notable for two reasons (1) glucose 6-phosphate cannot\ndiffuse through the membrane because of its negative charges, and <em>(2)\nthe addition of the phosphoryl group begins to destabilize glucose,\nthus facilitating its further metabolism.</em>”</p>\n</blockquote>\n<p>There is no explanation of the chemical nature of this ‘destabilization’ or, when the further metabolism is described subsequently, of how the phosphoryl group at the 6-position facilitates it. Moreover by the 9th edition there is no longer any mention of ‘destabilization’, with the second point becoming merely:</p>\n<blockquote>\n<p>“Also the addition of the phosphoryl group <em>facilitates the eventual\nmetabolism of glucose</em> into the three-carbon molecules with high\nphosphoryl group transfer potential.”</p>\n</blockquote>\n<p>But again, despite a detailed account of the subsequent reactions, there is no explanation of how the phosphoryl group is supposed to facilitate them.</p>\n<p>My chemistry is very rusty, but I do not see how the 6-phosphate can affect any of the subsequent reactions. In the absence of a precise chemical explanation, this cannot be accepted. (I shall post on SE regarding this specific point, but would welcome contributions from list members.)</p>\n<p><strong>Conclusion: Why not be satisfied with glucose trapping?</strong></p>\n<p>I detect a vague feeling of dissatisfaction with glucose trapping as the primary reason for the evolutionary emergence of the phosphorylation of glucose. If glycolysis evolved to generate ATP anaerobically, then the pyruvate kinase ‘payback’ stage of glycolysis would have had to evolve at the same time, unless it already existed for some other purpose. And raising the question of which pathways or reactions evolved first (what about the other fates of phosphorylated hexoses or trioses?) brings one into extremely difficult territory. This must have been considered by weightier minds than mine — does any one know where?</p>\n","answer_id":115920,"answer_text":"“Primary Function”: A Disclaimer\n\n\n\n\nAsking for the primary function of a biochemical process is akin to asking why it evolved. Such questions, by their very nature are impossible to answer. What may be answerable, and what I think is of interest in this case, is what positive effects the process elicits. Only then can one discuss which could have justified the emergence of the process.\n\n\n\n\nThis answer address the first point — which of the positive functions ascribed to the phosphorylation of glucose to glucose 6-phosphate is true.\n\n\n\n\nPossibility 1: Trapping Glucose in the cell\n\n\n\n\nThere is no doubt that the phosphorylation of glucose to glucose 6-phosphate (G6P) ‘traps’ glucose in the cell. The cell membrane is impermeable to this charged compound and the glucose transporters do not recognize the phosphorylated forms of glucose.\n\n\n\n\nIn addition, the conversion of intracellular glucose to G6P lowers the concentration of the former, maintaining an extracellular: intracellular glucose concentration gradient which facilitates further uptake of glucose.\n\n\n\n\nPossibility 2: Glucose ‘Activation’\n\n\n\n\nIn my opinion this is incorrect. As exemplified in another answer (https://biology.stackexchange.com/questions/115773/why-is-the-transfer-of-a-phosphoryl-group-used-by-atp-to-drive-reactions-rather/115858#115858), the activation of a molecule by phosphoryl group transfer from ATP facilitates bond formation, both by transfer of energy and provision of a suitable catalytic pathway. However the 6-phosphate group of G6P does not take part in any such reaction, and all it is ‘activated’ for is the phosphorylation of ADP to regenerate the ATP used in its formation.\n\n\n\n\nI can find no source for the claim of activation other than a single assertion on a discussion site: “Phosphorylation occurs in the first step of glycolysis to activate the glucose molecule and make it more reactive.” However the poster does not expand on this or develop his argument further. I shall consider the phrase “make it more reactive” under Possibility 3.\n\n\n\n\nIt should be emphasized that a phosphoryl group at the 1-hydroxyl position in glucose 1-phosphate (G1P) is involved in reaction with UTP to form UDP-glucose, which is an activated form of glucose. It is activated to form a glycosidic linkage to the terminal glucosyl residue in a glycogen chain. (G1P is formed from G6P in a reaction catalysed by phosphoglucomutase.)\n\n\n\n\nPossibility 3: Facilitating the subsequent reactions of glycolysis\n\n\n\n\nThe 5th edition of the respected text Biochemistry by Berg et al. (originally Streyer) has the following comment on the phosphorylation of glucose to G6P:\n\n\n\n\n\n\n\n“This step is notable for two reasons (1) glucose 6-phosphate cannot\ndiffuse through the membrane because of its negative charges, and (2)\nthe addition of the phosphoryl group begins to destabilize glucose,\nthus facilitating its further metabolism.”\n\n\n\n\n\n\n\nThere is no explanation of the chemical nature of this ‘destabilization’ or, when the further metabolism is described subsequently, of how the phosphoryl group at the 6-position facilitates it. Moreover by the 9th edition there is no longer any mention of ‘destabilization’, with the second point becoming merely:\n\n\n\n\n\n\n\n“Also the addition of the phosphoryl group facilitates the eventual\nmetabolism of glucose into the three-carbon molecules with high\nphosphoryl group transfer potential.”\n\n\n\n\n\n\n\nBut again, despite a detailed account of the subsequent reactions, there is no explanation of how the phosphoryl group is supposed to facilitate them.\n\n\n\n\nMy chemistry is very rusty, but I do not see how the 6-phosphate can affect any of the subsequent reactions. In the absence of a precise chemical explanation, this cannot be accepted. (I shall post on SE regarding this specific point, but would welcome contributions from list members.)\n\n\n\n\nConclusion: Why not be satisfied with glucose trapping?\n\n\n\n\nI detect a vague feeling of dissatisfaction with glucose trapping as the primary reason for the evolutionary emergence of the phosphorylation of glucose. If glycolysis evolved to generate ATP anaerobically, then the pyruvate kinase ‘payback’ stage of glycolysis would have had to evolve at the same time, unless it already existed for some other purpose. And raising the question of which pathways or reactions evolved first (what about the other fates of phosphorylated hexoses or trioses?) brings one into extremely difficult territory. This must have been considered by weightier minds than mine — does any one know where?","answer_url":"https://biology.stackexchange.com/a/115920","author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","created_at":"2025-01-07T17:42:19+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:22.614155+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2c8799380b8f5d7bf0fd42e594fd78a1835b27e1da9f481cc00f096bab9c01ca_0.json","raw_sha256":"348375a094fdfd6d9ca55d0bddc65d8dc7a7f0757e1e5a44c25e22a66b1a4892","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/116119;116113;116097;116096;116091;116087;116076;116067;116063;116059;116055;116037;116034;116028;116022;116012;116005;115997;115989;115988;115987;115979;115978;115976;115974;115973;115970;115966;115965;115957;115952;115939;115933;115932;115927;115921;115915;115903;115897;115894;115886;115885;115884;115881;115880;115868;115867;115857;115852;115840;115830;115825;115819;115815;115791;115780;115773;115764;115759;115756;115743;115736;115726;115723;115713;115699;115691;115689;115685;115678;115668;115664;115657;115650;115642;115639;115632;115627;115626;115609;115602;115598;115592;115588;115587;115580;115578;115570;115566;115562;115549;115537;115536;115531;115530;115528;115525;115521;115513;115510/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":115885,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2025-01-07T17:42:19+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"365A59B1-7774-4469-AFDE-1A51E4ECD3C3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/365A59B1-7774-4469-AFDE-1A51E4ECD3C3/view-source"}],"score":4},{"answer_html":"<p>In my view this can ultimately be traced back to evolution.\nOne important element of substrate control by an enzyme is via a phosphate group. This is very common and in my view a result of evolution.\nThe phosphorylation modifies the interaction of a substrate with its enzyme, e.g. binding more tightly.\nThe negative charge also helps to keep Glc in the cell, because it cannot pass back through the nonpolar membrane.</p>\n","answer_id":115925,"answer_text":"In my view this can ultimately be traced back to evolution.\nOne important element of substrate control by an enzyme is via a phosphate group. This is very common and in my view a result of evolution.\nThe phosphorylation modifies the interaction of a substrate with its enzyme, e.g. binding more tightly.\nThe negative charge also helps to keep Glc in the cell, because it cannot pass back through the nonpolar membrane.","answer_url":"https://biology.stackexchange.com/a/115925","author":"Willy England","author_url":"https://biology.stackexchange.com/users/96710/willy-england","content_license":"CC BY-SA 4.0","created_at":"2025-01-09T12:27:11+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:22.614155+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2c8799380b8f5d7bf0fd42e594fd78a1835b27e1da9f481cc00f096bab9c01ca_0.json","raw_sha256":"348375a094fdfd6d9ca55d0bddc65d8dc7a7f0757e1e5a44c25e22a66b1a4892","source_api":"Stack Exchange API 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England","profile_url":"https://biology.stackexchange.com/users/96710/willy-england","user_type":"registered"},"created_at":"2025-01-09T12:27:11+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"5320A13A-9528-4DDF-B220-3475F6A92FCA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5320A13A-9528-4DDF-B220-3475F6A92FCA/view-source"},{"content_license":null,"contributor":{"display_name":"Chris","profile_url":"https://biology.stackexchange.com/users/5144/chris","user_type":"moderator"},"created_at":"2025-01-10T17:04:45+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"7DA2C9EC-1D4C-44B2-86F7-994541B0470E","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/7DA2C9EC-1D4C-44B2-86F7-994541B0470E/view-source"}],"url":"https://biology.stackexchange.com/a/115925"}],"contexts":[{"context_id":"question","html":"<p>What is the primary function of the phosphorlyation of glucose in the first step of glycolysis?</p>\n<p>Some textbooks emphasize that it traps glucose in the cell, but some sources mention glucose &quot;activation.&quot; There is a <a href=\"https://www.quora.com/Why-are-2-ATPs-used-in-glycolysis\" rel=\"nofollow noreferrer\">response on Quora</a> that claims that energetics are irrelevant and that phosphorylation is solely about trapping glucose.</p>\n","text":"What is the primary function of the phosphorlyation of glucose in the first step of glycolysis?\n\n\n\n\nSome textbooks emphasize that it traps glucose in the cell, but some sources mention glucose \"activation.\" There is a response on Quora (https://www.quora.com/Why-are-2-ATPs-used-in-glycolysis) that claims that energetics are irrelevant and that phosphorylation is solely about trapping glucose."},{"context_id":"115920","html":"<p><strong>“Primary Function”: A Disclaimer</strong></p>\n<p>Asking for the primary function of a biochemical process is akin to asking why it evolved. Such questions, by their very nature are impossible to answer. What may be answerable, and what I think is of interest in this case, is <em>what positive effects the process elicits</em>. Only then can one discuss which could have justified the emergence of the process.</p>\n<p>This answer address the first point — <em>which of the positive functions ascribed to the phosphorylation of glucose to glucose 6-phosphate is true</em>.</p>\n<p><strong>Possibility 1: Trapping Glucose in the cell</strong></p>\n<p>There is no doubt that the phosphorylation of glucose to glucose 6-phosphate (G6P) ‘traps’ glucose in the cell. The cell membrane is impermeable to this charged compound and the glucose transporters do not recognize the phosphorylated forms of glucose.</p>\n<p>In addition, the conversion of intracellular glucose to G6P lowers the concentration of the former, maintaining an extracellular: intracellular glucose concentration gradient which facilitates further uptake of glucose.</p>\n<p><strong>Possibility 2: Glucose ‘Activation’</strong></p>\n<p>In my opinion this is incorrect. As exemplified in <a href=\"https://biology.stackexchange.com/questions/115773/why-is-the-transfer-of-a-phosphoryl-group-used-by-atp-to-drive-reactions-rather/115858#115858\">another answer</a>, the activation of a molecule by phosphoryl group transfer from ATP facilitates bond formation, both by transfer of energy and provision of a suitable catalytic pathway. However the 6-phosphate group of G6P does not take part in any such reaction, and all it is ‘activated’ for is the phosphorylation of ADP to regenerate the ATP used in its formation.</p>\n<p>I can find no source for the claim of activation other than a single assertion on a discussion site: <em>“Phosphorylation occurs in the first step of glycolysis to activate the glucose molecule and make it more reactive.”</em> However the poster does not expand on this or develop his argument further. I shall consider the phrase “make it more reactive” under Possibility 3.</p>\n<p>It should be emphasized that a phosphoryl group at the 1-hydroxyl position in glucose 1-phosphate (G1P) is involved in reaction with UTP to form UDP-glucose, which is an activated form of glucose. It is activated to form a glycosidic linkage to the terminal glucosyl residue in a glycogen chain. (G1P is formed from G6P in a reaction catalysed by phosphoglucomutase.)</p>\n<p><strong>Possibility 3: Facilitating the subsequent reactions of glycolysis</strong></p>\n<p>The 5th edition of the respected text <em>Biochemistry</em> by Berg <em>et al.</em> (originally Streyer) has the following comment on the phosphorylation of glucose to G6P:</p>\n<blockquote>\n<p>“This step is notable for two reasons (1) glucose 6-phosphate cannot\ndiffuse through the membrane because of its negative charges, and <em>(2)\nthe addition of the phosphoryl group begins to destabilize glucose,\nthus facilitating its further metabolism.</em>”</p>\n</blockquote>\n<p>There is no explanation of the chemical nature of this ‘destabilization’ or, when the further metabolism is described subsequently, of how the phosphoryl group at the 6-position facilitates it. Moreover by the 9th edition there is no longer any mention of ‘destabilization’, with the second point becoming merely:</p>\n<blockquote>\n<p>“Also the addition of the phosphoryl group <em>facilitates the eventual\nmetabolism of glucose</em> into the three-carbon molecules with high\nphosphoryl group transfer potential.”</p>\n</blockquote>\n<p>But again, despite a detailed account of the subsequent reactions, there is no explanation of how the phosphoryl group is supposed to facilitate them.</p>\n<p>My chemistry is very rusty, but I do not see how the 6-phosphate can affect any of the subsequent reactions. In the absence of a precise chemical explanation, this cannot be accepted. (I shall post on SE regarding this specific point, but would welcome contributions from list members.)</p>\n<p><strong>Conclusion: Why not be satisfied with glucose trapping?</strong></p>\n<p>I detect a vague feeling of dissatisfaction with glucose trapping as the primary reason for the evolutionary emergence of the phosphorylation of glucose. If glycolysis evolved to generate ATP anaerobically, then the pyruvate kinase ‘payback’ stage of glycolysis would have had to evolve at the same time, unless it already existed for some other purpose. And raising the question of which pathways or reactions evolved first (what about the other fates of phosphorylated hexoses or trioses?) brings one into extremely difficult territory. This must have been considered by weightier minds than mine — does any one know where?</p>\n","text":"“Primary Function”: A Disclaimer\n\n\n\n\nAsking for the primary function of a biochemical process is akin to asking why it evolved. Such questions, by their very nature are impossible to answer. What may be answerable, and what I think is of interest in this case, is what positive effects the process elicits. Only then can one discuss which could have justified the emergence of the process.\n\n\n\n\nThis answer address the first point — which of the positive functions ascribed to the phosphorylation of glucose to glucose 6-phosphate is true.\n\n\n\n\nPossibility 1: Trapping Glucose in the cell\n\n\n\n\nThere is no doubt that the phosphorylation of glucose to glucose 6-phosphate (G6P) ‘traps’ glucose in the cell. The cell membrane is impermeable to this charged compound and the glucose transporters do not recognize the phosphorylated forms of glucose.\n\n\n\n\nIn addition, the conversion of intracellular glucose to G6P lowers the concentration of the former, maintaining an extracellular: intracellular glucose concentration gradient which facilitates further uptake of glucose.\n\n\n\n\nPossibility 2: Glucose ‘Activation’\n\n\n\n\nIn my opinion this is incorrect. As exemplified in another answer (https://biology.stackexchange.com/questions/115773/why-is-the-transfer-of-a-phosphoryl-group-used-by-atp-to-drive-reactions-rather/115858#115858), the activation of a molecule by phosphoryl group transfer from ATP facilitates bond formation, both by transfer of energy and provision of a suitable catalytic pathway. However the 6-phosphate group of G6P does not take part in any such reaction, and all it is ‘activated’ for is the phosphorylation of ADP to regenerate the ATP used in its formation.\n\n\n\n\nI can find no source for the claim of activation other than a single assertion on a discussion site: “Phosphorylation occurs in the first step of glycolysis to activate the glucose molecule and make it more reactive.” However the poster does not expand on this or develop his argument further. I shall consider the phrase “make it more reactive” under Possibility 3.\n\n\n\n\nIt should be emphasized that a phosphoryl group at the 1-hydroxyl position in glucose 1-phosphate (G1P) is involved in reaction with UTP to form UDP-glucose, which is an activated form of glucose. It is activated to form a glycosidic linkage to the terminal glucosyl residue in a glycogen chain. (G1P is formed from G6P in a reaction catalysed by phosphoglucomutase.)\n\n\n\n\nPossibility 3: Facilitating the subsequent reactions of glycolysis\n\n\n\n\nThe 5th edition of the respected text Biochemistry by Berg et al. (originally Streyer) has the following comment on the phosphorylation of glucose to G6P:\n\n\n\n\n\n\n\n“This step is notable for two reasons (1) glucose 6-phosphate cannot\ndiffuse through the membrane because of its negative charges, and (2)\nthe addition of the phosphoryl group begins to destabilize glucose,\nthus facilitating its further metabolism.”\n\n\n\n\n\n\n\nThere is no explanation of the chemical nature of this ‘destabilization’ or, when the further metabolism is described subsequently, of how the phosphoryl group at the 6-position facilitates it. Moreover by the 9th edition there is no longer any mention of ‘destabilization’, with the second point becoming merely:\n\n\n\n\n\n\n\n“Also the addition of the phosphoryl group facilitates the eventual\nmetabolism of glucose into the three-carbon molecules with high\nphosphoryl group transfer potential.”\n\n\n\n\n\n\n\nBut again, despite a detailed account of the subsequent reactions, there is no explanation of how the phosphoryl group is supposed to facilitate them.\n\n\n\n\nMy chemistry is very rusty, but I do not see how the 6-phosphate can affect any of the subsequent reactions. In the absence of a precise chemical explanation, this cannot be accepted. (I shall post on SE regarding this specific point, but would welcome contributions from list members.)\n\n\n\n\nConclusion: Why not be satisfied with glucose trapping?\n\n\n\n\nI detect a vague feeling of dissatisfaction with glucose trapping as the primary reason for the evolutionary emergence of the phosphorylation of glucose. If glycolysis evolved to generate ATP anaerobically, then the pyruvate kinase ‘payback’ stage of glycolysis would have had to evolve at the same time, unless it already existed for some other purpose. And raising the question of which pathways or reactions evolved first (what about the other fates of phosphorylated hexoses or trioses?) brings one into extremely difficult territory. This must have been considered by weightier minds than mine — does any one know where?"},{"context_id":"115925","html":"<p>In my view this can ultimately be traced back to evolution.\nOne important element of substrate control by an enzyme is via a phosphate group. This is very common and in my view a result of evolution.\nThe phosphorylation modifies the interaction of a substrate with its enzyme, e.g. binding more tightly.\nThe negative charge also helps to keep Glc in the cell, because it cannot pass back through the nonpolar membrane.</p>\n","text":"In my view this can ultimately be traced back to evolution.\nOne important element of substrate control by an enzyme is via a phosphate group. This is very common and in my view a result of evolution.\nThe phosphorylation modifies the interaction of a substrate with its enzyme, e.g. binding more tightly.\nThe negative charge also helps to keep Glc in the cell, because it cannot pass back through the nonpolar membrane."}],"domain":"biology","external_citations":["https://biology.stackexchange.com/questions/115773/why-is-the-transfer-of-a-phosphoryl-group-used-by-atp-to-drive-reactions-rather/115858#115858","https://www.quora.com/Why-are-2-ATPs-used-in-glycolysis"],"ground_truth_type":"metadata_grounded","group_id":"b4f2483a6dca0bbfc525a13624bb8510176ecf1fa1719e2e94fec7553b20c2ad","hard_case_family":["multiple_sources","multiple_answer_candidates"],"id":"RHM-9a0c73a0a0ada8a11d73693d","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:04.377249+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/54ece81cba3a5a552bb15d6d3feedc4324a2ba2706d33480080ece9537efd4b1_0.json","raw_sha256":"f1eb8f7eda9336b81701b663029f9411e040c0bcf262148b7ede9a103ae73e69","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=4&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"elijah whipple","profile_url":"https://biology.stackexchange.com/users/95505/elijah-whipple","user_type":"registered"},"created_at":"2024-12-31T04:51:44+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"3BEC8E85-F377-49C3-B4A6-46B97BD264CB","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3BEC8E85-F377-49C3-B4A6-46B97BD264CB/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2025-01-07T17:43:39+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"49647A3A-BDDB-4D28-B453-8C4E4813EC3E","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/49647A3A-BDDB-4D28-B453-8C4E4813EC3E/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115885","source_record_sha256":"13d9fe7cf57e28680839d6a2cc70b677cd5127ad41da743850efbc7518c50fc6","source_url":"https://biology.stackexchange.com/questions/115885/what-is-the-primary-function-of-the-phosphorlyation-of-glucose-in-the-first-step","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What is the primary function of the phosphorlyation of glucose in the first step of glycolysis?\nWhat is the primary function of the phosphorlyation of glucose in the first step of glycolysis?\n\n\n\n\nSome textbooks emphasize that it traps glucose in the cell, but some sources mention glucose \"activation.\" There is a response on Quora (https://www.quora.com/Why-are-2-ATPs-used-in-glycolysis) that claims that energetics are irrelevant and that phosphorylation is solely about trapping glucose.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115920,"score":4},{"answer_id":115925,"score":0}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>It is possible that over time, they would diverge from each other solely from the effects of the slight differences in the gene pools. Even if you distributed the genotypes equally between each group, there will be average differences that can be amplified over generations of reproduction.</p>\n<p>How much would they diverge? That depends at which timepoint you analyze their differences. Since they begin with similar gene pools, the average genotype from each group will be similar at first, but become less and less similar over time. The rate of change would be linear(constant) without any external influences and if the populations reproduce at the same rate.</p>\n<p>Would they diverge into separate species eventually? Possibly, given enough time. Essentially, this question can be reworded to &quot;will they be able to produce fertile offspring with eachother?&quot; At some point, probably not, but it would take a while.</p>\n<p>(This assumes the isolated population groups are large enough to avoid negative effects of inbreeding, or the species is naturally not negatively affected by inbreeding.)</p>\n","answer_id":115969,"answer_text":"It is possible that over time, they would diverge from each other solely from the effects of the slight differences in the gene pools. Even if you distributed the genotypes equally between each group, there will be average differences that can be amplified over generations of reproduction.\n\n\n\n\nHow much would they diverge? That depends at which timepoint you analyze their differences. Since they begin with similar gene pools, the average genotype from each group will be similar at first, but become less and less similar over time. The rate of change would be linear(constant) without any external influences and if the populations reproduce at the same rate.\n\n\n\n\nWould they diverge into separate species eventually? Possibly, given enough time. Essentially, this question can be reworded to \"will they be able to produce fertile offspring with eachother?\" At some point, probably not, but it would take a while.\n\n\n\n\n(This assumes the isolated population groups are large enough to avoid negative effects of inbreeding, or the species is naturally not negatively affected by inbreeding.)","answer_url":"https://biology.stackexchange.com/a/115969","author":"boredatwork1234","author_url":"https://biology.stackexchange.com/users/98533/boredatwork1234","content_license":"CC BY-SA 4.0","created_at":"2025-01-16T15:33:42+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:22.614155+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2c8799380b8f5d7bf0fd42e594fd78a1835b27e1da9f481cc00f096bab9c01ca_0.json","raw_sha256":"348375a094fdfd6d9ca55d0bddc65d8dc7a7f0757e1e5a44c25e22a66b1a4892","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/116119;116113;116097;116096;116091;116087;116076;116067;116063;116059;116055;116037;116034;116028;116022;116012;116005;115997;115989;115988;115987;115979;115978;115976;115974;115973;115970;115966;115965;115957;115952;115939;115933;115932;115927;115921;115915;115903;115897;115894;115886;115885;115884;115881;115880;115868;115867;115857;115852;115840;115830;115825;115819;115815;115791;115780;115773;115764;115759;115756;115743;115736;115726;115723;115713;115699;115691;115689;115685;115678;115668;115664;115657;115650;115642;115639;115632;115627;115626;115609;115602;115598;115592;115588;115587;115580;115578;115570;115566;115562;115549;115537;115536;115531;115530;115528;115525;115521;115513;115510/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":115965,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"boredatwork1234","profile_url":"https://biology.stackexchange.com/users/98533/boredatwork1234","user_type":"registered"},"created_at":"2025-01-16T15:33:42+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"A6C26EA4-ADED-4723-9473-4B3963FC0170","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A6C26EA4-ADED-4723-9473-4B3963FC0170/view-source"}],"score":0},{"answer_html":"<p>The general topic you're looking for is <a href=\"https://pubmed.ncbi.nlm.nih.gov/?term=sympatric+speciation\" rel=\"nofollow noreferrer\">sympatric speciation</a>.  Some explanations given include <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC9060526/\" rel=\"nofollow noreferrer\">divergent selection</a> and <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC2141821/\" rel=\"nofollow noreferrer\">allochrony</a>.  There are some less-certain but intriguing explanations possible that are tied to genetics, besides the polyploidization that you mention.  Sometimes - as when a butterfly species mimics two different models - it pays to recombine all of the relevant traits into a <a href=\"https://pubmed.ncbi.nlm.nih.gov/33346837/\" rel=\"nofollow noreferrer\">supergene</a>.  If the supergene can become the basis of assortative mating, there should be a benefit in having fewer hybrids with non-mimetic wing patterns.</p>\n<p>A curious, similar phenomenon is <a href=\"https://pubmed.ncbi.nlm.nih.gov/?term=drosophila+inversion+polymorphism\" rel=\"nofollow noreferrer\">inversion polymorphism</a>, as seen in <em>Drosophila</em>.  While these by definition occur within one species, the inverted regions have a strong barrier to gene flow, since simple recombinants develop a chromosomal abnormality.  Cases of <a href=\"https://pubmed.ncbi.nlm.nih.gov/38482698/\" rel=\"nofollow noreferrer\">speciation</a> are believed to have arisen this way.</p>\n","answer_id":116114,"answer_text":"The general topic you're looking for is sympatric speciation (https://pubmed.ncbi.nlm.nih.gov/?term=sympatric+speciation).  Some explanations given include divergent selection (https://pmc.ncbi.nlm.nih.gov/articles/PMC9060526/) and allochrony (https://pmc.ncbi.nlm.nih.gov/articles/PMC2141821/).  There are some less-certain but intriguing explanations possible that are tied to genetics, besides the polyploidization that you mention.  Sometimes - as when a butterfly species mimics two different models - it pays to recombine all of the relevant traits into a supergene (https://pubmed.ncbi.nlm.nih.gov/33346837/).  If the supergene can become the basis of assortative mating, there should be a benefit in having fewer hybrids with non-mimetic wing patterns.\n\n\n\n\nA curious, similar phenomenon is inversion polymorphism (https://pubmed.ncbi.nlm.nih.gov/?term=drosophila+inversion+polymorphism), as seen in Drosophila.  While these by definition occur within one species, the inverted regions have a strong barrier to gene flow, since simple recombinants develop a chromosomal abnormality.  Cases of speciation (https://pubmed.ncbi.nlm.nih.gov/38482698/) are believed to have arisen this way.","answer_url":"https://biology.stackexchange.com/a/116114","author":"Mike Serfas","author_url":"https://biology.stackexchange.com/users/57271/mike-serfas","content_license":"CC BY-SA 4.0","created_at":"2025-02-16T23:20:27+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:24.022014+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/01aac796e48517b802ddadc0ad653c0cb9714bed9c7b63fe9d85feeb033045b4_0.json","raw_sha256":"78b00075a5e7010b6a99b251890c500809ce80227f5b68d26c5fa522422bf915","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/116119;116113;116097;116096;116091;116087;116076;116067;116063;116059;116055;116037;116034;116028;116022;116012;116005;115997;115989;115988;115987;115979;115978;115976;115974;115973;115970;115966;115965;115957;115952;115939;115933;115932;115927;115921;115915;115903;115897;115894;115886;115885;115884;115881;115880;115868;115867;115857;115852;115840;115830;115825;115819;115815;115791;115780;115773;115764;115759;115756;115743;115736;115726;115723;115713;115699;115691;115689;115685;115678;115668;115664;115657;115650;115642;115639;115632;115627;115626;115609;115602;115598;115592;115588;115587;115580;115578;115570;115566;115562;115549;115537;115536;115531;115530;115528;115525;115521;115513;115510/answers?filter=withbody&order=asc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":115965,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Mike Serfas","profile_url":"https://biology.stackexchange.com/users/57271/mike-serfas","user_type":"registered"},"created_at":"2025-02-16T23:20:27+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"58BB4721-86F5-4D09-BA4E-D9D603FDC827","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/58BB4721-86F5-4D09-BA4E-D9D603FDC827/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"user386598","author_url":"https://biology.stackexchange.com/users/87773/user386598","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user386598","profile_url":"https://biology.stackexchange.com/users/87773/user386598","user_type":"registered"},"created_at":"2025-01-15T22:55:14+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"3223C0BD-BB65-4057-BCD3-7F5FB8FFBAEE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3223C0BD-BB65-4057-BCD3-7F5FB8FFBAEE/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2025-02-15T16:04:35+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"25D462F1-79A8-4ED6-B1A6-637FA7EE1204","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/25D462F1-79A8-4ED6-B1A6-637FA7EE1204/view-source"}],"url":"https://biology.stackexchange.com/questions/115965/by-which-processes-can-speciation-occur"},{"author":"boredatwork1234","author_url":"https://biology.stackexchange.com/users/98533/boredatwork1234","content_license":"CC BY-SA 4.0","context_id":"115969","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"boredatwork1234","profile_url":"https://biology.stackexchange.com/users/98533/boredatwork1234","user_type":"registered"},"created_at":"2025-01-16T15:33:42+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"A6C26EA4-ADED-4723-9473-4B3963FC0170","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A6C26EA4-ADED-4723-9473-4B3963FC0170/view-source"}],"url":"https://biology.stackexchange.com/a/115969"},{"author":"Mike Serfas","author_url":"https://biology.stackexchange.com/users/57271/mike-serfas","content_license":"CC BY-SA 4.0","context_id":"116114","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Mike Serfas","profile_url":"https://biology.stackexchange.com/users/57271/mike-serfas","user_type":"registered"},"created_at":"2025-02-16T23:20:27+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"58BB4721-86F5-4D09-BA4E-D9D603FDC827","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/58BB4721-86F5-4D09-BA4E-D9D603FDC827/view-source"}],"url":"https://biology.stackexchange.com/a/116114"}],"contexts":[{"context_id":"question","html":"<p>I already know that the divergence of one species into two can happen through a variety of methods.</p>\n<ul>\n<li><p>part of a population is isolated and different environmental factors cause different selective pressures</p>\n</li>\n<li><p>sexual selection because certain traits are more considered more attractive in organisms</p>\n</li>\n<li><p>polyploidy</p>\n</li>\n<li><p>genetic drift/mutation/other random things</p>\n</li>\n<li><p>etc.</p>\n</li>\n</ul>\n<p>However, say a part of a species is isolated in similar conditions as the species in the main area. Ruling out random factors like genetic drift, mutation, etc., could the species still diverge? What I mean is, would it be possible for certain organisms to inherit unique combinations of genes from their parents so that they develop unique enough traits over a long period of time and can thus be classified as a separate species? I am basically wondering if simple inheritance and basic genetics, without any selective pressures or random occurences, can lead to the divergence of a species. Please let me know if the wording of this question doesn't make sense so I can fix it. Thanks!</p>\n","text":"I already know that the divergence of one species into two can happen through a variety of methods.\n\n\n\n\n\n\n\npart of a population is isolated and different environmental factors cause different selective pressures\n\n\n\n\n\n\n\n\n\nsexual selection because certain traits are more considered more attractive in organisms\n\n\n\n\n\n\n\n\n\npolyploidy\n\n\n\n\n\n\n\n\n\ngenetic drift/mutation/other random things\n\n\n\n\n\n\n\n\n\netc.\n\n\n\n\n\n\n\n\nHowever, say a part of a species is isolated in similar conditions as the species in the main area. Ruling out random factors like genetic drift, mutation, etc., could the species still diverge? What I mean is, would it be possible for certain organisms to inherit unique combinations of genes from their parents so that they develop unique enough traits over a long period of time and can thus be classified as a separate species? I am basically wondering if simple inheritance and basic genetics, without any selective pressures or random occurences, can lead to the divergence of a species. Please let me know if the wording of this question doesn't make sense so I can fix it. Thanks!"},{"context_id":"115969","html":"<p>It is possible that over time, they would diverge from each other solely from the effects of the slight differences in the gene pools. Even if you distributed the genotypes equally between each group, there will be average differences that can be amplified over generations of reproduction.</p>\n<p>How much would they diverge? That depends at which timepoint you analyze their differences. Since they begin with similar gene pools, the average genotype from each group will be similar at first, but become less and less similar over time. The rate of change would be linear(constant) without any external influences and if the populations reproduce at the same rate.</p>\n<p>Would they diverge into separate species eventually? Possibly, given enough time. Essentially, this question can be reworded to &quot;will they be able to produce fertile offspring with eachother?&quot; At some point, probably not, but it would take a while.</p>\n<p>(This assumes the isolated population groups are large enough to avoid negative effects of inbreeding, or the species is naturally not negatively affected by inbreeding.)</p>\n","text":"It is possible that over time, they would diverge from each other solely from the effects of the slight differences in the gene pools. Even if you distributed the genotypes equally between each group, there will be average differences that can be amplified over generations of reproduction.\n\n\n\n\nHow much would they diverge? That depends at which timepoint you analyze their differences. Since they begin with similar gene pools, the average genotype from each group will be similar at first, but become less and less similar over time. The rate of change would be linear(constant) without any external influences and if the populations reproduce at the same rate.\n\n\n\n\nWould they diverge into separate species eventually? Possibly, given enough time. Essentially, this question can be reworded to \"will they be able to produce fertile offspring with eachother?\" At some point, probably not, but it would take a while.\n\n\n\n\n(This assumes the isolated population groups are large enough to avoid negative effects of inbreeding, or the species is naturally not negatively affected by inbreeding.)"},{"context_id":"116114","html":"<p>The general topic you're looking for is <a href=\"https://pubmed.ncbi.nlm.nih.gov/?term=sympatric+speciation\" rel=\"nofollow noreferrer\">sympatric speciation</a>.  Some explanations given include <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC9060526/\" rel=\"nofollow noreferrer\">divergent selection</a> and <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC2141821/\" rel=\"nofollow noreferrer\">allochrony</a>.  There are some less-certain but intriguing explanations possible that are tied to genetics, besides the polyploidization that you mention.  Sometimes - as when a butterfly species mimics two different models - it pays to recombine all of the relevant traits into a <a href=\"https://pubmed.ncbi.nlm.nih.gov/33346837/\" rel=\"nofollow noreferrer\">supergene</a>.  If the supergene can become the basis of assortative mating, there should be a benefit in having fewer hybrids with non-mimetic wing patterns.</p>\n<p>A curious, similar phenomenon is <a href=\"https://pubmed.ncbi.nlm.nih.gov/?term=drosophila+inversion+polymorphism\" rel=\"nofollow noreferrer\">inversion polymorphism</a>, as seen in <em>Drosophila</em>.  While these by definition occur within one species, the inverted regions have a strong barrier to gene flow, since simple recombinants develop a chromosomal abnormality.  Cases of <a href=\"https://pubmed.ncbi.nlm.nih.gov/38482698/\" rel=\"nofollow noreferrer\">speciation</a> are believed to have arisen this way.</p>\n","text":"The general topic you're looking for is sympatric speciation (https://pubmed.ncbi.nlm.nih.gov/?term=sympatric+speciation).  Some explanations given include divergent selection (https://pmc.ncbi.nlm.nih.gov/articles/PMC9060526/) and allochrony (https://pmc.ncbi.nlm.nih.gov/articles/PMC2141821/).  There are some less-certain but intriguing explanations possible that are tied to genetics, besides the polyploidization that you mention.  Sometimes - as when a butterfly species mimics two different models - it pays to recombine all of the relevant traits into a supergene (https://pubmed.ncbi.nlm.nih.gov/33346837/).  If the supergene can become the basis of assortative mating, there should be a benefit in having fewer hybrids with non-mimetic wing patterns.\n\n\n\n\nA curious, similar phenomenon is inversion polymorphism (https://pubmed.ncbi.nlm.nih.gov/?term=drosophila+inversion+polymorphism), as seen in Drosophila.  While these by definition occur within one species, the inverted regions have a strong barrier to gene flow, since simple recombinants develop a chromosomal abnormality.  Cases of speciation (https://pubmed.ncbi.nlm.nih.gov/38482698/) are believed to have arisen this way."}],"domain":"biology","external_citations":["https://pmc.ncbi.nlm.nih.gov/articles/PMC2141821/","https://pmc.ncbi.nlm.nih.gov/articles/PMC9060526/","https://pubmed.ncbi.nlm.nih.gov/33346837/","https://pubmed.ncbi.nlm.nih.gov/38482698/","https://pubmed.ncbi.nlm.nih.gov/?term=drosophila+inversion+polymorphism","https://pubmed.ncbi.nlm.nih.gov/?term=sympatric+speciation"],"ground_truth_type":"metadata_grounded","group_id":"4679e0a0a88189cf42b5a43f32d8209957fa083ed62655342c45c38760cf3960","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-f3085bb21f0edaa8d6150396","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:04.377249+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/54ece81cba3a5a552bb15d6d3feedc4324a2ba2706d33480080ece9537efd4b1_0.json","raw_sha256":"f1eb8f7eda9336b81701b663029f9411e040c0bcf262148b7ede9a103ae73e69","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=4&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user386598","profile_url":"https://biology.stackexchange.com/users/87773/user386598","user_type":"registered"},"created_at":"2025-01-15T22:55:14+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"3223C0BD-BB65-4057-BCD3-7F5FB8FFBAEE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3223C0BD-BB65-4057-BCD3-7F5FB8FFBAEE/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2025-02-15T16:04:35+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"25D462F1-79A8-4ED6-B1A6-637FA7EE1204","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/25D462F1-79A8-4ED6-B1A6-637FA7EE1204/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115965","source_record_sha256":"d8bd3fd36b57fdbc8a31b4a0b14c70140ebeee59decc2b520d3b6a2fede7f8a8","source_url":"https://biology.stackexchange.com/questions/115965/by-which-processes-can-speciation-occur","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"By which processes can speciation occur?\nI already know that the divergence of one species into two can happen through a variety of methods.\n\n\n\n\n\n\n\npart of a population is isolated and different environmental factors cause different selective pressures\n\n\n\n\n\n\n\n\n\nsexual selection because certain traits are more considered more attractive in organisms\n\n\n\n\n\n\n\n\n\npolyploidy\n\n\n\n\n\n\n\n\n\ngenetic drift/mutation/other random things\n\n\n\n\n\n\n\n\n\netc.\n\n\n\n\n\n\n\n\nHowever, say a part of a species is isolated in similar conditions as the species in the main area. Ruling out random factors like genetic drift, mutation, etc., could the species still diverge? What I mean is, would it be possible for certain organisms to inherit unique combinations of genes from their parents so that they develop unique enough traits over a long period of time and can thus be classified as a separate species? I am basically wondering if simple inheritance and basic genetics, without any selective pressures or random occurences, can lead to the divergence of a species. Please let me know if the wording of this question doesn't make sense so I can fix it. Thanks!","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115969,"score":0},{"answer_id":116114,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<blockquote>\n<p>different females have different preferences for the coloring of male fish</p>\n</blockquote>\n<p>Let's imagine males are either red or blue, and assume that preference and coloring are genetically independent traits.</p>\n<p>If red-preferring females mate more with red males, they'll have offspring that are both more likely to be red-preferring among the females and red among the males than the previous generation, because those are the traits of their parents.</p>\n<p>If blue-preferring females mate more with blue males, they'll have offspring that are both more likely to be blue-preferring among the females and blue among the males than the previous generation, because those are the traits of their parents.</p>\n<p>If males that aren't red or blue (perhaps they're a hybrid purple, or some other color) are not preferred by anyone, these males will be selected against and be less likely to have descendants in the next generation (and, same for their mixed-color offspring, so also more pressure for females to have a stronger preference), discouraging cross-breeding further.</p>\n<p>If these preferences are strong enough, over time you've effectively created a <a href=\"https://en.wikipedia.org/wiki/Genetic_isolate\" rel=\"nofollow noreferrer\">genetic isolation</a> between the individuals where it's not just that red-preferring females are likely to have red male offspring, but that they have all or nearly all red male offspring, because their mother preferred red males and so their father was a red male, because their grandmother preferred red males so their grandfather was a red male, etc, and they don't interbreed with the blue anymore.</p>\n<p>Once populations are isolated reproductively, further deviation could happen randomly, called <a href=\"https://en.wikipedia.org/wiki/Genetic_drift\" rel=\"nofollow noreferrer\">genetic drift</a>, as well as by selection. If a new heritable trait arises alongside one color, it's not going to be shared with the other color through reproduction if there's no reproduction occurring across colors.</p>\n","answer_id":115971,"answer_text":"different females have different preferences for the coloring of male fish\n\n\n\n\n\n\n\nLet's imagine males are either red or blue, and assume that preference and coloring are genetically independent traits.\n\n\n\n\nIf red-preferring females mate more with red males, they'll have offspring that are both more likely to be red-preferring among the females and red among the males than the previous generation, because those are the traits of their parents.\n\n\n\n\nIf blue-preferring females mate more with blue males, they'll have offspring that are both more likely to be blue-preferring among the females and blue among the males than the previous generation, because those are the traits of their parents.\n\n\n\n\nIf males that aren't red or blue (perhaps they're a hybrid purple, or some other color) are not preferred by anyone, these males will be selected against and be less likely to have descendants in the next generation (and, same for their mixed-color offspring, so also more pressure for females to have a stronger preference), discouraging cross-breeding further.\n\n\n\n\nIf these preferences are strong enough, over time you've effectively created a genetic isolation (https://en.wikipedia.org/wiki/Genetic_isolate) between the individuals where it's not just that red-preferring females are likely to have red male offspring, but that they have all or nearly all red male offspring, because their mother preferred red males and so their father was a red male, because their grandmother preferred red males so their grandfather was a red male, etc, and they don't interbreed with the blue anymore.\n\n\n\n\nOnce populations are isolated reproductively, further deviation could happen randomly, called genetic drift (https://en.wikipedia.org/wiki/Genetic_drift), as well as by selection. If a new heritable trait arises alongside one color, it's not going to be shared with the other color through reproduction if there's no reproduction occurring across colors.","answer_url":"https://biology.stackexchange.com/a/115971","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2025-01-16T21:27:41+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:22.614155+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2c8799380b8f5d7bf0fd42e594fd78a1835b27e1da9f481cc00f096bab9c01ca_0.json","raw_sha256":"348375a094fdfd6d9ca55d0bddc65d8dc7a7f0757e1e5a44c25e22a66b1a4892","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/116119;116113;116097;116096;116091;116087;116076;116067;116063;116059;116055;116037;116034;116028;116022;116012;116005;115997;115989;115988;115987;115979;115978;115976;115974;115973;115970;115966;115965;115957;115952;115939;115933;115932;115927;115921;115915;115903;115897;115894;115886;115885;115884;115881;115880;115868;115867;115857;115852;115840;115830;115825;115819;115815;115791;115780;115773;115764;115759;115756;115743;115736;115726;115723;115713;115699;115691;115689;115685;115678;115668;115664;115657;115650;115642;115639;115632;115627;115626;115609;115602;115598;115592;115588;115587;115580;115578;115570;115566;115562;115549;115537;115536;115531;115530;115528;115525;115521;115513;115510/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":115970,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2025-01-16T21:27:41+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"C2985E38-952D-444F-9EB9-696D437B37A0","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C2985E38-952D-444F-9EB9-696D437B37A0/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2025-01-16T22:07:52+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"B5B782C7-6CF1-4149-A51E-AD8A382045EB","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B5B782C7-6CF1-4149-A51E-AD8A382045EB/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"user386598","author_url":"https://biology.stackexchange.com/users/87773/user386598","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user386598","profile_url":"https://biology.stackexchange.com/users/87773/user386598","user_type":"registered"},"created_at":"2025-01-16T21:03:25+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"31570B73-C092-4866-8690-B5E3D0EA485A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/31570B73-C092-4866-8690-B5E3D0EA485A/view-source"}],"url":"https://biology.stackexchange.com/questions/115970/impact-of-sexual-selection-on-the-divergence-of-species"},{"author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","context_id":"115971","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2025-01-16T21:27:41+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"C2985E38-952D-444F-9EB9-696D437B37A0","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C2985E38-952D-444F-9EB9-696D437B37A0/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2025-01-16T22:07:52+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"B5B782C7-6CF1-4149-A51E-AD8A382045EB","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B5B782C7-6CF1-4149-A51E-AD8A382045EB/view-source"}],"url":"https://biology.stackexchange.com/a/115971"}],"contexts":[{"context_id":"question","html":"<p>I understand that natural selection can cause a species to diverge because selective pressures influence species based on where they live. However, I am unclear how sexual selection plays a role in speciation. Wouldn't it have to be paired with another factor to be cause species to diverge?</p>\n<p>An example that comes up a lot are African cichlids, for different females have different preferences for the coloring of male fish. However, I don't understand how this can split apart a species and cause drastically different traits. I know that the offspring of a fish will inherit different traits depending on the coloring of the male, but I don't get how this plays a big role in speciation.</p>\n<p>Hopefully this question makes sense. Thanks.</p>\n","text":"I understand that natural selection can cause a species to diverge because selective pressures influence species based on where they live. However, I am unclear how sexual selection plays a role in speciation. Wouldn't it have to be paired with another factor to be cause species to diverge?\n\n\n\n\nAn example that comes up a lot are African cichlids, for different females have different preferences for the coloring of male fish. However, I don't understand how this can split apart a species and cause drastically different traits. I know that the offspring of a fish will inherit different traits depending on the coloring of the male, but I don't get how this plays a big role in speciation.\n\n\n\n\nHopefully this question makes sense. Thanks."},{"context_id":"115971","html":"<blockquote>\n<p>different females have different preferences for the coloring of male fish</p>\n</blockquote>\n<p>Let's imagine males are either red or blue, and assume that preference and coloring are genetically independent traits.</p>\n<p>If red-preferring females mate more with red males, they'll have offspring that are both more likely to be red-preferring among the females and red among the males than the previous generation, because those are the traits of their parents.</p>\n<p>If blue-preferring females mate more with blue males, they'll have offspring that are both more likely to be blue-preferring among the females and blue among the males than the previous generation, because those are the traits of their parents.</p>\n<p>If males that aren't red or blue (perhaps they're a hybrid purple, or some other color) are not preferred by anyone, these males will be selected against and be less likely to have descendants in the next generation (and, same for their mixed-color offspring, so also more pressure for females to have a stronger preference), discouraging cross-breeding further.</p>\n<p>If these preferences are strong enough, over time you've effectively created a <a href=\"https://en.wikipedia.org/wiki/Genetic_isolate\" rel=\"nofollow noreferrer\">genetic isolation</a> between the individuals where it's not just that red-preferring females are likely to have red male offspring, but that they have all or nearly all red male offspring, because their mother preferred red males and so their father was a red male, because their grandmother preferred red males so their grandfather was a red male, etc, and they don't interbreed with the blue anymore.</p>\n<p>Once populations are isolated reproductively, further deviation could happen randomly, called <a href=\"https://en.wikipedia.org/wiki/Genetic_drift\" rel=\"nofollow noreferrer\">genetic drift</a>, as well as by selection. If a new heritable trait arises alongside one color, it's not going to be shared with the other color through reproduction if there's no reproduction occurring across colors.</p>\n","text":"different females have different preferences for the coloring of male fish\n\n\n\n\n\n\n\nLet's imagine males are either red or blue, and assume that preference and coloring are genetically independent traits.\n\n\n\n\nIf red-preferring females mate more with red males, they'll have offspring that are both more likely to be red-preferring among the females and red among the males than the previous generation, because those are the traits of their parents.\n\n\n\n\nIf blue-preferring females mate more with blue males, they'll have offspring that are both more likely to be blue-preferring among the females and blue among the males than the previous generation, because those are the traits of their parents.\n\n\n\n\nIf males that aren't red or blue (perhaps they're a hybrid purple, or some other color) are not preferred by anyone, these males will be selected against and be less likely to have descendants in the next generation (and, same for their mixed-color offspring, so also more pressure for females to have a stronger preference), discouraging cross-breeding further.\n\n\n\n\nIf these preferences are strong enough, over time you've effectively created a genetic isolation (https://en.wikipedia.org/wiki/Genetic_isolate) between the individuals where it's not just that red-preferring females are likely to have red male offspring, but that they have all or nearly all red male offspring, because their mother preferred red males and so their father was a red male, because their grandmother preferred red males so their grandfather was a red male, etc, and they don't interbreed with the blue anymore.\n\n\n\n\nOnce populations are isolated reproductively, further deviation could happen randomly, called genetic drift (https://en.wikipedia.org/wiki/Genetic_drift), as well as by selection. If a new heritable trait arises alongside one color, it's not going to be shared with the other color through reproduction if there's no reproduction occurring across colors."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Genetic_drift","https://en.wikipedia.org/wiki/Genetic_isolate"],"ground_truth_type":"metadata_grounded","group_id":"da3765a1e19957bee9f918469bf99a8e2162165a9ee52ecd9659463edc524513","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-029fb16db42d4d654be456d5","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:04.377249+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/54ece81cba3a5a552bb15d6d3feedc4324a2ba2706d33480080ece9537efd4b1_0.json","raw_sha256":"f1eb8f7eda9336b81701b663029f9411e040c0bcf262148b7ede9a103ae73e69","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=4&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user386598","profile_url":"https://biology.stackexchange.com/users/87773/user386598","user_type":"registered"},"created_at":"2025-01-16T21:03:25+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"31570B73-C092-4866-8690-B5E3D0EA485A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/31570B73-C092-4866-8690-B5E3D0EA485A/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115970","source_record_sha256":"95ae1e7971dfa2b348da05d7b31da8765c690d4eaf89e1216ec3349a5e72dd5b","source_url":"https://biology.stackexchange.com/questions/115970/impact-of-sexual-selection-on-the-divergence-of-species","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Impact of sexual selection on the divergence of species\nI understand that natural selection can cause a species to diverge because selective pressures influence species based on where they live. However, I am unclear how sexual selection plays a role in speciation. Wouldn't it have to be paired with another factor to be cause species to diverge?\n\n\n\n\nAn example that comes up a lot are African cichlids, for different females have different preferences for the coloring of male fish. However, I don't understand how this can split apart a species and cause drastically different traits. I know that the offspring of a fish will inherit different traits depending on the coloring of the male, but I don't get how this plays a big role in speciation.\n\n\n\n\nHopefully this question makes sense. Thanks.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115971,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Without going into how much epinephrine you might find in food, whether any of it gets absorbed, whether it matters how an animal is killed before being eaten, etc., let's for a moment just think about epinephrine metabolism within the human body.</p>\n<p>Here's some drug information from a pharmaceutical company that sells epinephrine to be injected intravenously, right into the blood: <a href=\"https://www.pfizermedicalinformation.com/epinephrine-0/clinical-pharmacology\" rel=\"nofollow noreferrer\">https://www.pfizermedicalinformation.com/epinephrine-0/clinical-pharmacology</a></p>\n<blockquote>\n<p>Following intravenous injection, epinephrine is rapidly cleared from the plasma with an effective half-life of &lt; 5 min.</p>\n</blockquote>\n<p>Any epinephrine in the bloodstream is only around for a few minutes. To create a physiological response with epinephrine, your endocrine system needs to continually release it. If there is any epinephrine in your food, it's going to be absorbed over a long time period and then any amount absorbed will not have any effect at all within a few minutes. That's assuming it's in the food at all, after the food has sat for days before getting to your table.</p>\n<p>There might be some reasonable dietary concerns about eating a diet heavy in meat versus vegetables, both because of fat and cholesterol content in meat and lack of fiber that seems to be associated with better health outcomes, but this business about epinephrine is certainly not one of them. I'm not sure I'd take health advice from someone who hasn't thought out these aspects of biology.</p>\n","answer_id":115975,"answer_text":"Without going into how much epinephrine you might find in food, whether any of it gets absorbed, whether it matters how an animal is killed before being eaten, etc., let's for a moment just think about epinephrine metabolism within the human body.\n\n\n\n\nHere's some drug information from a pharmaceutical company that sells epinephrine to be injected intravenously, right into the blood: https://www.pfizermedicalinformation.com/epinephrine-0/clinical-pharmacology (https://www.pfizermedicalinformation.com/epinephrine-0/clinical-pharmacology)\n\n\n\n\n\n\n\nFollowing intravenous injection, epinephrine is rapidly cleared from the plasma with an effective half-life of < 5 min.\n\n\n\n\n\n\n\nAny epinephrine in the bloodstream is only around for a few minutes. To create a physiological response with epinephrine, your endocrine system needs to continually release it. If there is any epinephrine in your food, it's going to be absorbed over a long time period and then any amount absorbed will not have any effect at all within a few minutes. That's assuming it's in the food at all, after the food has sat for days before getting to your table.\n\n\n\n\nThere might be some reasonable dietary concerns about eating a diet heavy in meat versus vegetables, both because of fat and cholesterol content in meat and lack of fiber that seems to be associated with better health outcomes, but this business about epinephrine is certainly not one of them. I'm not sure I'd take health advice from someone who hasn't thought out these aspects of biology.","answer_url":"https://biology.stackexchange.com/a/115975","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2025-01-17T15:56:52+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:22.614155+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2c8799380b8f5d7bf0fd42e594fd78a1835b27e1da9f481cc00f096bab9c01ca_0.json","raw_sha256":"348375a094fdfd6d9ca55d0bddc65d8dc7a7f0757e1e5a44c25e22a66b1a4892","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/116119;116113;116097;116096;116091;116087;116076;116067;116063;116059;116055;116037;116034;116028;116022;116012;116005;115997;115989;115988;115987;115979;115978;115976;115974;115973;115970;115966;115965;115957;115952;115939;115933;115932;115927;115921;115915;115903;115897;115894;115886;115885;115884;115881;115880;115868;115867;115857;115852;115840;115830;115825;115819;115815;115791;115780;115773;115764;115759;115756;115743;115736;115726;115723;115713;115699;115691;115689;115685;115678;115668;115664;115657;115650;115642;115639;115632;115627;115626;115609;115602;115598;115592;115588;115587;115580;115578;115570;115566;115562;115549;115537;115536;115531;115530;115528;115525;115521;115513;115510/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":115973,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2025-01-17T15:56:52+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"B0ECEB35-01FA-4B2F-A8B6-2A97BB27C590","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B0ECEB35-01FA-4B2F-A8B6-2A97BB27C590/view-source"}],"score":2},{"answer_html":"<p>Answer: <strong>NO</strong>, epinephrine is not bioavailable when ingested. Hence Epipens.</p>\n<p>Ingested Epinephrine is extensively metabolized in the gut (monoamine oxidase) and liver. It is a polar molecule which is poorly absorbed by the lipid membranes in the gut. There is minimal bioavailability when taken orally. That's why it is administered by injection.</p>\n","answer_id":115982,"answer_text":"Answer: NO, epinephrine is not bioavailable when ingested. Hence Epipens.\n\n\n\n\nIngested Epinephrine is extensively metabolized in the gut (monoamine oxidase) and liver. It is a polar molecule which is poorly absorbed by the lipid membranes in the gut. There is minimal bioavailability when taken orally. That's why it is administered by injection.","answer_url":"https://biology.stackexchange.com/a/115982","author":"Woody","author_url":"https://biology.stackexchange.com/users/98830/woody","content_license":"CC BY-SA 4.0","created_at":"2025-01-20T07:00:28+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:22.614155+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2c8799380b8f5d7bf0fd42e594fd78a1835b27e1da9f481cc00f096bab9c01ca_0.json","raw_sha256":"348375a094fdfd6d9ca55d0bddc65d8dc7a7f0757e1e5a44c25e22a66b1a4892","source_api":"Stack Exchange API 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Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2025-01-17T15:56:52+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"B0ECEB35-01FA-4B2F-A8B6-2A97BB27C590","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B0ECEB35-01FA-4B2F-A8B6-2A97BB27C590/view-source"}],"url":"https://biology.stackexchange.com/a/115975"},{"author":"Woody","author_url":"https://biology.stackexchange.com/users/98830/woody","content_license":"CC BY-SA 4.0","context_id":"115982","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Woody","profile_url":"https://biology.stackexchange.com/users/98830/woody","user_type":"registered"},"created_at":"2025-01-20T07:00:28+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"81ECDF70-36E6-4A7A-8E9D-E183D5C92AEB","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/81ECDF70-36E6-4A7A-8E9D-E183D5C92AEB/view-source"}],"url":"https://biology.stackexchange.com/a/115982"}],"contexts":[{"context_id":"question","html":"<p>I have been confronted with the following argument for vegetarianism:</p>\n<blockquote>\n<p>Animals have a sense of fear, so will secrete stress hormones such as epinephrine when anticipating slaughter. These hormones will be consumed along with the meat, go into the bloodstream, and have harmful effects on the eater. For this reason meat-eating is unhealthy.</p>\n</blockquote>\n<p>Is that true? I would have thought that to a large extent such complex molecules would be degraded, either during meat storage or in the digestive tract.</p>\n","text":"I have been confronted with the following argument for vegetarianism:\n\n\n\n\n\n\n\nAnimals have a sense of fear, so will secrete stress hormones such as epinephrine when anticipating slaughter. These hormones will be consumed along with the meat, go into the bloodstream, and have harmful effects on the eater. For this reason meat-eating is unhealthy.\n\n\n\n\n\n\n\nIs that true? I would have thought that to a large extent such complex molecules would be degraded, either during meat storage or in the digestive tract."},{"context_id":"115975","html":"<p>Without going into how much epinephrine you might find in food, whether any of it gets absorbed, whether it matters how an animal is killed before being eaten, etc., let's for a moment just think about epinephrine metabolism within the human body.</p>\n<p>Here's some drug information from a pharmaceutical company that sells epinephrine to be injected intravenously, right into the blood: <a href=\"https://www.pfizermedicalinformation.com/epinephrine-0/clinical-pharmacology\" rel=\"nofollow noreferrer\">https://www.pfizermedicalinformation.com/epinephrine-0/clinical-pharmacology</a></p>\n<blockquote>\n<p>Following intravenous injection, epinephrine is rapidly cleared from the plasma with an effective half-life of &lt; 5 min.</p>\n</blockquote>\n<p>Any epinephrine in the bloodstream is only around for a few minutes. To create a physiological response with epinephrine, your endocrine system needs to continually release it. If there is any epinephrine in your food, it's going to be absorbed over a long time period and then any amount absorbed will not have any effect at all within a few minutes. That's assuming it's in the food at all, after the food has sat for days before getting to your table.</p>\n<p>There might be some reasonable dietary concerns about eating a diet heavy in meat versus vegetables, both because of fat and cholesterol content in meat and lack of fiber that seems to be associated with better health outcomes, but this business about epinephrine is certainly not one of them. I'm not sure I'd take health advice from someone who hasn't thought out these aspects of biology.</p>\n","text":"Without going into how much epinephrine you might find in food, whether any of it gets absorbed, whether it matters how an animal is killed before being eaten, etc., let's for a moment just think about epinephrine metabolism within the human body.\n\n\n\n\nHere's some drug information from a pharmaceutical company that sells epinephrine to be injected intravenously, right into the blood: https://www.pfizermedicalinformation.com/epinephrine-0/clinical-pharmacology (https://www.pfizermedicalinformation.com/epinephrine-0/clinical-pharmacology)\n\n\n\n\n\n\n\nFollowing intravenous injection, epinephrine is rapidly cleared from the plasma with an effective half-life of < 5 min.\n\n\n\n\n\n\n\nAny epinephrine in the bloodstream is only around for a few minutes. To create a physiological response with epinephrine, your endocrine system needs to continually release it. If there is any epinephrine in your food, it's going to be absorbed over a long time period and then any amount absorbed will not have any effect at all within a few minutes. That's assuming it's in the food at all, after the food has sat for days before getting to your table.\n\n\n\n\nThere might be some reasonable dietary concerns about eating a diet heavy in meat versus vegetables, both because of fat and cholesterol content in meat and lack of fiber that seems to be associated with better health outcomes, but this business about epinephrine is certainly not one of them. I'm not sure I'd take health advice from someone who hasn't thought out these aspects of biology."},{"context_id":"115982","html":"<p>Answer: <strong>NO</strong>, epinephrine is not bioavailable when ingested. Hence Epipens.</p>\n<p>Ingested Epinephrine is extensively metabolized in the gut (monoamine oxidase) and liver. It is a polar molecule which is poorly absorbed by the lipid membranes in the gut. There is minimal bioavailability when taken orally. That's why it is administered by injection.</p>\n","text":"Answer: NO, epinephrine is not bioavailable when ingested. Hence Epipens.\n\n\n\n\nIngested Epinephrine is extensively metabolized in the gut (monoamine oxidase) and liver. It is a polar molecule which is poorly absorbed by the lipid membranes in the gut. There is minimal bioavailability when taken orally. That's why it is administered by injection."}],"domain":"biology","external_citations":["https://www.pfizermedicalinformation.com/epinephrine-0/clinical-pharmacology"],"ground_truth_type":"metadata_grounded","group_id":"393e8df035c729407906d95a5aebfa403329c15b7da09058ac1f8f655582c021","hard_case_family":["no_accepted_answer","multiple_answer_candidates"],"id":"RHM-7056a1152892a577522cb323","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:04.377249+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/54ece81cba3a5a552bb15d6d3feedc4324a2ba2706d33480080ece9537efd4b1_0.json","raw_sha256":"f1eb8f7eda9336b81701b663029f9411e040c0bcf262148b7ede9a103ae73e69","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=4&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user96704","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-01-17T15:21:12+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"CDCE3523-B488-4A1F-94A8-3F013FEFB178","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CDCE3523-B488-4A1F-94A8-3F013FEFB178/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user96704","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-01-17T15:21:45+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"87206F00-C2FD-43C0-89BC-FD30DA32D2B8","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/87206F00-C2FD-43C0-89BC-FD30DA32D2B8/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user96704","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-01-17T15:22:01+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"B17B8A30-4482-40D0-9C03-937E6ED3E655","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B17B8A30-4482-40D0-9C03-937E6ED3E655/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user96704","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-01-17T15:22:26+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"DC9FB375-A5FE-4A19-8E59-D03F5045E4D1","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DC9FB375-A5FE-4A19-8E59-D03F5045E4D1/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2025-01-19T17:07:50+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"A1E929F2-49FF-4DDE-8FE3-0BAAE1487169","revision_number":5,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A1E929F2-49FF-4DDE-8FE3-0BAAE1487169/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115973","source_record_sha256":"60b1ccf25601d878f64f0c8408c771cf1b6eb0ddb9355ea5740aa3aa8ada72e9","source_url":"https://biology.stackexchange.com/questions/115973/are-epinephrine-or-other-stress-hormones-taken-up-with-potential-harmful-effect","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Are epinephrine or other stress hormones taken up, with potential harmful effects, when meat is consumed?\nI have been confronted with the following argument for vegetarianism:\n\n\n\n\n\n\n\nAnimals have a sense of fear, so will secrete stress hormones such as epinephrine when anticipating slaughter. These hormones will be consumed along with the meat, go into the bloodstream, and have harmful effects on the eater. For this reason meat-eating is unhealthy.\n\n\n\n\n\n\n\nIs that true? I would have thought that to a large extent such complex molecules would be degraded, either during meat storage or in the digestive tract.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115975,"score":2},{"answer_id":115982,"score":0}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p><a href=\"https://github.com/rrwick/Autocycler/issues/4#issuecomment-2605947209\" rel=\"nofollow noreferrer\">According to the author of Autocycler</a>:</p>\n<ul>\n<li>15× is the bare minimum for long-read assembly - any less than this and you'll likely only get short fragmented contigs.</li>\n<li>50× is a good general target - enough for a good assembly in most cases.</li>\n<li>100× or more is ideal if you want the best possible assembly.</li>\n<li>Read length matters too. If you have very long reads (e.g. &gt;25 kbp), you can get away with less depth, but if your reads are short (e.g. &lt;5 kbp), you will need more depth.</li>\n</ul>\n","answer_id":115995,"answer_text":"According to the author of Autocycler (https://github.com/rrwick/Autocycler/issues/4#issuecomment-2605947209):\n\n\n\n\n\n15× is the bare minimum for long-read assembly - any less than this and you'll likely only get short fragmented contigs.\n\n\n\n\n50× is a good general target - enough for a good assembly in most cases.\n\n\n\n\n100× or more is ideal if you want the best possible assembly.\n\n\n\n\nRead length matters too. If you have very long reads (e.g. >25 kbp), you can get away with less depth, but if your reads are short (e.g. <5 kbp), you will need more depth.","answer_url":"https://biology.stackexchange.com/a/115995","author":"bli","author_url":"https://biology.stackexchange.com/users/1486/bli","content_license":"CC BY-SA 4.0","created_at":"2025-01-23T10:42:58+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:22.614155+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2c8799380b8f5d7bf0fd42e594fd78a1835b27e1da9f481cc00f096bab9c01ca_0.json","raw_sha256":"348375a094fdfd6d9ca55d0bddc65d8dc7a7f0757e1e5a44c25e22a66b1a4892","source_api":"Stack Exchange API 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rewriting"},"question_id":115989,"revision_attribution":[{"content_license":null,"contributor":{"display_name":"bli","profile_url":"https://biology.stackexchange.com/users/1486/bli","user_type":"registered"},"created_at":"2025-01-23T10:42:58+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"6C3A8C5D-4C9C-4B93-936D-656C72FC296A","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/6C3A8C5D-4C9C-4B93-936D-656C72FC296A/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bli","profile_url":"https://biology.stackexchange.com/users/1486/bli","user_type":"registered"},"created_at":"2025-01-23T10:42:58+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"AA22B46B-C93E-4717-BB84-3CE6C7B2A7F3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AA22B46B-C93E-4717-BB84-3CE6C7B2A7F3/view-source"}],"score":3},{"answer_html":"<p>It's worth pointing out that <a href=\"https://en.wikipedia.org/wiki/DNA_sequencing_theory\" rel=\"nofollow noreferrer\">Lander-Waterman</a> and subsequent <a href=\"https://doi.org/10.1101%2Fgr.5.5.464\" rel=\"nofollow noreferrer\">work</a> (e.g. Roach 1995, <em>Genome Research</em>) provide a set of statistical tools for estimating the necessary coverage of sequencing given a genome length and read lengths.</p>\n<p>However, genome architecture and error models vary substantially enough that the practical rules of thumb such as that in the first answer and empirical tests are probably more informative for the average person wanting to do assembly.</p>\n","answer_id":116019,"answer_text":"It's worth pointing out that Lander-Waterman (https://en.wikipedia.org/wiki/DNA_sequencing_theory) and subsequent work (https://doi.org/10.1101%2Fgr.5.5.464) (e.g. Roach 1995, Genome Research) provide a set of statistical tools for estimating the necessary coverage of sequencing given a genome length and read lengths.\n\n\n\n\nHowever, genome architecture and error models vary substantially enough that the practical rules of thumb such as that in the first answer and empirical tests are probably more informative for the average person wanting to do assembly.","answer_url":"https://biology.stackexchange.com/a/116019","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2025-01-27T20:57:18+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:22.614155+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/2c8799380b8f5d7bf0fd42e594fd78a1835b27e1da9f481cc00f096bab9c01ca_0.json","raw_sha256":"348375a094fdfd6d9ca55d0bddc65d8dc7a7f0757e1e5a44c25e22a66b1a4892","source_api":"Stack Exchange API 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4.0","contributor":{"display_name":"bli","profile_url":"https://biology.stackexchange.com/users/1486/bli","user_type":"registered"},"created_at":"2025-01-23T10:42:58+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"AA22B46B-C93E-4717-BB84-3CE6C7B2A7F3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AA22B46B-C93E-4717-BB84-3CE6C7B2A7F3/view-source"}],"url":"https://biology.stackexchange.com/a/115995"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"116019","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2025-01-27T20:57:18+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"B3F9D08C-9CFD-4ABA-B80F-7C66760824C9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B3F9D08C-9CFD-4ABA-B80F-7C66760824C9/view-source"}],"url":"https://biology.stackexchange.com/a/116019"}],"contexts":[{"context_id":"question","html":"<p>The question is in the title: <strong>Are there typical minimal read depth recommendations to assemble a bacterial genome using long reads?</strong></p>\n<p>Some background: I'm supposed to build a semi-automated workflow performing long read assembly (based on <a href=\"https://github.com/rrwick/Autocycler\" rel=\"nofollow noreferrer\">https://github.com/rrwick/Autocycler</a>), and I'm considering adding some early sanity checks, in order to avoid useless automated processing (and possible failure).</p>\n","text":"The question is in the title: Are there typical minimal read depth recommendations to assemble a bacterial genome using long reads?\n\n\n\n\nSome background: I'm supposed to build a semi-automated workflow performing long read assembly (based on https://github.com/rrwick/Autocycler (https://github.com/rrwick/Autocycler)), and I'm considering adding some early sanity checks, in order to avoid useless automated processing (and possible failure)."},{"context_id":"115995","html":"<p><a href=\"https://github.com/rrwick/Autocycler/issues/4#issuecomment-2605947209\" rel=\"nofollow noreferrer\">According to the author of Autocycler</a>:</p>\n<ul>\n<li>15× is the bare minimum for long-read assembly - any less than this and you'll likely only get short fragmented contigs.</li>\n<li>50× is a good general target - enough for a good assembly in most cases.</li>\n<li>100× or more is ideal if you want the best possible assembly.</li>\n<li>Read length matters too. If you have very long reads (e.g. &gt;25 kbp), you can get away with less depth, but if your reads are short (e.g. &lt;5 kbp), you will need more depth.</li>\n</ul>\n","text":"According to the author of Autocycler (https://github.com/rrwick/Autocycler/issues/4#issuecomment-2605947209):\n\n\n\n\n\n15× is the bare minimum for long-read assembly - any less than this and you'll likely only get short fragmented contigs.\n\n\n\n\n50× is a good general target - enough for a good assembly in most cases.\n\n\n\n\n100× or more is ideal if you want the best possible assembly.\n\n\n\n\nRead length matters too. If you have very long reads (e.g. >25 kbp), you can get away with less depth, but if your reads are short (e.g. <5 kbp), you will need more depth."},{"context_id":"116019","html":"<p>It's worth pointing out that <a href=\"https://en.wikipedia.org/wiki/DNA_sequencing_theory\" rel=\"nofollow noreferrer\">Lander-Waterman</a> and subsequent <a href=\"https://doi.org/10.1101%2Fgr.5.5.464\" rel=\"nofollow noreferrer\">work</a> (e.g. Roach 1995, <em>Genome Research</em>) provide a set of statistical tools for estimating the necessary coverage of sequencing given a genome length and read lengths.</p>\n<p>However, genome architecture and error models vary substantially enough that the practical rules of thumb such as that in the first answer and empirical tests are probably more informative for the average person wanting to do assembly.</p>\n","text":"It's worth pointing out that Lander-Waterman (https://en.wikipedia.org/wiki/DNA_sequencing_theory) and subsequent work (https://doi.org/10.1101%2Fgr.5.5.464) (e.g. Roach 1995, Genome Research) provide a set of statistical tools for estimating the necessary coverage of sequencing given a genome length and read lengths.\n\n\n\n\nHowever, genome architecture and error models vary substantially enough that the practical rules of thumb such as that in the first answer and empirical tests are probably more informative for the average person wanting to do assembly."}],"domain":"biology","external_citations":["https://doi.org/10.1101%2Fgr.5.5.464","https://en.wikipedia.org/wiki/DNA_sequencing_theory","https://github.com/rrwick/Autocycler","https://github.com/rrwick/Autocycler/issues/4#issuecomment-2605947209"],"ground_truth_type":"metadata_grounded","group_id":"abe884c9cecafaa4951215e94ab5997c5915bca77faaee8e54a15efbfbe1fb73","hard_case_family":["no_accepted_answer","multiple_sources","multiple_answer_candidates"],"id":"RHM-c3aa61b5f495e8221db07acc","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:04.377249+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/54ece81cba3a5a552bb15d6d3feedc4324a2ba2706d33480080ece9537efd4b1_0.json","raw_sha256":"f1eb8f7eda9336b81701b663029f9411e040c0bcf262148b7ede9a103ae73e69","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=4&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bli","profile_url":"https://biology.stackexchange.com/users/1486/bli","user_type":"registered"},"created_at":"2025-01-21T11:55:17+00:00","raw_file":"raw/codex_api_v1/9208faf10edface85b193538ceee277a2c29dd57b691eaef3dbbd7fcb70c256f_1790824112025498400_0.json","raw_sha256":"cacf2fdbe629fb39b1a0932a5485abc61f5635b5e51482d0d3b8ab40f1450c36","revision_guid":"069A4176-B5EC-432D-B455-919AC800A588","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/069A4176-B5EC-432D-B455-919AC800A588/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"115989","source_record_sha256":"ebb2c71ab97470ae90ab90fb17ce04d13763f76dda71164799d6ecb8c038c84e","source_url":"https://biology.stackexchange.com/questions/115989/are-there-typical-minimal-read-depth-recommendations-to-assemble-a-bacterial-gen","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Are there typical minimal read depth recommendations to assemble a bacterial genome using long reads?\nThe question is in the title: Are there typical minimal read depth recommendations to assemble a bacterial genome using long reads?\n\n\n\n\nSome background: I'm supposed to build a semi-automated workflow performing long read assembly (based on https://github.com/rrwick/Autocycler (https://github.com/rrwick/Autocycler)), and I'm considering adding some early sanity checks, in order to avoid useless automated processing (and possible failure).","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115995,"score":3},{"answer_id":116019,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":116088,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>You can probably get pretty far with e.g. GFF3 annotations of the human genome. These are very targeted towards protein coding sequences.</p>\n<p>Here is one source for such annotations, Gencode: <a href=\"https://www.gencodegenes.org/human/\" rel=\"nofollow noreferrer\">https://www.gencodegenes.org/human/</a>.</p>\n<p>For repeat information, my recollection is that <a href=\"https://www.repeatmasker.org/\" rel=\"nofollow noreferrer\">RepeatMasker</a> does a basic annotation of the human genome.</p>\n<p>You can see the <a href=\"https://github.com/marbl/CHM13?tab=readme-ov-file\" rel=\"nofollow noreferrer\">T2T GitHub page</a> for a lot of e.g. tabular data formats annotating repeats, GFF3s etc. if you choose to go with that genome build version.</p>\n<p>For recent high level statistics, the recent <a href=\"https://ccb.jhu.edu/T2T.shtml\" rel=\"nofollow noreferrer\">T2T high-completeness genome project</a> might be a good resource.</p>\n<p>I'd recommend looking at both the <a href=\"https://www.nature.com/articles/35057062\" rel=\"nofollow noreferrer\">original human genome paper</a> and the <a href=\"https://www.science.org/doi/10.1126/science.abj6987\" rel=\"nofollow noreferrer\">T2T genome paper</a> for more information and high level stats.</p>\n","answer_id":116088,"answer_text":"You can probably get pretty far with e.g. GFF3 annotations of the human genome. These are very targeted towards protein coding sequences.\n\n\n\n\nHere is one source for such annotations, Gencode: https://www.gencodegenes.org/human/ (https://www.gencodegenes.org/human/).\n\n\n\n\nFor repeat information, my recollection is that RepeatMasker (https://www.repeatmasker.org/) does a basic annotation of the human genome.\n\n\n\n\nYou can see the T2T GitHub page (https://github.com/marbl/CHM13?tab=readme-ov-file) for a lot of e.g. tabular data formats annotating repeats, GFF3s etc. if you choose to go with that genome build version.\n\n\n\n\nFor recent high level statistics, the recent T2T high-completeness genome project (https://ccb.jhu.edu/T2T.shtml) might be a good resource.\n\n\n\n\nI'd recommend looking at both the original human genome paper (https://www.nature.com/articles/35057062) and the T2T genome paper (https://www.science.org/doi/10.1126/science.abj6987) for more information and high level stats.","answer_url":"https://biology.stackexchange.com/a/116088","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2025-02-10T17:44:43+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:24.022014+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/01aac796e48517b802ddadc0ad653c0cb9714bed9c7b63fe9d85feeb033045b4_0.json","raw_sha256":"78b00075a5e7010b6a99b251890c500809ce80227f5b68d26c5fa522422bf915","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/116119;116113;116097;116096;116091;116087;116076;116067;116063;116059;116055;116037;116034;116028;116022;116012;116005;115997;115989;115988;115987;115979;115978;115976;115974;115973;115970;115966;115965;115957;115952;115939;115933;115932;115927;115921;115915;115903;115897;115894;115886;115885;115884;115881;115880;115868;115867;115857;115852;115840;115830;115825;115819;115815;115791;115780;115773;115764;115759;115756;115743;115736;115726;115723;115713;115699;115691;115689;115685;115678;115668;115664;115657;115650;115642;115639;115632;115627;115626;115609;115602;115598;115592;115588;115587;115580;115578;115570;115566;115562;115549;115537;115536;115531;115530;115528;115525;115521;115513;115510/answers?filter=withbody&order=asc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":116087,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2025-02-10T17:44:43+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"B1B6108A-C756-433F-8221-502A7D2766AA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B1B6108A-C756-433F-8221-502A7D2766AA/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Francesco Ghizzo","author_url":"https://biology.stackexchange.com/users/78855/francesco-ghizzo","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Francesco Ghizzo","profile_url":"https://biology.stackexchange.com/users/78855/francesco-ghizzo","user_type":"registered"},"created_at":"2025-02-10T13:23:48+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"56730706-AD69-4CDC-ABFA-8216C84F7069","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/56730706-AD69-4CDC-ABFA-8216C84F7069/view-source"}],"url":"https://biology.stackexchange.com/questions/116087/where-and-how-can-i-download-the-human-genome-metadata-not-the-actual-sequence"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"116088","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2025-02-10T17:44:43+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"B1B6108A-C756-433F-8221-502A7D2766AA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B1B6108A-C756-433F-8221-502A7D2766AA/view-source"}],"url":"https://biology.stackexchange.com/a/116088"}],"contexts":[{"context_id":"question","html":"<p>Sorry if it may be a silly question for someone who works in the field.\nI'm a science communicator and I would like to create a few fancy visualizations of the human genome.\nFor example: which percentage of the human genome is comprised of coding genes, non coding genes, pseudogenes, ERV, transposable elements, repeats, etc.\nOr which percentage of coding genes is made of exons and introns.\nOr which percentage of the genome has been annotated.\nFor this purpose, I don't need the whole genome assembly (the actual sequence of nucleobases) I just need to download something like a table I could import in SQL, Python or R shaped like this:</p>\n<pre><code>ID.    Symbol.      Name.                Type               length\n\n01.    COL1A1.      Collagen Type I.     coding gene.       17,531\n02.    MIR21.       microRNA 21          non coding gene.   72 \n...    ...          ...                  ...                ...\n</code></pre>\n<p>This would allow me to easily calculate and plot any kind of aggregate statistics.\nDo you know if there is any way to download this whole metadata table from <a href=\"https://www.ncbi.nlm.nih.gov/datasets/taxonomy/9606/\" rel=\"nofollow noreferrer\">NCBI</a>?</p>\n","text":"Sorry if it may be a silly question for someone who works in the field.\nI'm a science communicator and I would like to create a few fancy visualizations of the human genome.\nFor example: which percentage of the human genome is comprised of coding genes, non coding genes, pseudogenes, ERV, transposable elements, repeats, etc.\nOr which percentage of coding genes is made of exons and introns.\nOr which percentage of the genome has been annotated.\nFor this purpose, I don't need the whole genome assembly (the actual sequence of nucleobases) I just need to download something like a table I could import in SQL, Python or R shaped like this:\n\n\n\n\nID.    Symbol.      Name.                Type               length\n\n01.    COL1A1.      Collagen Type I.     coding gene.       17,531\n02.    MIR21.       microRNA 21          non coding gene.   72 \n...    ...          ...                  ...                ...\n\n\n\n\n\nThis would allow me to easily calculate and plot any kind of aggregate statistics.\nDo you know if there is any way to download this whole metadata table from NCBI (https://www.ncbi.nlm.nih.gov/datasets/taxonomy/9606/)?"},{"context_id":"116088","html":"<p>You can probably get pretty far with e.g. GFF3 annotations of the human genome. These are very targeted towards protein coding sequences.</p>\n<p>Here is one source for such annotations, Gencode: <a href=\"https://www.gencodegenes.org/human/\" rel=\"nofollow noreferrer\">https://www.gencodegenes.org/human/</a>.</p>\n<p>For repeat information, my recollection is that <a href=\"https://www.repeatmasker.org/\" rel=\"nofollow noreferrer\">RepeatMasker</a> does a basic annotation of the human genome.</p>\n<p>You can see the <a href=\"https://github.com/marbl/CHM13?tab=readme-ov-file\" rel=\"nofollow noreferrer\">T2T GitHub page</a> for a lot of e.g. tabular data formats annotating repeats, GFF3s etc. if you choose to go with that genome build version.</p>\n<p>For recent high level statistics, the recent <a href=\"https://ccb.jhu.edu/T2T.shtml\" rel=\"nofollow noreferrer\">T2T high-completeness genome project</a> might be a good resource.</p>\n<p>I'd recommend looking at both the <a href=\"https://www.nature.com/articles/35057062\" rel=\"nofollow noreferrer\">original human genome paper</a> and the <a href=\"https://www.science.org/doi/10.1126/science.abj6987\" rel=\"nofollow noreferrer\">T2T genome paper</a> for more information and high level stats.</p>\n","text":"You can probably get pretty far with e.g. GFF3 annotations of the human genome. These are very targeted towards protein coding sequences.\n\n\n\n\nHere is one source for such annotations, Gencode: https://www.gencodegenes.org/human/ (https://www.gencodegenes.org/human/).\n\n\n\n\nFor repeat information, my recollection is that RepeatMasker (https://www.repeatmasker.org/) does a basic annotation of the human genome.\n\n\n\n\nYou can see the T2T GitHub page (https://github.com/marbl/CHM13?tab=readme-ov-file) for a lot of e.g. tabular data formats annotating repeats, GFF3s etc. if you choose to go with that genome build version.\n\n\n\n\nFor recent high level statistics, the recent T2T high-completeness genome project (https://ccb.jhu.edu/T2T.shtml) might be a good resource.\n\n\n\n\nI'd recommend looking at both the original human genome paper (https://www.nature.com/articles/35057062) and the T2T genome paper (https://www.science.org/doi/10.1126/science.abj6987) for more information and high level stats."}],"domain":"biology","external_citations":["https://ccb.jhu.edu/T2T.shtml","https://github.com/marbl/CHM13?tab=readme-ov-file","https://www.gencodegenes.org/human/","https://www.nature.com/articles/35057062","https://www.ncbi.nlm.nih.gov/datasets/taxonomy/9606/","https://www.repeatmasker.org/","https://www.science.org/doi/10.1126/science.abj6987"],"ground_truth_type":"metadata_grounded","group_id":"08d4a7a8720f278f3eee24cd6eb4ac88f74bfc497b65e96654abf6868ae90a38","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-f5ba167708a655ecb73c0447","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:04.377249+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/54ece81cba3a5a552bb15d6d3feedc4324a2ba2706d33480080ece9537efd4b1_0.json","raw_sha256":"f1eb8f7eda9336b81701b663029f9411e040c0bcf262148b7ede9a103ae73e69","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=4&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Francesco Ghizzo","profile_url":"https://biology.stackexchange.com/users/78855/francesco-ghizzo","user_type":"registered"},"created_at":"2025-02-10T13:23:48+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"56730706-AD69-4CDC-ABFA-8216C84F7069","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/56730706-AD69-4CDC-ABFA-8216C84F7069/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"116087","source_record_sha256":"3345c432f08e24dad63aa4cf333a535ea4c1491654166f50ed35dafdd0ca3187","source_url":"https://biology.stackexchange.com/questions/116087/where-and-how-can-i-download-the-human-genome-metadata-not-the-actual-sequence","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Where and how can I download the human genome metadata (not the actual sequence)?\nSorry if it may be a silly question for someone who works in the field.\nI'm a science communicator and I would like to create a few fancy visualizations of the human genome.\nFor example: which percentage of the human genome is comprised of coding genes, non coding genes, pseudogenes, ERV, transposable elements, repeats, etc.\nOr which percentage of coding genes is made of exons and introns.\nOr which percentage of the genome has been annotated.\nFor this purpose, I don't need the whole genome assembly (the actual sequence of nucleobases) I just need to download something like a table I could import in SQL, Python or R shaped like this:\n\n\n\n\nID.    Symbol.      Name.                Type               length\n\n01.    COL1A1.      Collagen Type I.     coding gene.       17,531\n02.    MIR21.       microRNA 21          non coding gene.   72 \n...    ...          ...                  ...                ...\n\n\n\n\n\nThis would allow me to easily calculate and plot any kind of aggregate statistics.\nDo you know if there is any way to download this whole metadata table from NCBI (https://www.ncbi.nlm.nih.gov/datasets/taxonomy/9606/)?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116088,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>As suggested in the comments, I transfer my comment to an answer:</p>\n<p>First of all, let me stress that the quote from the wikipedia article of the <a href=\"https://en.wikipedia.org/wiki/Blue_whale#Size\" rel=\"nofollow noreferrer\">blue whale</a></p>\n<blockquote>\n<p>The International Whaling Commission (IWC) whaling database reports 88 individuals longer than 30 meters (98 ft), including one of 33 meters (108 ft)</p>\n</blockquote>\n<p>is a bit unprecise, since it is actually not citing the IWC database, but rather the following article:</p>\n<ul>\n<li>C. R. McClain, et al. <em>Sizing ocean giants: patterns of intraspecific size variation in marine megafauna</em>. PeerJ. 2015 Jan 13;3:e715. doi: 10.7717/peerj.715. (the article is open access and can be read <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC4304853/\" rel=\"nofollow noreferrer\">here</a>).</li>\n</ul>\n<p>In this study, the authors analyze data from the IWC database, and they list a total of 88 blue whales exceeding 30 meters in length caught between 1916 and 1949, all of them in the Southern Ocean. While the IWC database in principle also includes records dating back to 1880, the authors argue that records before 1920 should be taken with caution, since the measurement methods are not always clearly stated and there is an ambiguity of whether Norwegian feet (0.314 m) or British feet (0.3048 m) were used. For example, the Guinness World Records <a href=\"https://www.guinnessworldrecords.com/world-records/69467-largest-whale\" rel=\"nofollow noreferrer\">lists a female blue whale</a> measuring 33.58 meters caught in 1909, but its accuracy remains uncertain. In fact, there is even a study argueing that blue whales should not be able to exceed 33 meters due to metabolic and energy constraints (see <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC3443106/\" rel=\"nofollow noreferrer\">here</a>).</p>\n<p>In any case, the following two graphs from the article of McClain et al. should be helpful in answering your question (source: McClaim et al., Figures 38 and 39):</p>\n<p><a href=\"https://i.sstatic.net/AJx5ol8Jl.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/AJx5ol8Jl.jpg\" alt=\"enter image description here\" /></a>\n<a href=\"https://i.sstatic.net/27Zf0kM6.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/27Zf0kM6.jpg\" alt=\"enter image description here\" /></a></p>\n<p>The full data set of McClain et al. was quite large and includes 288 551 indivduals, containing the 88 huge ones. From the first graph you can see that most of these 88 whales were caught in the pelagic zone (i.e. the open ocean) of the southern hemisphere. It seems, that most of them were femals, which also makes sense, since female blue whales tend to be a bit larger than males. Unfortunately, the figures and the paper of McClain et al. does not include information about age. Given the fact that many of them have probably been catched by commercial whale hunters, I think that this kind of information does not exist anyway.</p>\n","answer_id":116100,"answer_text":"As suggested in the comments, I transfer my comment to an answer:\n\n\n\n\nFirst of all, let me stress that the quote from the wikipedia article of the blue whale (https://en.wikipedia.org/wiki/Blue_whale#Size)\n\n\n\n\n\n\n\nThe International Whaling Commission (IWC) whaling database reports 88 individuals longer than 30 meters (98 ft), including one of 33 meters (108 ft)\n\n\n\n\n\n\n\nis a bit unprecise, since it is actually not citing the IWC database, but rather the following article:\n\n\n\n\n\nC. R. McClain, et al. Sizing ocean giants: patterns of intraspecific size variation in marine megafauna. PeerJ. 2015 Jan 13;3:e715. doi: 10.7717/peerj.715. (the article is open access and can be read here (https://pmc.ncbi.nlm.nih.gov/articles/PMC4304853/)).\n\n\n\n\n\nIn this study, the authors analyze data from the IWC database, and they list a total of 88 blue whales exceeding 30 meters in length caught between 1916 and 1949, all of them in the Southern Ocean. While the IWC database in principle also includes records dating back to 1880, the authors argue that records before 1920 should be taken with caution, since the measurement methods are not always clearly stated and there is an ambiguity of whether Norwegian feet (0.314 m) or British feet (0.3048 m) were used. For example, the Guinness World Records lists a female blue whale (https://www.guinnessworldrecords.com/world-records/69467-largest-whale) measuring 33.58 meters caught in 1909, but its accuracy remains uncertain. In fact, there is even a study argueing that blue whales should not be able to exceed 33 meters due to metabolic and energy constraints (see here (https://pmc.ncbi.nlm.nih.gov/articles/PMC3443106/)).\n\n\n\n\nIn any case, the following two graphs from the article of McClain et al. should be helpful in answering your question (source: McClaim et al., Figures 38 and 39):\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/AJx5ol8Jl.jpg] (https://i.sstatic.net/AJx5ol8Jl.jpg)\n[image: enter image description here; source: https://i.sstatic.net/27Zf0kM6.jpg] (https://i.sstatic.net/27Zf0kM6.jpg)\n\n\n\n\nThe full data set of McClain et al. was quite large and includes 288 551 indivduals, containing the 88 huge ones. From the first graph you can see that most of these 88 whales were caught in the pelagic zone (i.e. the open ocean) of the southern hemisphere. It seems, that most of them were femals, which also makes sense, since female blue whales tend to be a bit larger than males. Unfortunately, the figures and the paper of McClain et al. does not include information about age. Given the fact that many of them have probably been catched by commercial whale hunters, I think that this kind of information does not exist anyway.","answer_url":"https://biology.stackexchange.com/a/116100","author":"G. Blaickner","author_url":"https://biology.stackexchange.com/users/76678/g-blaickner","content_license":"CC BY-SA 4.0","created_at":"2025-02-13T22:08:48+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:24.022014+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/01aac796e48517b802ddadc0ad653c0cb9714bed9c7b63fe9d85feeb033045b4_0.json","raw_sha256":"78b00075a5e7010b6a99b251890c500809ce80227f5b68d26c5fa522422bf915","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/116119;116113;116097;116096;116091;116087;116076;116067;116063;116059;116055;116037;116034;116028;116022;116012;116005;115997;115989;115988;115987;115979;115978;115976;115974;115973;115970;115966;115965;115957;115952;115939;115933;115932;115927;115921;115915;115903;115897;115894;115886;115885;115884;115881;115880;115868;115867;115857;115852;115840;115830;115825;115819;115815;115791;115780;115773;115764;115759;115756;115743;115736;115726;115723;115713;115699;115691;115689;115685;115678;115668;115664;115657;115650;115642;115639;115632;115627;115626;115609;115602;115598;115592;115588;115587;115580;115578;115570;115566;115562;115549;115537;115536;115531;115530;115528;115525;115521;115513;115510/answers?filter=withbody&order=asc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":116096,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"G. Blaickner","profile_url":"https://biology.stackexchange.com/users/76678/g-blaickner","user_type":"registered"},"created_at":"2025-02-13T22:08:48+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"AC8667C3-75E2-4EF1-B9EB-65C4C1F23291","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AC8667C3-75E2-4EF1-B9EB-65C4C1F23291/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"G. Blaickner","profile_url":"https://biology.stackexchange.com/users/76678/g-blaickner","user_type":"registered"},"created_at":"2025-02-14T08:22:05+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"9F840BFE-FD6D-4E1C-91D1-DC10044F1D55","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9F840BFE-FD6D-4E1C-91D1-DC10044F1D55/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"ggk hj","author_url":"https://biology.stackexchange.com/users/75189/ggk-hj","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"ggk hj","profile_url":"https://biology.stackexchange.com/users/75189/ggk-hj","user_type":"registered"},"created_at":"2025-02-12T12:03:45+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"B27BD523-0C2D-4ACE-BEA9-9AD4A909B69B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B27BD523-0C2D-4ACE-BEA9-9AD4A909B69B/view-source"}],"url":"https://biology.stackexchange.com/questions/116096/where-can-i-find-information-on-blue-whales-longer-than-30-meters"},{"author":"G. Blaickner","author_url":"https://biology.stackexchange.com/users/76678/g-blaickner","content_license":"CC BY-SA 4.0","context_id":"116100","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"G. Blaickner","profile_url":"https://biology.stackexchange.com/users/76678/g-blaickner","user_type":"registered"},"created_at":"2025-02-13T22:08:48+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"AC8667C3-75E2-4EF1-B9EB-65C4C1F23291","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AC8667C3-75E2-4EF1-B9EB-65C4C1F23291/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"G. Blaickner","profile_url":"https://biology.stackexchange.com/users/76678/g-blaickner","user_type":"registered"},"created_at":"2025-02-14T08:22:05+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"9F840BFE-FD6D-4E1C-91D1-DC10044F1D55","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9F840BFE-FD6D-4E1C-91D1-DC10044F1D55/view-source"}],"url":"https://biology.stackexchange.com/a/116100"}],"contexts":[{"context_id":"question","html":"<p>Can anyone provide information from the IWC database or another source on the 88 blue whales over 30 meters in length (year, sex, age, region, etc.)?</p>\n<p>Wikipedia mentions this, but I don't know where to find more detailed information.</p>\n<p><a href=\"https://en.wikipedia.org/wiki/Blue_whale#Size\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/Blue_whale#Size</a></p>\n","text":"Can anyone provide information from the IWC database or another source on the 88 blue whales over 30 meters in length (year, sex, age, region, etc.)?\n\n\n\n\nWikipedia mentions this, but I don't know where to find more detailed information.\n\n\n\n\nhttps://en.wikipedia.org/wiki/Blue_whale#Size (https://en.wikipedia.org/wiki/Blue_whale#Size)"},{"context_id":"116100","html":"<p>As suggested in the comments, I transfer my comment to an answer:</p>\n<p>First of all, let me stress that the quote from the wikipedia article of the <a href=\"https://en.wikipedia.org/wiki/Blue_whale#Size\" rel=\"nofollow noreferrer\">blue whale</a></p>\n<blockquote>\n<p>The International Whaling Commission (IWC) whaling database reports 88 individuals longer than 30 meters (98 ft), including one of 33 meters (108 ft)</p>\n</blockquote>\n<p>is a bit unprecise, since it is actually not citing the IWC database, but rather the following article:</p>\n<ul>\n<li>C. R. McClain, et al. <em>Sizing ocean giants: patterns of intraspecific size variation in marine megafauna</em>. PeerJ. 2015 Jan 13;3:e715. doi: 10.7717/peerj.715. (the article is open access and can be read <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC4304853/\" rel=\"nofollow noreferrer\">here</a>).</li>\n</ul>\n<p>In this study, the authors analyze data from the IWC database, and they list a total of 88 blue whales exceeding 30 meters in length caught between 1916 and 1949, all of them in the Southern Ocean. While the IWC database in principle also includes records dating back to 1880, the authors argue that records before 1920 should be taken with caution, since the measurement methods are not always clearly stated and there is an ambiguity of whether Norwegian feet (0.314 m) or British feet (0.3048 m) were used. For example, the Guinness World Records <a href=\"https://www.guinnessworldrecords.com/world-records/69467-largest-whale\" rel=\"nofollow noreferrer\">lists a female blue whale</a> measuring 33.58 meters caught in 1909, but its accuracy remains uncertain. In fact, there is even a study argueing that blue whales should not be able to exceed 33 meters due to metabolic and energy constraints (see <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC3443106/\" rel=\"nofollow noreferrer\">here</a>).</p>\n<p>In any case, the following two graphs from the article of McClain et al. should be helpful in answering your question (source: McClaim et al., Figures 38 and 39):</p>\n<p><a href=\"https://i.sstatic.net/AJx5ol8Jl.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/AJx5ol8Jl.jpg\" alt=\"enter image description here\" /></a>\n<a href=\"https://i.sstatic.net/27Zf0kM6.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/27Zf0kM6.jpg\" alt=\"enter image description here\" /></a></p>\n<p>The full data set of McClain et al. was quite large and includes 288 551 indivduals, containing the 88 huge ones. From the first graph you can see that most of these 88 whales were caught in the pelagic zone (i.e. the open ocean) of the southern hemisphere. It seems, that most of them were femals, which also makes sense, since female blue whales tend to be a bit larger than males. Unfortunately, the figures and the paper of McClain et al. does not include information about age. Given the fact that many of them have probably been catched by commercial whale hunters, I think that this kind of information does not exist anyway.</p>\n","text":"As suggested in the comments, I transfer my comment to an answer:\n\n\n\n\nFirst of all, let me stress that the quote from the wikipedia article of the blue whale (https://en.wikipedia.org/wiki/Blue_whale#Size)\n\n\n\n\n\n\n\nThe International Whaling Commission (IWC) whaling database reports 88 individuals longer than 30 meters (98 ft), including one of 33 meters (108 ft)\n\n\n\n\n\n\n\nis a bit unprecise, since it is actually not citing the IWC database, but rather the following article:\n\n\n\n\n\nC. R. McClain, et al. Sizing ocean giants: patterns of intraspecific size variation in marine megafauna. PeerJ. 2015 Jan 13;3:e715. doi: 10.7717/peerj.715. (the article is open access and can be read here (https://pmc.ncbi.nlm.nih.gov/articles/PMC4304853/)).\n\n\n\n\n\nIn this study, the authors analyze data from the IWC database, and they list a total of 88 blue whales exceeding 30 meters in length caught between 1916 and 1949, all of them in the Southern Ocean. While the IWC database in principle also includes records dating back to 1880, the authors argue that records before 1920 should be taken with caution, since the measurement methods are not always clearly stated and there is an ambiguity of whether Norwegian feet (0.314 m) or British feet (0.3048 m) were used. For example, the Guinness World Records lists a female blue whale (https://www.guinnessworldrecords.com/world-records/69467-largest-whale) measuring 33.58 meters caught in 1909, but its accuracy remains uncertain. In fact, there is even a study argueing that blue whales should not be able to exceed 33 meters due to metabolic and energy constraints (see here (https://pmc.ncbi.nlm.nih.gov/articles/PMC3443106/)).\n\n\n\n\nIn any case, the following two graphs from the article of McClain et al. should be helpful in answering your question (source: McClaim et al., Figures 38 and 39):\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/AJx5ol8Jl.jpg] (https://i.sstatic.net/AJx5ol8Jl.jpg)\n[image: enter image description here; source: https://i.sstatic.net/27Zf0kM6.jpg] (https://i.sstatic.net/27Zf0kM6.jpg)\n\n\n\n\nThe full data set of McClain et al. was quite large and includes 288 551 indivduals, containing the 88 huge ones. From the first graph you can see that most of these 88 whales were caught in the pelagic zone (i.e. the open ocean) of the southern hemisphere. It seems, that most of them were femals, which also makes sense, since female blue whales tend to be a bit larger than males. Unfortunately, the figures and the paper of McClain et al. does not include information about age. Given the fact that many of them have probably been catched by commercial whale hunters, I think that this kind of information does not exist anyway."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Blue_whale#Size","https://i.sstatic.net/27Zf0kM6.jpg","https://i.sstatic.net/AJx5ol8Jl.jpg","https://pmc.ncbi.nlm.nih.gov/articles/PMC3443106/","https://pmc.ncbi.nlm.nih.gov/articles/PMC4304853/","https://www.guinnessworldrecords.com/world-records/69467-largest-whale"],"ground_truth_type":"metadata_grounded","group_id":"77de3e730171e09914a764c23a3c8f603bacb3924f6dea4e5fb0ce6936436b0b","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-2de57f1693c27bbb47b884dd","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:04.377249+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/54ece81cba3a5a552bb15d6d3feedc4324a2ba2706d33480080ece9537efd4b1_0.json","raw_sha256":"f1eb8f7eda9336b81701b663029f9411e040c0bcf262148b7ede9a103ae73e69","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=4&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"ggk hj","profile_url":"https://biology.stackexchange.com/users/75189/ggk-hj","user_type":"registered"},"created_at":"2025-02-12T12:03:45+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"B27BD523-0C2D-4ACE-BEA9-9AD4A909B69B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B27BD523-0C2D-4ACE-BEA9-9AD4A909B69B/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"116096","source_record_sha256":"0b45a3e2f4554ae4962455012597db706ae36c3c8df51003b5e2c7dfda4b659c","source_url":"https://biology.stackexchange.com/questions/116096/where-can-i-find-information-on-blue-whales-longer-than-30-meters","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Where can I find information on blue whales longer than 30 meters?\nCan anyone provide information from the IWC database or another source on the 88 blue whales over 30 meters in length (year, sex, age, region, etc.)?\n\n\n\n\nWikipedia mentions this, but I don't know where to find more detailed information.\n\n\n\n\nhttps://en.wikipedia.org/wiki/Blue_whale#Size (https://en.wikipedia.org/wiki/Blue_whale#Size)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116100,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The single key question in the poster’s shopping list can, I think, be reduced to</p>\n<blockquote>\n<p>“Why don’t the experimental results bear out the predictions?”</p>\n</blockquote>\n<p>The answer would seem self-evident:</p>\n<blockquote>\n<p>“Because the predictions, based as they are on sequence comparison, are incorrect.”</p>\n</blockquote>\n<p>It would seem rather naive to be surprised about this as the graveyard of biology is populated by the remains of many a beautiful hypothesis.</p>\n<p>The purpose of this site is not to try to provide detailed advice on research programmes, but in similar circumstances I personally would accept the experimental results and either look for another target for the mir or give up the idea that its changes are the cause of the biological changes observed.</p>\n","answer_id":116169,"answer_text":"The single key question in the poster’s shopping list can, I think, be reduced to\n\n\n\n\n\n\n\n“Why don’t the experimental results bear out the predictions?”\n\n\n\n\n\n\n\nThe answer would seem self-evident:\n\n\n\n\n\n\n\n“Because the predictions, based as they are on sequence comparison, are incorrect.”\n\n\n\n\n\n\n\nIt would seem rather naive to be surprised about this as the graveyard of biology is populated by the remains of many a beautiful hypothesis.\n\n\n\n\nThe purpose of this site is not to try to provide detailed advice on research programmes, but in similar circumstances I personally would accept the experimental results and either look for another target for the mir or give up the idea that its changes are the cause of the biological changes observed.","answer_url":"https://biology.stackexchange.com/a/116169","author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","created_at":"2025-02-28T23:35:24+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:19.947691+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/df693642d727b738d2a533740632235c18a06cefec7a1e337c9589214a4ec91e_0.json","raw_sha256":"9df534f437f3b2f12d33db8536999ec4e6ffa10f2f59394799d9fe01c3c1ad16","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/117606;117602;117598;117594;117585;117579;117570;117568;117565;117559;117558;117555;117552;117548;117538;117524;117523;117522;117520;117515;117510;116509;116508;116504;116499;116491;116485;116483;116461;116454;116453;116445;116441;116435;116430;116426;116425;116414;116412;116406;116401;116399;116396;116395;116394;116392;116389;116384;116370;116367;116363;116361;116352;116351;116347;116345;116343;116338;116337;116332;116331;116324;116320;116316;116314;116312;116306;116292;116290;116284;116280;116277;116271;116270;116268;116267;116257;116256;116253;116250;116249;116240;116237;116233;116219;116214;116212;116205;116204;116200;116198;116187;116184;116173;116172;116167;116162;116149;116142;116129/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":116162,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2025-02-28T23:35:24+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"90750D86-DBD5-4171-989A-3083C74C20CC","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/90750D86-DBD5-4171-989A-3083C74C20CC/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"H Lily","author_url":"https://biology.stackexchange.com/users/101954/h-lily","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"H Lily","profile_url":"https://biology.stackexchange.com/users/101954/h-lily","user_type":"registered"},"created_at":"2025-02-26T16:28:22+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"90403C31-3670-4AB9-8204-E1C321A09A6E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/90403C31-3670-4AB9-8204-E1C321A09A6E/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2025-02-26T20:42:37+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"CF364875-8DD0-4539-BC8A-E5441CB81A98","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CF364875-8DD0-4539-BC8A-E5441CB81A98/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2025-03-31T00:05:25+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"9737B421-F277-46F8-8436-8E94B32677A3","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/9737B421-F277-46F8-8436-8E94B32677A3/view-source"}],"url":"https://biology.stackexchange.com/questions/116162/bioinformatics-prediction-vs-experimental-results-mirna-regulation-of-ampk-wnt"},{"author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","context_id":"116169","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2025-02-28T23:35:24+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"90750D86-DBD5-4171-989A-3083C74C20CC","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/90750D86-DBD5-4171-989A-3083C74C20CC/view-source"}],"url":"https://biology.stackexchange.com/a/116169"}],"contexts":[{"context_id":"question","html":"<p>I am investigating the role of a specific miRNA in high-glucose conditions, particularly its effects on cell proliferation, migration, and metabolism. However, I have encountered a significant discrepancy between bioinformatics predictions and experimental results, and I would appreciate insights on potential explanations and next steps.</p>\n<h2>Background &amp; Bioinformatics Predictions:</h2>\n<p>Using TargetScan and miRDB, my bioinformatics analysis suggests that this miRNA targets PRKAA1 (AMPK) and WNT pathway components, implying that it may suppress autophagy and cell growth.</p>\n<p>In a high-glucose environment, RNA-seq data shows that this miRNA is downregulated, which theoretically should:</p>\n<ul>\n<li>Release AMPK inhibition → promote autophagy.</li>\n<li>Suppress WNT signaling → inhibit proliferation.</li>\n</ul>\n<h2>Experimental Results (Contradictory to Predictions):</h2>\n<p>Overexpressing the miRNA in high-glucose conditions reduces cellular damage, contrary to the expectation that it should further suppress AMPK/WNT.</p>\n<p>Inhibiting the miRNA in normal conditions leads to reduced proliferation and migration, contradicting the assumption that it suppresses growth.</p>\n<p>This contradicts previous literature where AMPK activation is typically protective in high-glucose stress conditions.</p>\n<p>Methods Used for Validation:</p>\n<ul>\n<li>qPCR: Confirmed miRNA expression changes in high-glucose conditions.</li>\n<li>CCK-8 Assay: Measured proliferation.</li>\n<li>Transwell Assay: Evaluated cell migration.</li>\n</ul>\n<h2>Key Questions:</h2>\n<p>What could explain this discrepancy between bioinformatics predictions and experimental results?</p>\n<p>Could this be due to context-dependent miRNA regulation, indirect compensatory mechanisms, or database biases?</p>\n<p>Are there known cases where AMPK suppression is protective in a high-glucose environment rather than harmful?</p>\n<p>Could WNT signaling be altered differently in this metabolic condition?</p>\n<p>Should I continue pursuing this pathway if no prior literature supports this specific mechanism?</p>\n<p>Is it common for miRNA bioinformatics predictions to significantly differ from in vitro results?</p>\n<p>Should I validate additional targets or check for compensatory signaling pathways?</p>\n<p>Any insights, relevant studies, or alternative explanations would be greatly appreciated!</p>\n","text":"I am investigating the role of a specific miRNA in high-glucose conditions, particularly its effects on cell proliferation, migration, and metabolism. However, I have encountered a significant discrepancy between bioinformatics predictions and experimental results, and I would appreciate insights on potential explanations and next steps.\n\n\n\n\nBackground & Bioinformatics Predictions:\n\n\n\n\nUsing TargetScan and miRDB, my bioinformatics analysis suggests that this miRNA targets PRKAA1 (AMPK) and WNT pathway components, implying that it may suppress autophagy and cell growth.\n\n\n\n\nIn a high-glucose environment, RNA-seq data shows that this miRNA is downregulated, which theoretically should:\n\n\n\n\n\nRelease AMPK inhibition → promote autophagy.\n\n\n\n\nSuppress WNT signaling → inhibit proliferation.\n\n\n\n\n\nExperimental Results (Contradictory to Predictions):\n\n\n\n\nOverexpressing the miRNA in high-glucose conditions reduces cellular damage, contrary to the expectation that it should further suppress AMPK/WNT.\n\n\n\n\nInhibiting the miRNA in normal conditions leads to reduced proliferation and migration, contradicting the assumption that it suppresses growth.\n\n\n\n\nThis contradicts previous literature where AMPK activation is typically protective in high-glucose stress conditions.\n\n\n\n\nMethods Used for Validation:\n\n\n\n\n\nqPCR: Confirmed miRNA expression changes in high-glucose conditions.\n\n\n\n\nCCK-8 Assay: Measured proliferation.\n\n\n\n\nTranswell Assay: Evaluated cell migration.\n\n\n\n\n\nKey Questions:\n\n\n\n\nWhat could explain this discrepancy between bioinformatics predictions and experimental results?\n\n\n\n\nCould this be due to context-dependent miRNA regulation, indirect compensatory mechanisms, or database biases?\n\n\n\n\nAre there known cases where AMPK suppression is protective in a high-glucose environment rather than harmful?\n\n\n\n\nCould WNT signaling be altered differently in this metabolic condition?\n\n\n\n\nShould I continue pursuing this pathway if no prior literature supports this specific mechanism?\n\n\n\n\nIs it common for miRNA bioinformatics predictions to significantly differ from in vitro results?\n\n\n\n\nShould I validate additional targets or check for compensatory signaling pathways?\n\n\n\n\nAny insights, relevant studies, or alternative explanations would be greatly appreciated!"},{"context_id":"116169","html":"<p>The single key question in the poster’s shopping list can, I think, be reduced to</p>\n<blockquote>\n<p>“Why don’t the experimental results bear out the predictions?”</p>\n</blockquote>\n<p>The answer would seem self-evident:</p>\n<blockquote>\n<p>“Because the predictions, based as they are on sequence comparison, are incorrect.”</p>\n</blockquote>\n<p>It would seem rather naive to be surprised about this as the graveyard of biology is populated by the remains of many a beautiful hypothesis.</p>\n<p>The purpose of this site is not to try to provide detailed advice on research programmes, but in similar circumstances I personally would accept the experimental results and either look for another target for the mir or give up the idea that its changes are the cause of the biological changes observed.</p>\n","text":"The single key question in the poster’s shopping list can, I think, be reduced to\n\n\n\n\n\n\n\n“Why don’t the experimental results bear out the predictions?”\n\n\n\n\n\n\n\nThe answer would seem self-evident:\n\n\n\n\n\n\n\n“Because the predictions, based as they are on sequence comparison, are incorrect.”\n\n\n\n\n\n\n\nIt would seem rather naive to be surprised about this as the graveyard of biology is populated by the remains of many a beautiful hypothesis.\n\n\n\n\nThe purpose of this site is not to try to provide detailed advice on research programmes, but in similar circumstances I personally would accept the experimental results and either look for another target for the mir or give up the idea that its changes are the cause of the biological changes observed."}],"domain":"biology","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"0eea56127b6d555605632244fd4925f5d95dac54e0b46ca82269892b4f16aec6","hard_case_family":["no_accepted_answer"],"id":"RHM-0246f3bbd97ef799a0dca77f","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:02.598621+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/5d480e4bd1bd45ab525a4baf3227fba404f89b6af9dad33215fd9fa7c302a211_0.json","raw_sha256":"d723c7a62c8386d143891d26ae30b2234242ed3dac9599b11f141712ea994a96","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=3&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"H Lily","profile_url":"https://biology.stackexchange.com/users/101954/h-lily","user_type":"registered"},"created_at":"2025-02-26T16:28:22+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"90403C31-3670-4AB9-8204-E1C321A09A6E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/90403C31-3670-4AB9-8204-E1C321A09A6E/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2025-02-26T20:42:37+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"CF364875-8DD0-4539-BC8A-E5441CB81A98","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CF364875-8DD0-4539-BC8A-E5441CB81A98/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2025-03-31T00:05:25+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"9737B421-F277-46F8-8436-8E94B32677A3","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/9737B421-F277-46F8-8436-8E94B32677A3/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"116162","source_record_sha256":"b881c37af004bd4ad991816aaf140d4d146aae654ad51a5b177b375c148b1755","source_url":"https://biology.stackexchange.com/questions/116162/bioinformatics-prediction-vs-experimental-results-mirna-regulation-of-ampk-wnt","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Bioinformatics Prediction vs. Experimental Results: miRNA Regulation of AMPK/WNT Pathway in High-Glucose Conditions\nI am investigating the role of a specific miRNA in high-glucose conditions, particularly its effects on cell proliferation, migration, and metabolism. However, I have encountered a significant discrepancy between bioinformatics predictions and experimental results, and I would appreciate insights on potential explanations and next steps.\n\n\n\n\nBackground & Bioinformatics Predictions:\n\n\n\n\nUsing TargetScan and miRDB, my bioinformatics analysis suggests that this miRNA targets PRKAA1 (AMPK) and WNT pathway components, implying that it may suppress autophagy and cell growth.\n\n\n\n\nIn a high-glucose environment, RNA-seq data shows that this miRNA is downregulated, which theoretically should:\n\n\n\n\n\nRelease AMPK inhibition → promote autophagy.\n\n\n\n\nSuppress WNT signaling → inhibit proliferation.\n\n\n\n\n\nExperimental Results (Contradictory to Predictions):\n\n\n\n\nOverexpressing the miRNA in high-glucose conditions reduces cellular damage, contrary to the expectation that it should further suppress AMPK/WNT.\n\n\n\n\nInhibiting the miRNA in normal conditions leads to reduced proliferation and migration, contradicting the assumption that it suppresses growth.\n\n\n\n\nThis contradicts previous literature where AMPK activation is typically protective in high-glucose stress conditions.\n\n\n\n\nMethods Used for Validation:\n\n\n\n\n\nqPCR: Confirmed miRNA expression changes in high-glucose conditions.\n\n\n\n\nCCK-8 Assay: Measured proliferation.\n\n\n\n\nTranswell Assay: Evaluated cell migration.\n\n\n\n\n\nKey Questions:\n\n\n\n\nWhat could explain this discrepancy between bioinformatics predictions and experimental results?\n\n\n\n\nCould this be due to context-dependent miRNA regulation, indirect compensatory mechanisms, or database biases?\n\n\n\n\nAre there known cases where AMPK suppression is protective in a high-glucose environment rather than harmful?\n\n\n\n\nCould WNT signaling be altered differently in this metabolic condition?\n\n\n\n\nShould I continue pursuing this pathway if no prior literature supports this specific mechanism?\n\n\n\n\nIs it common for miRNA bioinformatics predictions to significantly differ from in vitro results?\n\n\n\n\nShould I validate additional targets or check for compensatory signaling pathways?\n\n\n\n\nAny insights, relevant studies, or alternative explanations would be greatly appreciated!","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116169,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>As far as I can tell, there are a range of proteins in teff, and they all seem to be members of known families of proteins, <a href=\"https://en.wikipedia.org/wiki/Prolamin\" rel=\"nofollow noreferrer\">prolamins</a>, <a href=\"https://en.wikipedia.org/wiki/Glutelin\" rel=\"nofollow noreferrer\">glutelins</a> (which are actually part of the prolamin family anyway) and <a href=\"https://en.wikipedia.org/wiki/Albumin\" rel=\"nofollow noreferrer\">albumins</a>. <a href=\"https://www.sciencedirect.com/science/article/pii/S0733521011001317\" rel=\"nofollow noreferrer\">Abedowale <em>et al</em> 2011</a><sup>1</sup> seems to be the most recent paper referenced on the protein content, which is shown in the table below (source: ref 1). Other papers have found differences in percentage content, such as Bekele <em>et al</em> , 1995<sup>2</sup> and Tathum <em>et al.</em>, 1996<sup>3</sup>, so there is some disagreement on this.</p>\n<p><a href=\"https://i.sstatic.net/wj4Rd7hY.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/wj4Rd7hY.png\" alt=\"Teff protein fractions from Abedowale 2011\" /></a></p>\n<p>As teff is relatively unknown in the western world and hence understudied, I wouldn't be at all surprised if there is no name for teff's variant on these proteins yet, though I am sure it will be named eventually.</p>\n<p>Ref:</p>\n<ol>\n<li><p>Adebowale, Abdul-Rasaq A., et al. &quot;Fractionation and characterization of teff proteins.&quot; Journal of Cereal science 54.3 (2011): 380-386.</p>\n</li>\n<li><p>Bekele, E., Fido, R.J., Tatham, A.S. and Shewry, P.R. (1995), Heterogeneity and Polymorphism of Seed Proteins in Tef (Eragrotis Tef). Hereditas, 122: 67-72. <a href=\"https://doi.org/10.1111/j.1601-5223.1995.00067.x\" rel=\"nofollow noreferrer\">https://doi.org/10.1111/j.1601-5223.1995.00067.x</a></p>\n</li>\n<li><p>Tatham, A. S., Fido, R. J., Moore, C. M., Kasarda, D. D., Kuzmicky, D. D., Keen, J. N., &amp; Shewry, P. R. (1996). Characterisation of the major prolamins of tef (Eragrostis tef) and finger millet (Eleusine coracana). Journal of Cereal Science, 24(1), 65-71. <a href=\"https://doi.org/10.1006/jcrs.1996.0038\" rel=\"nofollow noreferrer\">https://doi.org/10.1006/jcrs.1996.0038</a></p>\n</li>\n</ol>\n","answer_id":116217,"answer_text":"As far as I can tell, there are a range of proteins in teff, and they all seem to be members of known families of proteins, prolamins (https://en.wikipedia.org/wiki/Prolamin), glutelins (https://en.wikipedia.org/wiki/Glutelin) (which are actually part of the prolamin family anyway) and albumins (https://en.wikipedia.org/wiki/Albumin). Abedowale et al 2011 (https://www.sciencedirect.com/science/article/pii/S0733521011001317)1 seems to be the most recent paper referenced on the protein content, which is shown in the table below (source: ref 1). Other papers have found differences in percentage content, such as Bekele et al , 19952 and Tathum et al., 19963, so there is some disagreement on this.\n\n\n\n\n[image: Teff protein fractions from Abedowale 2011; source: https://i.sstatic.net/wj4Rd7hY.png] (https://i.sstatic.net/wj4Rd7hY.png)\n\n\n\n\nAs teff is relatively unknown in the western world and hence understudied, I wouldn't be at all surprised if there is no name for teff's variant on these proteins yet, though I am sure it will be named eventually.\n\n\n\n\nRef:\n\n\n\n\n\n\n\nAdebowale, Abdul-Rasaq A., et al. \"Fractionation and characterization of teff proteins.\" Journal of Cereal science 54.3 (2011): 380-386.\n\n\n\n\n\n\n\n\n\nBekele, E., Fido, R.J., Tatham, A.S. and Shewry, P.R. (1995), Heterogeneity and Polymorphism of Seed Proteins in Tef (Eragrotis Tef). Hereditas, 122: 67-72. https://doi.org/10.1111/j.1601-5223.1995.00067.x (https://doi.org/10.1111/j.1601-5223.1995.00067.x)\n\n\n\n\n\n\n\n\n\nTatham, A. S., Fido, R. J., Moore, C. M., Kasarda, D. D., Kuzmicky, D. D., Keen, J. N., & Shewry, P. R. (1996). Characterisation of the major prolamins of tef (Eragrostis tef) and finger millet (Eleusine coracana). Journal of Cereal Science, 24(1), 65-71. https://doi.org/10.1006/jcrs.1996.0038 (https://doi.org/10.1006/jcrs.1996.0038)","answer_url":"https://biology.stackexchange.com/a/116217","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2025-03-11T20:17:17+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:19.947691+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/df693642d727b738d2a533740632235c18a06cefec7a1e337c9589214a4ec91e_0.json","raw_sha256":"9df534f437f3b2f12d33db8536999ec4e6ffa10f2f59394799d9fe01c3c1ad16","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/117606;117602;117598;117594;117585;117579;117570;117568;117565;117559;117558;117555;117552;117548;117538;117524;117523;117522;117520;117515;117510;116509;116508;116504;116499;116491;116485;116483;116461;116454;116453;116445;116441;116435;116430;116426;116425;116414;116412;116406;116401;116399;116396;116395;116394;116392;116389;116384;116370;116367;116363;116361;116352;116351;116347;116345;116343;116338;116337;116332;116331;116324;116320;116316;116314;116312;116306;116292;116290;116284;116280;116277;116271;116270;116268;116267;116257;116256;116253;116250;116249;116240;116237;116233;116219;116214;116212;116205;116204;116200;116198;116187;116184;116173;116172;116167;116162;116149;116142;116129/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":116214,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2025-03-11T20:17:17+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"64F9A60B-A08D-4899-9DE5-6FE5CEA1097D","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/64F9A60B-A08D-4899-9DE5-6FE5CEA1097D/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Kurt Hikes","author_url":"https://biology.stackexchange.com/users/39747/kurt-hikes","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Kurt Hikes","profile_url":"https://biology.stackexchange.com/users/39747/kurt-hikes","user_type":"registered"},"created_at":"2025-03-11T17:26:06+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"9FA410EC-7D6B-4B57-84D9-D91757CC02CF","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9FA410EC-7D6B-4B57-84D9-D91757CC02CF/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2025-04-10T21:05:35+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"B36E40FB-9078-4FC2-9F91-59E776EB20A1","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/B36E40FB-9078-4FC2-9F91-59E776EB20A1/view-source"}],"url":"https://biology.stackexchange.com/questions/116214/what-is-the-names-of-the-proteins-in-teff-injera"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"116217","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2025-03-11T20:17:17+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"64F9A60B-A08D-4899-9DE5-6FE5CEA1097D","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/64F9A60B-A08D-4899-9DE5-6FE5CEA1097D/view-source"}],"url":"https://biology.stackexchange.com/a/116217"}],"contexts":[{"context_id":"question","html":"<p>Supposedly, teff bread (injera) is higher than average among grains in protein, but lacks the problematic gluten....</p>\n<p>Sorghum also generally lacks gluten, but I had no problem tracking down which protein it did have (a prolamine called kafirin)...</p>\n","text":"Supposedly, teff bread (injera) is higher than average among grains in protein, but lacks the problematic gluten....\n\n\n\n\nSorghum also generally lacks gluten, but I had no problem tracking down which protein it did have (a prolamine called kafirin)..."},{"context_id":"116217","html":"<p>As far as I can tell, there are a range of proteins in teff, and they all seem to be members of known families of proteins, <a href=\"https://en.wikipedia.org/wiki/Prolamin\" rel=\"nofollow noreferrer\">prolamins</a>, <a href=\"https://en.wikipedia.org/wiki/Glutelin\" rel=\"nofollow noreferrer\">glutelins</a> (which are actually part of the prolamin family anyway) and <a href=\"https://en.wikipedia.org/wiki/Albumin\" rel=\"nofollow noreferrer\">albumins</a>. <a href=\"https://www.sciencedirect.com/science/article/pii/S0733521011001317\" rel=\"nofollow noreferrer\">Abedowale <em>et al</em> 2011</a><sup>1</sup> seems to be the most recent paper referenced on the protein content, which is shown in the table below (source: ref 1). Other papers have found differences in percentage content, such as Bekele <em>et al</em> , 1995<sup>2</sup> and Tathum <em>et al.</em>, 1996<sup>3</sup>, so there is some disagreement on this.</p>\n<p><a href=\"https://i.sstatic.net/wj4Rd7hY.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/wj4Rd7hY.png\" alt=\"Teff protein fractions from Abedowale 2011\" /></a></p>\n<p>As teff is relatively unknown in the western world and hence understudied, I wouldn't be at all surprised if there is no name for teff's variant on these proteins yet, though I am sure it will be named eventually.</p>\n<p>Ref:</p>\n<ol>\n<li><p>Adebowale, Abdul-Rasaq A., et al. &quot;Fractionation and characterization of teff proteins.&quot; Journal of Cereal science 54.3 (2011): 380-386.</p>\n</li>\n<li><p>Bekele, E., Fido, R.J., Tatham, A.S. and Shewry, P.R. (1995), Heterogeneity and Polymorphism of Seed Proteins in Tef (Eragrotis Tef). Hereditas, 122: 67-72. <a href=\"https://doi.org/10.1111/j.1601-5223.1995.00067.x\" rel=\"nofollow noreferrer\">https://doi.org/10.1111/j.1601-5223.1995.00067.x</a></p>\n</li>\n<li><p>Tatham, A. S., Fido, R. J., Moore, C. M., Kasarda, D. D., Kuzmicky, D. D., Keen, J. N., &amp; Shewry, P. R. (1996). Characterisation of the major prolamins of tef (Eragrostis tef) and finger millet (Eleusine coracana). Journal of Cereal Science, 24(1), 65-71. <a href=\"https://doi.org/10.1006/jcrs.1996.0038\" rel=\"nofollow noreferrer\">https://doi.org/10.1006/jcrs.1996.0038</a></p>\n</li>\n</ol>\n","text":"As far as I can tell, there are a range of proteins in teff, and they all seem to be members of known families of proteins, prolamins (https://en.wikipedia.org/wiki/Prolamin), glutelins (https://en.wikipedia.org/wiki/Glutelin) (which are actually part of the prolamin family anyway) and albumins (https://en.wikipedia.org/wiki/Albumin). Abedowale et al 2011 (https://www.sciencedirect.com/science/article/pii/S0733521011001317)1 seems to be the most recent paper referenced on the protein content, which is shown in the table below (source: ref 1). Other papers have found differences in percentage content, such as Bekele et al , 19952 and Tathum et al., 19963, so there is some disagreement on this.\n\n\n\n\n[image: Teff protein fractions from Abedowale 2011; source: https://i.sstatic.net/wj4Rd7hY.png] (https://i.sstatic.net/wj4Rd7hY.png)\n\n\n\n\nAs teff is relatively unknown in the western world and hence understudied, I wouldn't be at all surprised if there is no name for teff's variant on these proteins yet, though I am sure it will be named eventually.\n\n\n\n\nRef:\n\n\n\n\n\n\n\nAdebowale, Abdul-Rasaq A., et al. \"Fractionation and characterization of teff proteins.\" Journal of Cereal science 54.3 (2011): 380-386.\n\n\n\n\n\n\n\n\n\nBekele, E., Fido, R.J., Tatham, A.S. and Shewry, P.R. (1995), Heterogeneity and Polymorphism of Seed Proteins in Tef (Eragrotis Tef). Hereditas, 122: 67-72. https://doi.org/10.1111/j.1601-5223.1995.00067.x (https://doi.org/10.1111/j.1601-5223.1995.00067.x)\n\n\n\n\n\n\n\n\n\nTatham, A. S., Fido, R. J., Moore, C. M., Kasarda, D. D., Kuzmicky, D. D., Keen, J. N., & Shewry, P. R. (1996). Characterisation of the major prolamins of tef (Eragrostis tef) and finger millet (Eleusine coracana). Journal of Cereal Science, 24(1), 65-71. https://doi.org/10.1006/jcrs.1996.0038 (https://doi.org/10.1006/jcrs.1996.0038)"}],"domain":"biology","external_citations":["https://doi.org/10.1006/jcrs.1996.0038","https://doi.org/10.1111/j.1601-5223.1995.00067.x","https://en.wikipedia.org/wiki/Albumin","https://en.wikipedia.org/wiki/Glutelin","https://en.wikipedia.org/wiki/Prolamin","https://i.sstatic.net/wj4Rd7hY.png","https://www.sciencedirect.com/science/article/pii/S0733521011001317"],"ground_truth_type":"metadata_grounded","group_id":"7dd2b8da003e10eb0765a2267a5dced1262d29cdd490bdd0d22054707015a29e","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-8cb9d4e9c27c2bc31aed3aa9","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:02.598621+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/5d480e4bd1bd45ab525a4baf3227fba404f89b6af9dad33215fd9fa7c302a211_0.json","raw_sha256":"d723c7a62c8386d143891d26ae30b2234242ed3dac9599b11f141712ea994a96","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=3&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Kurt Hikes","profile_url":"https://biology.stackexchange.com/users/39747/kurt-hikes","user_type":"registered"},"created_at":"2025-03-11T17:26:06+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"9FA410EC-7D6B-4B57-84D9-D91757CC02CF","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9FA410EC-7D6B-4B57-84D9-D91757CC02CF/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2025-04-10T21:05:35+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"B36E40FB-9078-4FC2-9F91-59E776EB20A1","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/B36E40FB-9078-4FC2-9F91-59E776EB20A1/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"116214","source_record_sha256":"0bff8fca4068edbd096bfba1bf534bea70cc772842db1cf3b8a9cb877f58fa2a","source_url":"https://biology.stackexchange.com/questions/116214/what-is-the-names-of-the-proteins-in-teff-injera","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What is the name(s) of the protein(s) in teff (injera)?\nSupposedly, teff bread (injera) is higher than average among grains in protein, but lacks the problematic gluten....\n\n\n\n\nSorghum also generally lacks gluten, but I had no problem tracking down which protein it did have (a prolamine called kafirin)...","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116217,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":116286,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<h2>It's probably all three</h2>\n<p>keep in mind 40,000 years is 15-20,000 generations for dogs, humans take forever to breed but dogs can manage in 2-3 years. We have been domesticating dogs for a LOT longer than any other species so it makes sense we produced more variation. We didn't go right from wolves to chihuahua, there is a lot of time in between.</p>\n<p>Artificial selection is faster than normal natural in many ways. Well faster than the average rate anyway. Mostly this is becasue it is hyperselection for one or two traits where natural selction works on a whole mosaic at the same time. It also tends to be very strong selection, breed or not levels not just differential survival.</p>\n<p>Dogs and wolves are known to have especially plastic genomes, plus unlike humans dogs started with rather diverse genomes. there are several proposed reasons for this and work is only in the early stages but one leading idea is the sheer number of repeating silenced elements in the dog genome which allows for easy mutations and reactivation. The studies on foxes shows there may also be some linked traits that make certain stages of domestication easier. that is certain behavioral genes may be linked to physical traits making them easy to identify.</p>\n<p><a href=\"https://www.researchgate.net/publication/375242159_Duplications_and_retrogenes_are_numerous_and_widespread_in_modern_canine_genomic_assemblies\" rel=\"noreferrer\">source</a></p>\n<p><a href=\"https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0010058\" rel=\"noreferrer\">source 2</a></p>\n<p><a href=\"https://evolution-outreach.biomedcentral.com/articles/10.1186/s12052-018-0090-x\" rel=\"noreferrer\">fox source</a></p>\n<p><a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC2763232/\" rel=\"noreferrer\">fox source 2</a></p>\n<p><a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC7109016/\" rel=\"noreferrer\">source 6</a></p>\n","answer_id":116286,"answer_text":"It's probably all three\n\n\n\n\nkeep in mind 40,000 years is 15-20,000 generations for dogs, humans take forever to breed but dogs can manage in 2-3 years. We have been domesticating dogs for a LOT longer than any other species so it makes sense we produced more variation. We didn't go right from wolves to chihuahua, there is a lot of time in between.\n\n\n\n\nArtificial selection is faster than normal natural in many ways. Well faster than the average rate anyway. Mostly this is becasue it is hyperselection for one or two traits where natural selction works on a whole mosaic at the same time. It also tends to be very strong selection, breed or not levels not just differential survival.\n\n\n\n\nDogs and wolves are known to have especially plastic genomes, plus unlike humans dogs started with rather diverse genomes. there are several proposed reasons for this and work is only in the early stages but one leading idea is the sheer number of repeating silenced elements in the dog genome which allows for easy mutations and reactivation. The studies on foxes shows there may also be some linked traits that make certain stages of domestication easier. that is certain behavioral genes may be linked to physical traits making them easy to identify.\n\n\n\n\nsource (https://www.researchgate.net/publication/375242159_Duplications_and_retrogenes_are_numerous_and_widespread_in_modern_canine_genomic_assemblies)\n\n\n\n\nsource 2 (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0010058)\n\n\n\n\nfox source (https://evolution-outreach.biomedcentral.com/articles/10.1186/s12052-018-0090-x)\n\n\n\n\nfox source 2 (https://pmc.ncbi.nlm.nih.gov/articles/PMC2763232/)\n\n\n\n\nsource 6 (https://pmc.ncbi.nlm.nih.gov/articles/PMC7109016/)","answer_url":"https://biology.stackexchange.com/a/116286","author":"John","author_url":"https://biology.stackexchange.com/users/28022/john","content_license":"CC BY-SA 4.0","created_at":"2025-03-27T01:11:16+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:19.947691+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/df693642d727b738d2a533740632235c18a06cefec7a1e337c9589214a4ec91e_0.json","raw_sha256":"9df534f437f3b2f12d33db8536999ec4e6ffa10f2f59394799d9fe01c3c1ad16","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/117606;117602;117598;117594;117585;117579;117570;117568;117565;117559;117558;117555;117552;117548;117538;117524;117523;117522;117520;117515;117510;116509;116508;116504;116499;116491;116485;116483;116461;116454;116453;116445;116441;116435;116430;116426;116425;116414;116412;116406;116401;116399;116396;116395;116394;116392;116389;116384;116370;116367;116363;116361;116352;116351;116347;116345;116343;116338;116337;116332;116331;116324;116320;116316;116314;116312;116306;116292;116290;116284;116280;116277;116271;116270;116268;116267;116257;116256;116253;116250;116249;116240;116237;116233;116219;116214;116212;116205;116204;116200;116198;116187;116184;116173;116172;116167;116162;116149;116142;116129/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":116277,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"John","profile_url":"https://biology.stackexchange.com/users/28022/john","user_type":"registered"},"created_at":"2025-03-27T01:11:16+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"DC8B12CA-F1E1-4118-9DF2-4FD4DC63A2FA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DC8B12CA-F1E1-4118-9DF2-4FD4DC63A2FA/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2025-03-27T17:13:37+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"54FD0DD5-7790-4BBC-B5E7-79291316E395","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/54FD0DD5-7790-4BBC-B5E7-79291316E395/view-source"}],"score":7}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Riemann'sPointyNose","author_url":"https://biology.stackexchange.com/users/64385/riemannspointynose","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Riemann'sPointyNose","profile_url":"https://biology.stackexchange.com/users/64385/riemannspointynose","user_type":"registered"},"created_at":"2025-03-24T22:40:20+00:00","raw_file":"raw/codex_api_v1/6a8d1217a71337b035f168c28f3cef00c95606938297595ce7816a6ee2aabc47_1790824139846857200_0.json","raw_sha256":"915362f28bff22e7e44f536acc7b10e33f23a77bbb5e547906a8fdc7cf7e3e89","revision_guid":"1C47B2F6-7061-4518-94C0-42A729ADE971","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/1C47B2F6-7061-4518-94C0-42A729ADE971/view-source"}],"url":"https://biology.stackexchange.com/questions/116277/dog-domestication-timeline"},{"author":"John","author_url":"https://biology.stackexchange.com/users/28022/john","content_license":"CC BY-SA 4.0","context_id":"116286","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"John","profile_url":"https://biology.stackexchange.com/users/28022/john","user_type":"registered"},"created_at":"2025-03-27T01:11:16+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"DC8B12CA-F1E1-4118-9DF2-4FD4DC63A2FA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DC8B12CA-F1E1-4118-9DF2-4FD4DC63A2FA/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2025-03-27T17:13:37+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"54FD0DD5-7790-4BBC-B5E7-79291316E395","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/54FD0DD5-7790-4BBC-B5E7-79291316E395/view-source"}],"url":"https://biology.stackexchange.com/a/116286"}],"contexts":[{"context_id":"question","html":"<p>Full disclosure: not a biologist, I am pretty much a noobie when it comes to biology.</p>\n<p>I was shocked to find out that the domestication of dogs is believed really to have only taken around 40,000 years. On an evolutionary timescale, this seems absolutely miniscule, right? It's hard to look at a Chihuahua and reconcile the fact that a measly 40,000 years ago it had a wolf-like great great ... great grandparent.</p>\n<p>The only ideas I can come up with are that,</p>\n<ol>\n<li>In fact, this is not that short of a timeframe, and I am mistaken. Or maybe in fact the change we see in 40,000 years is not that drastic at all.</li>\n<li>Artificial selection is simply much more efficient than natural selection.</li>\n<li>There is something specific genetically about dogs that make them much easier to select for?</li>\n</ol>\n<p>Or maybe it's a combination of the above. I'm not sure. What is it?</p>\n","text":"Full disclosure: not a biologist, I am pretty much a noobie when it comes to biology.\n\n\n\n\nI was shocked to find out that the domestication of dogs is believed really to have only taken around 40,000 years. On an evolutionary timescale, this seems absolutely miniscule, right? It's hard to look at a Chihuahua and reconcile the fact that a measly 40,000 years ago it had a wolf-like great great ... great grandparent.\n\n\n\n\nThe only ideas I can come up with are that,\n\n\n\n\n\nIn fact, this is not that short of a timeframe, and I am mistaken. Or maybe in fact the change we see in 40,000 years is not that drastic at all.\n\n\n\n\nArtificial selection is simply much more efficient than natural selection.\n\n\n\n\nThere is something specific genetically about dogs that make them much easier to select for?\n\n\n\n\n\nOr maybe it's a combination of the above. I'm not sure. What is it?"},{"context_id":"116286","html":"<h2>It's probably all three</h2>\n<p>keep in mind 40,000 years is 15-20,000 generations for dogs, humans take forever to breed but dogs can manage in 2-3 years. We have been domesticating dogs for a LOT longer than any other species so it makes sense we produced more variation. We didn't go right from wolves to chihuahua, there is a lot of time in between.</p>\n<p>Artificial selection is faster than normal natural in many ways. Well faster than the average rate anyway. Mostly this is becasue it is hyperselection for one or two traits where natural selction works on a whole mosaic at the same time. It also tends to be very strong selection, breed or not levels not just differential survival.</p>\n<p>Dogs and wolves are known to have especially plastic genomes, plus unlike humans dogs started with rather diverse genomes. there are several proposed reasons for this and work is only in the early stages but one leading idea is the sheer number of repeating silenced elements in the dog genome which allows for easy mutations and reactivation. The studies on foxes shows there may also be some linked traits that make certain stages of domestication easier. that is certain behavioral genes may be linked to physical traits making them easy to identify.</p>\n<p><a href=\"https://www.researchgate.net/publication/375242159_Duplications_and_retrogenes_are_numerous_and_widespread_in_modern_canine_genomic_assemblies\" rel=\"noreferrer\">source</a></p>\n<p><a href=\"https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0010058\" rel=\"noreferrer\">source 2</a></p>\n<p><a href=\"https://evolution-outreach.biomedcentral.com/articles/10.1186/s12052-018-0090-x\" rel=\"noreferrer\">fox source</a></p>\n<p><a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC2763232/\" rel=\"noreferrer\">fox source 2</a></p>\n<p><a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC7109016/\" rel=\"noreferrer\">source 6</a></p>\n","text":"It's probably all three\n\n\n\n\nkeep in mind 40,000 years is 15-20,000 generations for dogs, humans take forever to breed but dogs can manage in 2-3 years. We have been domesticating dogs for a LOT longer than any other species so it makes sense we produced more variation. We didn't go right from wolves to chihuahua, there is a lot of time in between.\n\n\n\n\nArtificial selection is faster than normal natural in many ways. Well faster than the average rate anyway. Mostly this is becasue it is hyperselection for one or two traits where natural selction works on a whole mosaic at the same time. It also tends to be very strong selection, breed or not levels not just differential survival.\n\n\n\n\nDogs and wolves are known to have especially plastic genomes, plus unlike humans dogs started with rather diverse genomes. there are several proposed reasons for this and work is only in the early stages but one leading idea is the sheer number of repeating silenced elements in the dog genome which allows for easy mutations and reactivation. The studies on foxes shows there may also be some linked traits that make certain stages of domestication easier. that is certain behavioral genes may be linked to physical traits making them easy to identify.\n\n\n\n\nsource (https://www.researchgate.net/publication/375242159_Duplications_and_retrogenes_are_numerous_and_widespread_in_modern_canine_genomic_assemblies)\n\n\n\n\nsource 2 (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0010058)\n\n\n\n\nfox source (https://evolution-outreach.biomedcentral.com/articles/10.1186/s12052-018-0090-x)\n\n\n\n\nfox source 2 (https://pmc.ncbi.nlm.nih.gov/articles/PMC2763232/)\n\n\n\n\nsource 6 (https://pmc.ncbi.nlm.nih.gov/articles/PMC7109016/)"}],"domain":"biology","external_citations":["https://evolution-outreach.biomedcentral.com/articles/10.1186/s12052-018-0090-x","https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0010058","https://pmc.ncbi.nlm.nih.gov/articles/PMC2763232/","https://pmc.ncbi.nlm.nih.gov/articles/PMC7109016/","https://www.researchgate.net/publication/375242159_Duplications_and_retrogenes_are_numerous_and_widespread_in_modern_canine_genomic_assemblies"],"ground_truth_type":"metadata_grounded","group_id":"9af72fc080dfae8822e955692a5e4340300d784d4411edb7a8aa57be15eef70a","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-66f2141cdcdd806ff406e643","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:02.598621+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/5d480e4bd1bd45ab525a4baf3227fba404f89b6af9dad33215fd9fa7c302a211_0.json","raw_sha256":"d723c7a62c8386d143891d26ae30b2234242ed3dac9599b11f141712ea994a96","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=3&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Riemann'sPointyNose","profile_url":"https://biology.stackexchange.com/users/64385/riemannspointynose","user_type":"registered"},"created_at":"2025-03-24T22:40:20+00:00","raw_file":"raw/codex_api_v1/6a8d1217a71337b035f168c28f3cef00c95606938297595ce7816a6ee2aabc47_1790824139846857200_0.json","raw_sha256":"915362f28bff22e7e44f536acc7b10e33f23a77bbb5e547906a8fdc7cf7e3e89","revision_guid":"1C47B2F6-7061-4518-94C0-42A729ADE971","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/1C47B2F6-7061-4518-94C0-42A729ADE971/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"116277","source_record_sha256":"40d84c87fcb3cf29b2a1cd2a63227edb56b265fb856bea5dd0de4d707311b77b","source_url":"https://biology.stackexchange.com/questions/116277/dog-domestication-timeline","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Dog domestication timeline?\nFull disclosure: not a biologist, I am pretty much a noobie when it comes to biology.\n\n\n\n\nI was shocked to find out that the domestication of dogs is believed really to have only taken around 40,000 years. On an evolutionary timescale, this seems absolutely miniscule, right? It's hard to look at a Chihuahua and reconcile the fact that a measly 40,000 years ago it had a wolf-like great great ... great grandparent.\n\n\n\n\nThe only ideas I can come up with are that,\n\n\n\n\n\nIn fact, this is not that short of a timeframe, and I am mistaken. Or maybe in fact the change we see in 40,000 years is not that drastic at all.\n\n\n\n\nArtificial selection is simply much more efficient than natural selection.\n\n\n\n\nThere is something specific genetically about dogs that make them much easier to select for?\n\n\n\n\n\nOr maybe it's a combination of the above. I'm not sure. What is it?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116286,"score":7}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>If I understand the question correctly, it's not that far-fetched. But there are various systems, for example, online, that represent corresponding hierarchies and manage them in the background at the database level (e.g., <a href=\"https://www.floraweb.de/\" rel=\"nofollow noreferrer\">https://www.floraweb.de/</a>). Computer-based classification, for example, using corresponding hierarchical keys that map parent-child relationships, makes sense (see example).</p>\n<p><a href=\"https://i.sstatic.net/WxveehZw.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/WxveehZw.png\" alt=\"Example of a hierarchical list of vegetation science\" /></a></p>\n","answer_id":116293,"answer_text":"If I understand the question correctly, it's not that far-fetched. But there are various systems, for example, online, that represent corresponding hierarchies and manage them in the background at the database level (e.g., https://www.floraweb.de/ (https://www.floraweb.de/)). Computer-based classification, for example, using corresponding hierarchical keys that map parent-child relationships, makes sense (see example).\n\n\n\n\n[image: Example of a hierarchical list of vegetation science; source: https://i.sstatic.net/WxveehZw.png] (https://i.sstatic.net/WxveehZw.png)","answer_url":"https://biology.stackexchange.com/a/116293","author":"Detlev Finke","author_url":"https://biology.stackexchange.com/users/103641/detlev-finke","content_license":"CC BY-SA 4.0","created_at":"2025-03-28T13:24:55+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:19.947691+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/df693642d727b738d2a533740632235c18a06cefec7a1e337c9589214a4ec91e_0.json","raw_sha256":"9df534f437f3b2f12d33db8536999ec4e6ffa10f2f59394799d9fe01c3c1ad16","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/117606;117602;117598;117594;117585;117579;117570;117568;117565;117559;117558;117555;117552;117548;117538;117524;117523;117522;117520;117515;117510;116509;116508;116504;116499;116491;116485;116483;116461;116454;116453;116445;116441;116435;116430;116426;116425;116414;116412;116406;116401;116399;116396;116395;116394;116392;116389;116384;116370;116367;116363;116361;116352;116351;116347;116345;116343;116338;116337;116332;116331;116324;116320;116316;116314;116312;116306;116292;116290;116284;116280;116277;116271;116270;116268;116267;116257;116256;116253;116250;116249;116240;116237;116233;116219;116214;116212;116205;116204;116200;116198;116187;116184;116173;116172;116167;116162;116149;116142;116129/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":116284,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Detlev Finke","profile_url":"https://biology.stackexchange.com/users/103641/detlev-finke","user_type":"registered"},"created_at":"2025-03-28T13:24:55+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"E24A538B-9245-4C62-89EA-4A46CADEA068","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E24A538B-9245-4C62-89EA-4A46CADEA068/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Laszlo Pav","author_url":"https://biology.stackexchange.com/users/103448/laszlo-pav","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Laszlo Pav","profile_url":"https://biology.stackexchange.com/users/103448/laszlo-pav","user_type":"registered"},"created_at":"2025-03-25T22:42:54+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"302B837B-3F35-4D4A-BC87-F4F31A2B0577","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/302B837B-3F35-4D4A-BC87-F4F31A2B0577/view-source"}],"url":"https://biology.stackexchange.com/questions/116284/taxonomic-hierarchy-represented-as-a-computer-directory-hierarchy"},{"author":"Detlev Finke","author_url":"https://biology.stackexchange.com/users/103641/detlev-finke","content_license":"CC BY-SA 4.0","context_id":"116293","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Detlev Finke","profile_url":"https://biology.stackexchange.com/users/103641/detlev-finke","user_type":"registered"},"created_at":"2025-03-28T13:24:55+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"E24A538B-9245-4C62-89EA-4A46CADEA068","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E24A538B-9245-4C62-89EA-4A46CADEA068/view-source"}],"url":"https://biology.stackexchange.com/a/116293"}],"contexts":[{"context_id":"question","html":"<p>Is there any representation of the taxonomic hierarchy as a computer directory, where in the root directory, there would be domains (also directories), and inside those, kingdoms and so on and so on? I couldn't find anything about it anywhere.</p>\n<p>Thank you!</p>\n","text":"Is there any representation of the taxonomic hierarchy as a computer directory, where in the root directory, there would be domains (also directories), and inside those, kingdoms and so on and so on? I couldn't find anything about it anywhere.\n\n\n\n\nThank you!"},{"context_id":"116293","html":"<p>If I understand the question correctly, it's not that far-fetched. But there are various systems, for example, online, that represent corresponding hierarchies and manage them in the background at the database level (e.g., <a href=\"https://www.floraweb.de/\" rel=\"nofollow noreferrer\">https://www.floraweb.de/</a>). Computer-based classification, for example, using corresponding hierarchical keys that map parent-child relationships, makes sense (see example).</p>\n<p><a href=\"https://i.sstatic.net/WxveehZw.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/WxveehZw.png\" alt=\"Example of a hierarchical list of vegetation science\" /></a></p>\n","text":"If I understand the question correctly, it's not that far-fetched. But there are various systems, for example, online, that represent corresponding hierarchies and manage them in the background at the database level (e.g., https://www.floraweb.de/ (https://www.floraweb.de/)). Computer-based classification, for example, using corresponding hierarchical keys that map parent-child relationships, makes sense (see example).\n\n\n\n\n[image: Example of a hierarchical list of vegetation science; source: https://i.sstatic.net/WxveehZw.png] (https://i.sstatic.net/WxveehZw.png)"}],"domain":"biology","external_citations":["https://i.sstatic.net/WxveehZw.png","https://www.floraweb.de/"],"ground_truth_type":"metadata_grounded","group_id":"a06715f21fb98f32c445e433ad88b3ee764262101b9674c7d3affbe42314ca27","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-a26ba474afcae665d8716c1a","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:02.598621+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/5d480e4bd1bd45ab525a4baf3227fba404f89b6af9dad33215fd9fa7c302a211_0.json","raw_sha256":"d723c7a62c8386d143891d26ae30b2234242ed3dac9599b11f141712ea994a96","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=3&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Laszlo Pav","profile_url":"https://biology.stackexchange.com/users/103448/laszlo-pav","user_type":"registered"},"created_at":"2025-03-25T22:42:54+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"302B837B-3F35-4D4A-BC87-F4F31A2B0577","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/302B837B-3F35-4D4A-BC87-F4F31A2B0577/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"116284","source_record_sha256":"84d715043b73fa344d6ebaeeda7e1059db448b1d56188200777d239a23239d74","source_url":"https://biology.stackexchange.com/questions/116284/taxonomic-hierarchy-represented-as-a-computer-directory-hierarchy","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Taxonomic hierarchy represented as a computer directory hierarchy?\nIs there any representation of the taxonomic hierarchy as a computer directory, where in the root directory, there would be domains (also directories), and inside those, kingdoms and so on and so on? I couldn't find anything about it anywhere.\n\n\n\n\nThank you!","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116293,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>This trait is believed to have evolved independently numerous times, and can be male-to-female and female-to-male, and can even result/start with simultaneous hermaphrodites. Hermaphrodites are also found in many different distinct phylogenetic groups, from <a href=\"https://www.sciencedirect.com/science/article/abs/pii/S0024406683710035\" rel=\"nofollow noreferrer\">molluscs</a>, <a href=\"https://link.springer.com/article/10.1007/s10228-020-00754-6\" rel=\"nofollow noreferrer\">fish</a>, to <a href=\"https://www.jstor.org/stable/2097186\" rel=\"nofollow noreferrer\">plants</a>, making generalisations quite difficult.</p>\n<p>Regardless, the general evolutionary pressures in non-plants are relatively easy to follow. I've not read much about the plant side, but it might also apply there.</p>\n<p>There are currently two dominant theories to the evolution of sequential hermaphroditism in animals, the <strong>size advantage</strong> and <strong>low density</strong> models of evolution [<a href=\"https://www.jstor.org/stable/2097186\" rel=\"nofollow noreferrer\">1</a>].</p>\n<h3>Size Advantage:</h3>\n<p>This model describes a process when an individual's reproductive success changes over their lifetime. This could either be when smaller males <em>or</em> smaller females have an advantage in early life. The starting point for sequential hermaphrodites can either be separate sex populations or simultaneous hermaphrodite populations.</p>\n<p>The clownfish is a good example here. In this species, smaller young males are still able to fertilise eggs, but smaller females produce less eggs, so males have the reproductive success advantage when small, and when they get bigger, the females have the advantage. And by being both through a lifetime, each individual has higher reproductive success than populations where they are only 1 sex for their entire lifetime.</p>\n<p>The opposite can also be true, when smaller females are able to produce enough eggs to be reproductively successful, but in populations where male competition is a more dominant factor. Here, small males are at a disadvantage, so larger males are selected for.</p>\n<h3>Low density:</h3>\n<p>This model is even easier to follow and essentially suggests that for populations with a low density, it can be beneficial to be flexible. If one individual has an overlapping home range with another, they might initially be incompatible because they are both the same sex. But by changing sex during their lifetime, these individuals can be compatible later in life, so long as the sex change doesn't occur at the same time.</p>\n<p>However, it should be noted that there are many factors at play in any given populations which can contribute to everything above, including resource availability, predation, and parasitism pressures. Some interesting relevant reading: [<a href=\"https://onlinelibrary.wiley.com/doi/full/10.1111/\" rel=\"nofollow noreferrer\">2</a>, <a href=\"https://www.nature.com/articles/s41467-022-30419-z\" rel=\"nofollow noreferrer\">3</a>, <a href=\"https://www.journals.uchicago.edu/doi/abs/10.1086/282974\" rel=\"nofollow noreferrer\">4</a>]</p>\n","answer_id":116334,"answer_text":"This trait is believed to have evolved independently numerous times, and can be male-to-female and female-to-male, and can even result/start with simultaneous hermaphrodites. Hermaphrodites are also found in many different distinct phylogenetic groups, from molluscs (https://www.sciencedirect.com/science/article/abs/pii/S0024406683710035), fish (https://link.springer.com/article/10.1007/s10228-020-00754-6), to plants (https://www.jstor.org/stable/2097186), making generalisations quite difficult.\n\n\n\n\nRegardless, the general evolutionary pressures in non-plants are relatively easy to follow. I've not read much about the plant side, but it might also apply there.\n\n\n\n\nThere are currently two dominant theories to the evolution of sequential hermaphroditism in animals, the size advantage and low density models of evolution [1 (https://www.jstor.org/stable/2097186)].\n\n\n\n\nSize Advantage:\n\n\n\n\nThis model describes a process when an individual's reproductive success changes over their lifetime. This could either be when smaller males or smaller females have an advantage in early life. The starting point for sequential hermaphrodites can either be separate sex populations or simultaneous hermaphrodite populations.\n\n\n\n\nThe clownfish is a good example here. In this species, smaller young males are still able to fertilise eggs, but smaller females produce less eggs, so males have the reproductive success advantage when small, and when they get bigger, the females have the advantage. And by being both through a lifetime, each individual has higher reproductive success than populations where they are only 1 sex for their entire lifetime.\n\n\n\n\nThe opposite can also be true, when smaller females are able to produce enough eggs to be reproductively successful, but in populations where male competition is a more dominant factor. Here, small males are at a disadvantage, so larger males are selected for.\n\n\n\n\nLow density:\n\n\n\n\nThis model is even easier to follow and essentially suggests that for populations with a low density, it can be beneficial to be flexible. If one individual has an overlapping home range with another, they might initially be incompatible because they are both the same sex. But by changing sex during their lifetime, these individuals can be compatible later in life, so long as the sex change doesn't occur at the same time.\n\n\n\n\nHowever, it should be noted that there are many factors at play in any given populations which can contribute to everything above, including resource availability, predation, and parasitism pressures. Some interesting relevant reading: [2 (https://onlinelibrary.wiley.com/doi/full/10.1111/), 3 (https://www.nature.com/articles/s41467-022-30419-z), 4 (https://www.journals.uchicago.edu/doi/abs/10.1086/282974)]","answer_url":"https://biology.stackexchange.com/a/116334","author":"dthorbur","author_url":"https://biology.stackexchange.com/users/97760/dthorbur","content_license":"CC BY-SA 4.0","created_at":"2025-04-07T09:15:07+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:19.947691+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/df693642d727b738d2a533740632235c18a06cefec7a1e337c9589214a4ec91e_0.json","raw_sha256":"9df534f437f3b2f12d33db8536999ec4e6ffa10f2f59394799d9fe01c3c1ad16","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/117606;117602;117598;117594;117585;117579;117570;117568;117565;117559;117558;117555;117552;117548;117538;117524;117523;117522;117520;117515;117510;116509;116508;116504;116499;116491;116485;116483;116461;116454;116453;116445;116441;116435;116430;116426;116425;116414;116412;116406;116401;116399;116396;116395;116394;116392;116389;116384;116370;116367;116363;116361;116352;116351;116347;116345;116343;116338;116337;116332;116331;116324;116320;116316;116314;116312;116306;116292;116290;116284;116280;116277;116271;116270;116268;116267;116257;116256;116253;116250;116249;116240;116237;116233;116219;116214;116212;116205;116204;116200;116198;116187;116184;116173;116172;116167;116162;116149;116142;116129/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":116332,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"dthorbur","profile_url":"https://biology.stackexchange.com/users/97760/dthorbur","user_type":"registered"},"created_at":"2025-04-07T09:15:07+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"C73EB8F6-E0D3-4D22-AE9C-D083C562ABB7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C73EB8F6-E0D3-4D22-AE9C-D083C562ABB7/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Sharkey Malarkey","author_url":"https://biology.stackexchange.com/users/104078/sharkey-malarkey","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Sharkey Malarkey","profile_url":"https://biology.stackexchange.com/users/104078/sharkey-malarkey","user_type":"registered"},"created_at":"2025-04-07T04:53:37+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"B1443073-8BF2-4996-AFCE-FB5F3F221971","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B1443073-8BF2-4996-AFCE-FB5F3F221971/view-source"}],"url":"https://biology.stackexchange.com/questions/116332/how-does-sequential-hermaphroditism-evolve"},{"author":"dthorbur","author_url":"https://biology.stackexchange.com/users/97760/dthorbur","content_license":"CC BY-SA 4.0","context_id":"116334","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"dthorbur","profile_url":"https://biology.stackexchange.com/users/97760/dthorbur","user_type":"registered"},"created_at":"2025-04-07T09:15:07+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"C73EB8F6-E0D3-4D22-AE9C-D083C562ABB7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C73EB8F6-E0D3-4D22-AE9C-D083C562ABB7/view-source"}],"url":"https://biology.stackexchange.com/a/116334"}],"contexts":[{"context_id":"question","html":"<p>sequential hermaphroditism is the process of changing one’s biological gender. I’m just curious how this evolved. I understand why it evolved but how did this evolve? Evolution is a gradual process, so how did swapping genders evolve gradually?</p>\n","text":"sequential hermaphroditism is the process of changing one’s biological gender. I’m just curious how this evolved. I understand why it evolved but how did this evolve? Evolution is a gradual process, so how did swapping genders evolve gradually?"},{"context_id":"116334","html":"<p>This trait is believed to have evolved independently numerous times, and can be male-to-female and female-to-male, and can even result/start with simultaneous hermaphrodites. Hermaphrodites are also found in many different distinct phylogenetic groups, from <a href=\"https://www.sciencedirect.com/science/article/abs/pii/S0024406683710035\" rel=\"nofollow noreferrer\">molluscs</a>, <a href=\"https://link.springer.com/article/10.1007/s10228-020-00754-6\" rel=\"nofollow noreferrer\">fish</a>, to <a href=\"https://www.jstor.org/stable/2097186\" rel=\"nofollow noreferrer\">plants</a>, making generalisations quite difficult.</p>\n<p>Regardless, the general evolutionary pressures in non-plants are relatively easy to follow. I've not read much about the plant side, but it might also apply there.</p>\n<p>There are currently two dominant theories to the evolution of sequential hermaphroditism in animals, the <strong>size advantage</strong> and <strong>low density</strong> models of evolution [<a href=\"https://www.jstor.org/stable/2097186\" rel=\"nofollow noreferrer\">1</a>].</p>\n<h3>Size Advantage:</h3>\n<p>This model describes a process when an individual's reproductive success changes over their lifetime. This could either be when smaller males <em>or</em> smaller females have an advantage in early life. The starting point for sequential hermaphrodites can either be separate sex populations or simultaneous hermaphrodite populations.</p>\n<p>The clownfish is a good example here. In this species, smaller young males are still able to fertilise eggs, but smaller females produce less eggs, so males have the reproductive success advantage when small, and when they get bigger, the females have the advantage. And by being both through a lifetime, each individual has higher reproductive success than populations where they are only 1 sex for their entire lifetime.</p>\n<p>The opposite can also be true, when smaller females are able to produce enough eggs to be reproductively successful, but in populations where male competition is a more dominant factor. Here, small males are at a disadvantage, so larger males are selected for.</p>\n<h3>Low density:</h3>\n<p>This model is even easier to follow and essentially suggests that for populations with a low density, it can be beneficial to be flexible. If one individual has an overlapping home range with another, they might initially be incompatible because they are both the same sex. But by changing sex during their lifetime, these individuals can be compatible later in life, so long as the sex change doesn't occur at the same time.</p>\n<p>However, it should be noted that there are many factors at play in any given populations which can contribute to everything above, including resource availability, predation, and parasitism pressures. Some interesting relevant reading: [<a href=\"https://onlinelibrary.wiley.com/doi/full/10.1111/\" rel=\"nofollow noreferrer\">2</a>, <a href=\"https://www.nature.com/articles/s41467-022-30419-z\" rel=\"nofollow noreferrer\">3</a>, <a href=\"https://www.journals.uchicago.edu/doi/abs/10.1086/282974\" rel=\"nofollow noreferrer\">4</a>]</p>\n","text":"This trait is believed to have evolved independently numerous times, and can be male-to-female and female-to-male, and can even result/start with simultaneous hermaphrodites. Hermaphrodites are also found in many different distinct phylogenetic groups, from molluscs (https://www.sciencedirect.com/science/article/abs/pii/S0024406683710035), fish (https://link.springer.com/article/10.1007/s10228-020-00754-6), to plants (https://www.jstor.org/stable/2097186), making generalisations quite difficult.\n\n\n\n\nRegardless, the general evolutionary pressures in non-plants are relatively easy to follow. I've not read much about the plant side, but it might also apply there.\n\n\n\n\nThere are currently two dominant theories to the evolution of sequential hermaphroditism in animals, the size advantage and low density models of evolution [1 (https://www.jstor.org/stable/2097186)].\n\n\n\n\nSize Advantage:\n\n\n\n\nThis model describes a process when an individual's reproductive success changes over their lifetime. This could either be when smaller males or smaller females have an advantage in early life. The starting point for sequential hermaphrodites can either be separate sex populations or simultaneous hermaphrodite populations.\n\n\n\n\nThe clownfish is a good example here. In this species, smaller young males are still able to fertilise eggs, but smaller females produce less eggs, so males have the reproductive success advantage when small, and when they get bigger, the females have the advantage. And by being both through a lifetime, each individual has higher reproductive success than populations where they are only 1 sex for their entire lifetime.\n\n\n\n\nThe opposite can also be true, when smaller females are able to produce enough eggs to be reproductively successful, but in populations where male competition is a more dominant factor. Here, small males are at a disadvantage, so larger males are selected for.\n\n\n\n\nLow density:\n\n\n\n\nThis model is even easier to follow and essentially suggests that for populations with a low density, it can be beneficial to be flexible. If one individual has an overlapping home range with another, they might initially be incompatible because they are both the same sex. But by changing sex during their lifetime, these individuals can be compatible later in life, so long as the sex change doesn't occur at the same time.\n\n\n\n\nHowever, it should be noted that there are many factors at play in any given populations which can contribute to everything above, including resource availability, predation, and parasitism pressures. Some interesting relevant reading: [2 (https://onlinelibrary.wiley.com/doi/full/10.1111/), 3 (https://www.nature.com/articles/s41467-022-30419-z), 4 (https://www.journals.uchicago.edu/doi/abs/10.1086/282974)]"}],"domain":"biology","external_citations":["https://link.springer.com/article/10.1007/s10228-020-00754-6","https://onlinelibrary.wiley.com/doi/full/10.1111/","https://www.journals.uchicago.edu/doi/abs/10.1086/282974","https://www.jstor.org/stable/2097186","https://www.nature.com/articles/s41467-022-30419-z","https://www.sciencedirect.com/science/article/abs/pii/S0024406683710035"],"ground_truth_type":"metadata_grounded","group_id":"22143efa5fed6305a09df95cc97a151b2fc56d6093cfdcfdb51c6ca3779c6f21","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-141d6e72cbc14d6dba388bd1","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:02.598621+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/5d480e4bd1bd45ab525a4baf3227fba404f89b6af9dad33215fd9fa7c302a211_0.json","raw_sha256":"d723c7a62c8386d143891d26ae30b2234242ed3dac9599b11f141712ea994a96","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=3&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Sharkey Malarkey","profile_url":"https://biology.stackexchange.com/users/104078/sharkey-malarkey","user_type":"registered"},"created_at":"2025-04-07T04:53:37+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"B1443073-8BF2-4996-AFCE-FB5F3F221971","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B1443073-8BF2-4996-AFCE-FB5F3F221971/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"116332","source_record_sha256":"d37ae6ef03cc48a39520883e63f8e945601af51df079c59f03c602e567999ae7","source_url":"https://biology.stackexchange.com/questions/116332/how-does-sequential-hermaphroditism-evolve","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How does sequential hermaphroditism evolve?\nsequential hermaphroditism is the process of changing one’s biological gender. I’m just curious how this evolved. I understand why it evolved but how did this evolve? Evolution is a gradual process, so how did swapping genders evolve gradually?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116334,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I would suggest instead looking at the mtDNA sequence deposited in NCBI: <a href=\"https://www.ncbi.nlm.nih.gov/nuccore/KC879692.1\" rel=\"nofollow noreferrer\">https://www.ncbi.nlm.nih.gov/nuccore/KC879692.1</a></p>\n<p>I am not sure how this was generated exactly so maybe look into that more. But as far as I can tell it's what you want:</p>\n<pre><code>LOCUS       KC879692               16567 bp    DNA     circular PRI 24-JUN-2013\nDEFINITION  Homo sapiens neanderthalensis mitochondrion, complete genome.\nACCESSION   KC879692\nVERSION     KC879692.1\nKEYWORDS    .\nSOURCE      mitochondrion Homo sapiens neanderthalensis (Neandertal)\n  ORGANISM  Homo sapiens neanderthalensis\n            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;\n            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;\n            Catarrhini; Hominidae; Homo.\nREFERENCE   1  (bases 1 to 16567)\n  AUTHORS   Consortium,H.C.N.G.\n  TITLE     The high-coverage genome sequence of a Neandertal individual from\n            Denisova cave in the Altai\n  JOURNAL   Unpublished\nREFERENCE   2  (bases 1 to 16567)\n  AUTHORS   Sawyer,S.\n  TITLE     Direct Submission\n  JOURNAL   Submitted (09-APR-2013) Genetics, Max Planck Institute for\n            Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Saxony\n            04103, Germany\n</code></pre>\n","answer_id":116397,"answer_text":"I would suggest instead looking at the mtDNA sequence deposited in NCBI: https://www.ncbi.nlm.nih.gov/nuccore/KC879692.1 (https://www.ncbi.nlm.nih.gov/nuccore/KC879692.1)\n\n\n\n\nI am not sure how this was generated exactly so maybe look into that more. But as far as I can tell it's what you want:\n\n\n\n\nLOCUS       KC879692               16567 bp    DNA     circular PRI 24-JUN-2013\nDEFINITION  Homo sapiens neanderthalensis mitochondrion, complete genome.\nACCESSION   KC879692\nVERSION     KC879692.1\nKEYWORDS    .\nSOURCE      mitochondrion Homo sapiens neanderthalensis (Neandertal)\n  ORGANISM  Homo sapiens neanderthalensis\n            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;\n            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;\n            Catarrhini; Hominidae; Homo.\nREFERENCE   1  (bases 1 to 16567)\n  AUTHORS   Consortium,H.C.N.G.\n  TITLE     The high-coverage genome sequence of a Neandertal individual from\n            Denisova cave in the Altai\n  JOURNAL   Unpublished\nREFERENCE   2  (bases 1 to 16567)\n  AUTHORS   Sawyer,S.\n  TITLE     Direct Submission\n  JOURNAL   Submitted (09-APR-2013) Genetics, Max Planck Institute for\n            Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Saxony\n            04103, Germany","answer_url":"https://biology.stackexchange.com/a/116397","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2025-04-23T00:14:09+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:19.947691+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/df693642d727b738d2a533740632235c18a06cefec7a1e337c9589214a4ec91e_0.json","raw_sha256":"9df534f437f3b2f12d33db8536999ec4e6ffa10f2f59394799d9fe01c3c1ad16","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/117606;117602;117598;117594;117585;117579;117570;117568;117565;117559;117558;117555;117552;117548;117538;117524;117523;117522;117520;117515;117510;116509;116508;116504;116499;116491;116485;116483;116461;116454;116453;116445;116441;116435;116430;116426;116425;116414;116412;116406;116401;116399;116396;116395;116394;116392;116389;116384;116370;116367;116363;116361;116352;116351;116347;116345;116343;116338;116337;116332;116331;116324;116320;116316;116314;116312;116306;116292;116290;116284;116280;116277;116271;116270;116268;116267;116257;116256;116253;116250;116249;116240;116237;116233;116219;116214;116212;116205;116204;116200;116198;116187;116184;116173;116172;116167;116162;116149;116142;116129/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":116396,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2025-04-23T00:14:09+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"ADFDA359-C7DC-4A0D-8A16-F7F2B59E4E7F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/ADFDA359-C7DC-4A0D-8A16-F7F2B59E4E7F/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Mehdi Saada","author_url":"https://biology.stackexchange.com/users/82694/mehdi-saada","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Mehdi Saada","profile_url":"https://biology.stackexchange.com/users/82694/mehdi-saada","user_type":"registered"},"created_at":"2025-04-22T23:19:27+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"641BDAAF-0DF0-4DF6-A92F-9796B028FB47","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/641BDAAF-0DF0-4DF6-A92F-9796B028FB47/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Mehdi Saada","profile_url":"https://biology.stackexchange.com/users/82694/mehdi-saada","user_type":"registered"},"created_at":"2025-04-22T23:22:21+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"FA98BB5E-D9FA-4C7D-AB0A-E887F6F7067E","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FA98BB5E-D9FA-4C7D-AB0A-E887F6F7067E/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2025-05-23T01:03:20+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"2B8DE90A-567F-4469-A500-58C9EF0A1B1D","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/2B8DE90A-567F-4469-A500-58C9EF0A1B1D/view-source"}],"url":"https://biology.stackexchange.com/questions/116396/how-to-find-the-hvrii-locus-on-the-altai-neandertal"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"116397","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maximilian Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2025-04-23T00:14:09+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"ADFDA359-C7DC-4A0D-8A16-F7F2B59E4E7F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/ADFDA359-C7DC-4A0D-8A16-F7F2B59E4E7F/view-source"}],"url":"https://biology.stackexchange.com/a/116397"}],"contexts":[{"context_id":"question","html":"<p>I am looking for the HVRII locus on the Altai Neandertal sequence. Its accession number is ERP002097, but it's the raw resequencing data so it is not on NCBI. You can download the relevant file (for the mtDNA here) on <a href=\"http://cdna.eva.mpg.de/neandertal/altai/AltaiNeandertal/bam/\" rel=\"nofollow noreferrer\">http://cdna.eva.mpg.de/neandertal/altai/AltaiNeandertal/bam/</a>.\nThe file is huge, needless to say, but the problem is because those are the contigs, translating it into FASTA doesn't help as I get millions of small reads, what can I do with that ?\nI have the HVRII from the OG neandertal genome, and it has the tri-thymine insertion in the polycysteine tract from the HVRII. That is what I want to check on the Altai.\nDo I have to assemble it myself to give it to Blast ?\nThank you.</p>\n","text":"I am looking for the HVRII locus on the Altai Neandertal sequence. Its accession number is ERP002097, but it's the raw resequencing data so it is not on NCBI. You can download the relevant file (for the mtDNA here) on http://cdna.eva.mpg.de/neandertal/altai/AltaiNeandertal/bam/ (http://cdna.eva.mpg.de/neandertal/altai/AltaiNeandertal/bam/).\nThe file is huge, needless to say, but the problem is because those are the contigs, translating it into FASTA doesn't help as I get millions of small reads, what can I do with that ?\nI have the HVRII from the OG neandertal genome, and it has the tri-thymine insertion in the polycysteine tract from the HVRII. That is what I want to check on the Altai.\nDo I have to assemble it myself to give it to Blast ?\nThank you."},{"context_id":"116397","html":"<p>I would suggest instead looking at the mtDNA sequence deposited in NCBI: <a href=\"https://www.ncbi.nlm.nih.gov/nuccore/KC879692.1\" rel=\"nofollow noreferrer\">https://www.ncbi.nlm.nih.gov/nuccore/KC879692.1</a></p>\n<p>I am not sure how this was generated exactly so maybe look into that more. But as far as I can tell it's what you want:</p>\n<pre><code>LOCUS       KC879692               16567 bp    DNA     circular PRI 24-JUN-2013\nDEFINITION  Homo sapiens neanderthalensis mitochondrion, complete genome.\nACCESSION   KC879692\nVERSION     KC879692.1\nKEYWORDS    .\nSOURCE      mitochondrion Homo sapiens neanderthalensis (Neandertal)\n  ORGANISM  Homo sapiens neanderthalensis\n            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;\n            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;\n            Catarrhini; Hominidae; Homo.\nREFERENCE   1  (bases 1 to 16567)\n  AUTHORS   Consortium,H.C.N.G.\n  TITLE     The high-coverage genome sequence of a Neandertal individual from\n            Denisova cave in the Altai\n  JOURNAL   Unpublished\nREFERENCE   2  (bases 1 to 16567)\n  AUTHORS   Sawyer,S.\n  TITLE     Direct Submission\n  JOURNAL   Submitted (09-APR-2013) Genetics, Max Planck Institute for\n            Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Saxony\n            04103, Germany\n</code></pre>\n","text":"I would suggest instead looking at the mtDNA sequence deposited in NCBI: https://www.ncbi.nlm.nih.gov/nuccore/KC879692.1 (https://www.ncbi.nlm.nih.gov/nuccore/KC879692.1)\n\n\n\n\nI am not sure how this was generated exactly so maybe look into that more. But as far as I can tell it's what you want:\n\n\n\n\nLOCUS       KC879692               16567 bp    DNA     circular PRI 24-JUN-2013\nDEFINITION  Homo sapiens neanderthalensis mitochondrion, complete genome.\nACCESSION   KC879692\nVERSION     KC879692.1\nKEYWORDS    .\nSOURCE      mitochondrion Homo sapiens neanderthalensis (Neandertal)\n  ORGANISM  Homo sapiens neanderthalensis\n            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;\n            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;\n            Catarrhini; Hominidae; Homo.\nREFERENCE   1  (bases 1 to 16567)\n  AUTHORS   Consortium,H.C.N.G.\n  TITLE     The high-coverage genome sequence of a Neandertal individual from\n            Denisova cave in the Altai\n  JOURNAL   Unpublished\nREFERENCE   2  (bases 1 to 16567)\n  AUTHORS   Sawyer,S.\n  TITLE     Direct Submission\n  JOURNAL   Submitted (09-APR-2013) Genetics, Max Planck Institute for\n            Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Saxony\n            04103, Germany"}],"domain":"biology","external_citations":["http://cdna.eva.mpg.de/neandertal/altai/AltaiNeandertal/bam/","https://www.ncbi.nlm.nih.gov/nuccore/KC879692.1"],"ground_truth_type":"metadata_grounded","group_id":"8909fa445a12aa523ea13f6f9f5e64165fd0bcd4bf08283e343f39fdeea0c1d6","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-017aac528e26242f29c9e2c1","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:02.598621+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/5d480e4bd1bd45ab525a4baf3227fba404f89b6af9dad33215fd9fa7c302a211_0.json","raw_sha256":"d723c7a62c8386d143891d26ae30b2234242ed3dac9599b11f141712ea994a96","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=3&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Mehdi Saada","profile_url":"https://biology.stackexchange.com/users/82694/mehdi-saada","user_type":"registered"},"created_at":"2025-04-22T23:19:27+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"641BDAAF-0DF0-4DF6-A92F-9796B028FB47","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/641BDAAF-0DF0-4DF6-A92F-9796B028FB47/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Mehdi Saada","profile_url":"https://biology.stackexchange.com/users/82694/mehdi-saada","user_type":"registered"},"created_at":"2025-04-22T23:22:21+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"FA98BB5E-D9FA-4C7D-AB0A-E887F6F7067E","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FA98BB5E-D9FA-4C7D-AB0A-E887F6F7067E/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2025-05-23T01:03:20+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"2B8DE90A-567F-4469-A500-58C9EF0A1B1D","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/2B8DE90A-567F-4469-A500-58C9EF0A1B1D/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"116396","source_record_sha256":"704022626335419300b4aef24969034056a47440a2d3699ed6905796b77c6cbe","source_url":"https://biology.stackexchange.com/questions/116396/how-to-find-the-hvrii-locus-on-the-altai-neandertal","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How to find the HVRII locus on the Altai Neandertal\nI am looking for the HVRII locus on the Altai Neandertal sequence. Its accession number is ERP002097, but it's the raw resequencing data so it is not on NCBI. You can download the relevant file (for the mtDNA here) on http://cdna.eva.mpg.de/neandertal/altai/AltaiNeandertal/bam/ (http://cdna.eva.mpg.de/neandertal/altai/AltaiNeandertal/bam/).\nThe file is huge, needless to say, but the problem is because those are the contigs, translating it into FASTA doesn't help as I get millions of small reads, what can I do with that ?\nI have the HVRII from the OG neandertal genome, and it has the tri-thymine insertion in the polycysteine tract from the HVRII. That is what I want to check on the Altai.\nDo I have to assemble it myself to give it to Blast ?\nThank you.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116397,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The &quot;bulb&quot; isn't a bulb, it is called a <a href=\"https://en.wikipedia.org/wiki/Plant_stem\" rel=\"nofollow noreferrer\">node</a>. This is the point on a stem where branches/leaves come off the stem.</p>\n<p>In your case you have a point where there have been multiple small branches come off this point. These may have been below the bark in the form of <a href=\"https://en.wikipedia.org/wiki/Epicormic_shoot\" rel=\"nofollow noreferrer\">epicormic shoots</a>, so were potential new branches/buds but not fully formed. At some point during the plant's life the bark and shoots have rotted away and you are left with the holes you see. In your top picture, you can see five prominent holes arranged more or less like the pattern of the &quot;5&quot; side\non a <a href=\"https://en.wikipedia.org/wiki/Dice\" rel=\"nofollow noreferrer\">die</a>. Directly below this pattern is a small knob, which is the remains of a stick that hasn't fully rotted out yet.</p>\n","answer_id":116416,"answer_text":"The \"bulb\" isn't a bulb, it is called a node (https://en.wikipedia.org/wiki/Plant_stem). This is the point on a stem where branches/leaves come off the stem.\n\n\n\n\nIn your case you have a point where there have been multiple small branches come off this point. These may have been below the bark in the form of epicormic shoots (https://en.wikipedia.org/wiki/Epicormic_shoot), so were potential new branches/buds but not fully formed. At some point during the plant's life the bark and shoots have rotted away and you are left with the holes you see. In your top picture, you can see five prominent holes arranged more or less like the pattern of the \"5\" side\non a die (https://en.wikipedia.org/wiki/Dice). Directly below this pattern is a small knob, which is the remains of a stick that hasn't fully rotted out yet.","answer_url":"https://biology.stackexchange.com/a/116416","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2025-04-27T23:20:51+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:19.947691+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/df693642d727b738d2a533740632235c18a06cefec7a1e337c9589214a4ec91e_0.json","raw_sha256":"9df534f437f3b2f12d33db8536999ec4e6ffa10f2f59394799d9fe01c3c1ad16","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/117606;117602;117598;117594;117585;117579;117570;117568;117565;117559;117558;117555;117552;117548;117538;117524;117523;117522;117520;117515;117510;116509;116508;116504;116499;116491;116485;116483;116461;116454;116453;116445;116441;116435;116430;116426;116425;116414;116412;116406;116401;116399;116396;116395;116394;116392;116389;116384;116370;116367;116363;116361;116352;116351;116347;116345;116343;116338;116337;116332;116331;116324;116320;116316;116314;116312;116306;116292;116290;116284;116280;116277;116271;116270;116268;116267;116257;116256;116253;116250;116249;116240;116237;116233;116219;116214;116212;116205;116204;116200;116198;116187;116184;116173;116172;116167;116162;116149;116142;116129/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":116414,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2025-04-27T23:20:51+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"EA6B26B9-A49B-44D2-831E-82C9A62C1D60","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/EA6B26B9-A49B-44D2-831E-82C9A62C1D60/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"charlip","author_url":"https://biology.stackexchange.com/users/105654/charlip","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"charlip","profile_url":"https://biology.stackexchange.com/users/105654/charlip","user_type":"registered"},"created_at":"2025-04-27T02:19:47+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"0ABCA181-BBE9-4E08-8F6A-30B8E757DE9A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0ABCA181-BBE9-4E08-8F6A-30B8E757DE9A/view-source"}],"url":"https://biology.stackexchange.com/questions/116414/stick-with-hollow-round-bulb-with-holes"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"116416","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2025-04-27T23:20:51+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"EA6B26B9-A49B-44D2-831E-82C9A62C1D60","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/EA6B26B9-A49B-44D2-831E-82C9A62C1D60/view-source"}],"url":"https://biology.stackexchange.com/a/116416"}],"contexts":[{"context_id":"question","html":"<p>I found this wooden stick while walking in a brushy area. I do not have it with me anymore but I have photos attached. The bulb (I don’t really know what to call it) is hollow with holes and a little smaller than a ping-pong ball.\nWhat is this bulb? How did it get there?</p>\n<p><a href=\"https://i.sstatic.net/3KrowxTl.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/3KrowxTl.jpg\" alt=\"stick with a small, round, hollow formation, which has holes in it\" /></a></p>\n<p><a href=\"https://i.sstatic.net/4hnTafjL.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/4hnTafjL.jpg\" alt=\"stick with a small, round, hollow formation, which has holes in it\" /></a></p>\n","text":"I found this wooden stick while walking in a brushy area. I do not have it with me anymore but I have photos attached. The bulb (I don’t really know what to call it) is hollow with holes and a little smaller than a ping-pong ball.\nWhat is this bulb? How did it get there?\n\n\n\n\n[image: stick with a small, round, hollow formation, which has holes in it; source: https://i.sstatic.net/3KrowxTl.jpg] (https://i.sstatic.net/3KrowxTl.jpg)\n\n\n\n\n[image: stick with a small, round, hollow formation, which has holes in it; source: https://i.sstatic.net/4hnTafjL.jpg] (https://i.sstatic.net/4hnTafjL.jpg)"},{"context_id":"116416","html":"<p>The &quot;bulb&quot; isn't a bulb, it is called a <a href=\"https://en.wikipedia.org/wiki/Plant_stem\" rel=\"nofollow noreferrer\">node</a>. This is the point on a stem where branches/leaves come off the stem.</p>\n<p>In your case you have a point where there have been multiple small branches come off this point. These may have been below the bark in the form of <a href=\"https://en.wikipedia.org/wiki/Epicormic_shoot\" rel=\"nofollow noreferrer\">epicormic shoots</a>, so were potential new branches/buds but not fully formed. At some point during the plant's life the bark and shoots have rotted away and you are left with the holes you see. In your top picture, you can see five prominent holes arranged more or less like the pattern of the &quot;5&quot; side\non a <a href=\"https://en.wikipedia.org/wiki/Dice\" rel=\"nofollow noreferrer\">die</a>. Directly below this pattern is a small knob, which is the remains of a stick that hasn't fully rotted out yet.</p>\n","text":"The \"bulb\" isn't a bulb, it is called a node (https://en.wikipedia.org/wiki/Plant_stem). This is the point on a stem where branches/leaves come off the stem.\n\n\n\n\nIn your case you have a point where there have been multiple small branches come off this point. These may have been below the bark in the form of epicormic shoots (https://en.wikipedia.org/wiki/Epicormic_shoot), so were potential new branches/buds but not fully formed. At some point during the plant's life the bark and shoots have rotted away and you are left with the holes you see. In your top picture, you can see five prominent holes arranged more or less like the pattern of the \"5\" side\non a die (https://en.wikipedia.org/wiki/Dice). Directly below this pattern is a small knob, which is the remains of a stick that hasn't fully rotted out yet."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Dice","https://en.wikipedia.org/wiki/Epicormic_shoot","https://en.wikipedia.org/wiki/Plant_stem","https://i.sstatic.net/3KrowxTl.jpg","https://i.sstatic.net/4hnTafjL.jpg"],"ground_truth_type":"metadata_grounded","group_id":"a790754a91939ef96d07d0487e508dd462aa0dc8136d3ecd71968fa969db334d","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-ff9b77759cd91342cf61ac03","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:02.598621+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/5d480e4bd1bd45ab525a4baf3227fba404f89b6af9dad33215fd9fa7c302a211_0.json","raw_sha256":"d723c7a62c8386d143891d26ae30b2234242ed3dac9599b11f141712ea994a96","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=3&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"charlip","profile_url":"https://biology.stackexchange.com/users/105654/charlip","user_type":"registered"},"created_at":"2025-04-27T02:19:47+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"0ABCA181-BBE9-4E08-8F6A-30B8E757DE9A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0ABCA181-BBE9-4E08-8F6A-30B8E757DE9A/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"116414","source_record_sha256":"2b1e9fe3c0146ed2d5c2d761f5009278b79e8f64572a51ffc11668c016a2f69a","source_url":"https://biology.stackexchange.com/questions/116414/stick-with-hollow-round-bulb-with-holes","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Stick with hollow, round bulb with holes\nI found this wooden stick while walking in a brushy area. I do not have it with me anymore but I have photos attached. The bulb (I don’t really know what to call it) is hollow with holes and a little smaller than a ping-pong ball.\nWhat is this bulb? How did it get there?\n\n\n\n\n[image: stick with a small, round, hollow formation, which has holes in it; source: https://i.sstatic.net/3KrowxTl.jpg] (https://i.sstatic.net/3KrowxTl.jpg)\n\n\n\n\n[image: stick with a small, round, hollow formation, which has holes in it; source: https://i.sstatic.net/4hnTafjL.jpg] (https://i.sstatic.net/4hnTafjL.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116416,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p><strong>Not an answer, but some thoughts until an answer comes along.</strong></p>\n<p>I can't seem to find much in the scientific literature, but I suspect I just don't know the key words or phrases. But I'm sure you could go down a reference rabbit hole with the paper I did find.</p>\n<p>This example you've posted appears to be from the genus <em>Danaus</em>, which are common in Taiwan. Though it looks really similar to the Monarch butterfly chrysalis. There are some pretty extreme examples of the &quot;metallic&quot; or reflective elements from the genus <a href=\"https://en.wikipedia.org/wiki/Mechanitis\" rel=\"nofollow noreferrer\">Mechanitis</a>, which are really interesting. A <a href=\"https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2435.13963\" rel=\"nofollow noreferrer\">2021 study</a> tested the theory a metallic reflective coat would decrease predation, but found no difference in predation risk when more reflective.</p>\n<p><a href=\"https://i.sstatic.net/pBD04rkf.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/pBD04rkf.jpg\" alt=\"enter image description here\" /></a></p>\n<p>Lepidoptera (butterflies and moths) are known for their ability to advertise their unpleasant taste to predators (<a href=\"https://resjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2311.2009.01137.x\" rel=\"nofollow noreferrer\">1</a>). So a simple explanation could just be a unique pattern to identify itself to predators, especially if another palatable species has started to mimic it. But there are plenty of other explanations, including the idea the reflections help camouflage the chrysalis (though less likely IMO).</p>\n","answer_id":116458,"answer_text":"Not an answer, but some thoughts until an answer comes along.\n\n\n\n\nI can't seem to find much in the scientific literature, but I suspect I just don't know the key words or phrases. But I'm sure you could go down a reference rabbit hole with the paper I did find.\n\n\n\n\nThis example you've posted appears to be from the genus Danaus, which are common in Taiwan. Though it looks really similar to the Monarch butterfly chrysalis. There are some pretty extreme examples of the \"metallic\" or reflective elements from the genus Mechanitis (https://en.wikipedia.org/wiki/Mechanitis), which are really interesting. A 2021 study (https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2435.13963) tested the theory a metallic reflective coat would decrease predation, but found no difference in predation risk when more reflective.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/pBD04rkf.jpg] (https://i.sstatic.net/pBD04rkf.jpg)\n\n\n\n\nLepidoptera (butterflies and moths) are known for their ability to advertise their unpleasant taste to predators (1 (https://resjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2311.2009.01137.x)). So a simple explanation could just be a unique pattern to identify itself to predators, especially if another palatable species has started to mimic it. But there are plenty of other explanations, including the idea the reflections help camouflage the chrysalis (though less likely IMO).","answer_url":"https://biology.stackexchange.com/a/116458","author":"dthorbur","author_url":"https://biology.stackexchange.com/users/97760/dthorbur","content_license":"CC BY-SA 4.0","created_at":"2025-05-07T13:24:55+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:19.947691+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/df693642d727b738d2a533740632235c18a06cefec7a1e337c9589214a4ec91e_0.json","raw_sha256":"9df534f437f3b2f12d33db8536999ec4e6ffa10f2f59394799d9fe01c3c1ad16","source_api":"Stack Exchange API 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BY-SA 4.0","context_id":"116458","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"dthorbur","profile_url":"https://biology.stackexchange.com/users/97760/dthorbur","user_type":"registered"},"created_at":"2025-05-07T13:24:55+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"28F97FF8-0F32-470B-9CB6-6C09473DC4DD","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/28F97FF8-0F32-470B-9CB6-6C09473DC4DD/view-source"},{"content_license":"CC BY-SA 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Taiwan in late April something sparkly under a leaf caught my eye as I walked by. Upon investigating, I found a 20 x 9 mm very bright green chrysalis hanging under a leaf. It has some black dots patterned on it, and a short black &quot;stem&quot; connected by white fibers to the leaf's underside.</p>\n<p>But what really amazed me are the patterns of silvery &quot;glitter&quot; or bright, shiny, reflective areas, some random, but some in a line or row as well.</p>\n<p><strong>Question:</strong> What caterpillar makes such a chrysalis, what butterfly then emerges, and why/how are these glittery spots made?</p>\n<hr />\n<p>Since I'm not sure which features or angles are important to show to address both parts fo the question, I've included several more photos. Click images for full size.</p>\n<p><a href=\"https://i.sstatic.net/TCziCRJj.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/TCziCRJjm.jpg\" alt=\"bright green 20x8 mm chrysalis with black and glittery spots, Hsinchu county, Taiwan, late April\" /></a> <a href=\"https://i.sstatic.net/8qbLO1TK.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/8qbLO1TKm.jpg\" alt=\"bright green 20x8 mm chrysalis with black and glittery spots, Hsinchu county, Taiwan, late April\" /></a>\n<a href=\"https://i.sstatic.net/zOqBYGn5.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/zOqBYGn5m.jpg\" alt=\"bright green 20x8 mm chrysalis with black and glittery spots, Hsinchu county, Taiwan, late April\" /></a> <a href=\"https://i.sstatic.net/tCHDtFZy.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/tCHDtFZym.jpg\" alt=\"bright green 20x8 mm chrysalis with black and glittery spots, Hsinchu county, Taiwan, late April\" /></a></p>\n","text":"[image: bright green 20x8 mm chrysalis with black and glittery spots, Hsinchu county, Taiwan, late April; source: https://i.sstatic.net/8esr3oTK.jpg] (https://i.sstatic.net/8esr3oTK.jpg)\n\n\n\n\nHiking in a low elevation area in Hsinchu county Taiwan in late April something sparkly under a leaf caught my eye as I walked by. Upon investigating, I found a 20 x 9 mm very bright green chrysalis hanging under a leaf. It has some black dots patterned on it, and a short black \"stem\" connected by white fibers to the leaf's underside.\n\n\n\n\nBut what really amazed me are the patterns of silvery \"glitter\" or bright, shiny, reflective areas, some random, but some in a line or row as well.\n\n\n\n\nQuestion: What caterpillar makes such a chrysalis, what butterfly then emerges, and why/how are these glittery spots made?\n\n\n\n\n\n\n\nSince I'm not sure which features or angles are important to show to address both parts fo the question, I've included several more photos. Click images for full size.\n\n\n\n\n[image: bright green 20x8 mm chrysalis with black and glittery spots, Hsinchu county, Taiwan, late April; source: https://i.sstatic.net/TCziCRJjm.jpg] (https://i.sstatic.net/TCziCRJj.jpg) [image: bright green 20x8 mm chrysalis with black and glittery spots, Hsinchu county, Taiwan, late April; source: https://i.sstatic.net/8qbLO1TKm.jpg] (https://i.sstatic.net/8qbLO1TK.jpg)\n[image: bright green 20x8 mm chrysalis with black and glittery spots, Hsinchu county, Taiwan, late April; source: https://i.sstatic.net/zOqBYGn5m.jpg] (https://i.sstatic.net/zOqBYGn5.jpg) [image: bright green 20x8 mm chrysalis with black and glittery spots, Hsinchu county, Taiwan, late April; source: https://i.sstatic.net/tCHDtFZym.jpg] (https://i.sstatic.net/tCHDtFZy.jpg)"},{"context_id":"116458","html":"<p><strong>Not an answer, but some thoughts until an answer comes along.</strong></p>\n<p>I can't seem to find much in the scientific literature, but I suspect I just don't know the key words or phrases. But I'm sure you could go down a reference rabbit hole with the paper I did find.</p>\n<p>This example you've posted appears to be from the genus <em>Danaus</em>, which are common in Taiwan. Though it looks really similar to the Monarch butterfly chrysalis. There are some pretty extreme examples of the &quot;metallic&quot; or reflective elements from the genus <a href=\"https://en.wikipedia.org/wiki/Mechanitis\" rel=\"nofollow noreferrer\">Mechanitis</a>, which are really interesting. A <a href=\"https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2435.13963\" rel=\"nofollow noreferrer\">2021 study</a> tested the theory a metallic reflective coat would decrease predation, but found no difference in predation risk when more reflective.</p>\n<p><a href=\"https://i.sstatic.net/pBD04rkf.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/pBD04rkf.jpg\" alt=\"enter image description here\" /></a></p>\n<p>Lepidoptera (butterflies and moths) are known for their ability to advertise their unpleasant taste to predators (<a href=\"https://resjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2311.2009.01137.x\" rel=\"nofollow noreferrer\">1</a>). So a simple explanation could just be a unique pattern to identify itself to predators, especially if another palatable species has started to mimic it. But there are plenty of other explanations, including the idea the reflections help camouflage the chrysalis (though less likely IMO).</p>\n","text":"Not an answer, but some thoughts until an answer comes along.\n\n\n\n\nI can't seem to find much in the scientific literature, but I suspect I just don't know the key words or phrases. But I'm sure you could go down a reference rabbit hole with the paper I did find.\n\n\n\n\nThis example you've posted appears to be from the genus Danaus, which are common in Taiwan. Though it looks really similar to the Monarch butterfly chrysalis. There are some pretty extreme examples of the \"metallic\" or reflective elements from the genus Mechanitis (https://en.wikipedia.org/wiki/Mechanitis), which are really interesting. A 2021 study (https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2435.13963) tested the theory a metallic reflective coat would decrease predation, but found no difference in predation risk when more reflective.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/pBD04rkf.jpg] (https://i.sstatic.net/pBD04rkf.jpg)\n\n\n\n\nLepidoptera (butterflies and moths) are known for their ability to advertise their unpleasant taste to predators (1 (https://resjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2311.2009.01137.x)). So a simple explanation could just be a unique pattern to identify itself to predators, especially if another palatable species has started to mimic it. But there are plenty of other explanations, including the idea the reflections help camouflage the chrysalis (though less likely IMO)."}],"domain":"biology","external_citations":["https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2435.13963","https://en.wikipedia.org/wiki/Mechanitis","https://i.sstatic.net/8esr3oTK.jpg","https://i.sstatic.net/8qbLO1TK.jpg","https://i.sstatic.net/TCziCRJj.jpg","https://i.sstatic.net/pBD04rkf.jpg","https://i.sstatic.net/tCHDtFZy.jpg","https://i.sstatic.net/zOqBYGn5.jpg","https://resjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2311.2009.01137.x"],"ground_truth_type":"metadata_grounded","group_id":"d925f66a5d4a4dee8ac8de1327b4c671128b9cb05a53804c556d1cc3cc9a3a48","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-5635e700771535bad9c5a45a","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:02.598621+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/5d480e4bd1bd45ab525a4baf3227fba404f89b6af9dad33215fd9fa7c302a211_0.json","raw_sha256":"d723c7a62c8386d143891d26ae30b2234242ed3dac9599b11f141712ea994a96","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=3&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"uhoh","profile_url":"https://biology.stackexchange.com/users/27918/uhoh","user_type":"registered"},"created_at":"2025-05-07T10:01:54+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"903F2E51-AAE1-4BB4-A1D1-6A1E8A594787","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/903F2E51-AAE1-4BB4-A1D1-6A1E8A594787/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"uhoh","profile_url":"https://biology.stackexchange.com/users/27918/uhoh","user_type":"registered"},"created_at":"2025-05-07T10:08:25+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"4ED8B498-97D4-4780-9C71-4E6574F1F20B","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4ED8B498-97D4-4780-9C71-4E6574F1F20B/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2025-05-07T14:35:10+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"A33A5CE2-2B90-491B-BE6D-054B16E2FBD6","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A33A5CE2-2B90-491B-BE6D-054B16E2FBD6/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-05-07T18:03:30+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"DE92EBDA-67B1-47CE-B71D-FA7016D5B277","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/DE92EBDA-67B1-47CE-B71D-FA7016D5B277/view-source"},{"content_license":null,"contributor":{"display_name":"uhoh","profile_url":"https://biology.stackexchange.com/users/27918/uhoh","user_type":"registered"},"created_at":"2025-05-08T19:59:17+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"323AFDF7-C06D-4095-9D6E-5A1EFB1C345B","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/323AFDF7-C06D-4095-9D6E-5A1EFB1C345B/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"116454","source_record_sha256":"364c59f5721ca1eccfdcc1481f70111ba960c2bee3faa806644d7f1d4d504b57","source_url":"https://biology.stackexchange.com/questions/116454/who-puts-glitter-on-their-chrysalis-and-how-is-it-produced","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Who puts glitter on their chrysalis? And how is it produced?\n[image: bright green 20x8 mm chrysalis with black and glittery spots, Hsinchu county, Taiwan, late April; source: https://i.sstatic.net/8esr3oTK.jpg] (https://i.sstatic.net/8esr3oTK.jpg)\n\n\n\n\nHiking in a low elevation area in Hsinchu county Taiwan in late April something sparkly under a leaf caught my eye as I walked by. Upon investigating, I found a 20 x 9 mm very bright green chrysalis hanging under a leaf. It has some black dots patterned on it, and a short black \"stem\" connected by white fibers to the leaf's underside.\n\n\n\n\nBut what really amazed me are the patterns of silvery \"glitter\" or bright, shiny, reflective areas, some random, but some in a line or row as well.\n\n\n\n\nQuestion: What caterpillar makes such a chrysalis, what butterfly then emerges, and why/how are these glittery spots made?\n\n\n\n\n\n\n\nSince I'm not sure which features or angles are important to show to address both parts fo the question, I've included several more photos. Click images for full size.\n\n\n\n\n[image: bright green 20x8 mm chrysalis with black and glittery spots, Hsinchu county, Taiwan, late April; source: https://i.sstatic.net/TCziCRJjm.jpg] (https://i.sstatic.net/TCziCRJj.jpg) [image: bright green 20x8 mm chrysalis with black and glittery spots, Hsinchu county, Taiwan, late April; source: https://i.sstatic.net/8qbLO1TKm.jpg] (https://i.sstatic.net/8qbLO1TK.jpg)\n[image: bright green 20x8 mm chrysalis with black and glittery spots, Hsinchu county, Taiwan, late April; source: https://i.sstatic.net/zOqBYGn5m.jpg] (https://i.sstatic.net/zOqBYGn5.jpg) [image: bright green 20x8 mm chrysalis with black and glittery spots, Hsinchu county, Taiwan, late April; source: https://i.sstatic.net/tCHDtFZym.jpg] (https://i.sstatic.net/tCHDtFZy.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116458,"score":5}],"split":"test"}
{"accepted_status":{"accepted_answer_id":116506,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>These are most likely Red Spider Mites (<em><a href=\"https://en.wikipedia.org/wiki/Tetranychus_urticae\" rel=\"nofollow noreferrer\">Tetranychus urticae</a></em>), which are found world-wide. They are <a href=\"https://en.wikipedia.org/wiki/Mite\" rel=\"nofollow noreferrer\">mites</a>, so arthropods within the arachnid family, but not spiders. They feed on plants and you can often see them scrambling over rocks or dirt in sunny spots, particularly where there is plant material for it to feed on.</p>\n<p>They are of no risk to you, but are a serious pest of crop and domestic plants.</p>\n","answer_id":116506,"answer_text":"These are most likely Red Spider Mites (Tetranychus urticae (https://en.wikipedia.org/wiki/Tetranychus_urticae)), which are found world-wide. They are mites (https://en.wikipedia.org/wiki/Mite), so arthropods within the arachnid family, but not spiders. They feed on plants and you can often see them scrambling over rocks or dirt in sunny spots, particularly where there is plant material for it to feed on.\n\n\n\n\nThey are of no risk to you, but are a serious pest of crop and domestic plants.","answer_url":"https://biology.stackexchange.com/a/116506","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2025-05-19T21:46:48+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:19.947691+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/df693642d727b738d2a533740632235c18a06cefec7a1e337c9589214a4ec91e_0.json","raw_sha256":"9df534f437f3b2f12d33db8536999ec4e6ffa10f2f59394799d9fe01c3c1ad16","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/117606;117602;117598;117594;117585;117579;117570;117568;117565;117559;117558;117555;117552;117548;117538;117524;117523;117522;117520;117515;117510;116509;116508;116504;116499;116491;116485;116483;116461;116454;116453;116445;116441;116435;116430;116426;116425;116414;116412;116406;116401;116399;116396;116395;116394;116392;116389;116384;116370;116367;116363;116361;116352;116351;116347;116345;116343;116338;116337;116332;116331;116324;116320;116316;116314;116312;116306;116292;116290;116284;116280;116277;116271;116270;116268;116267;116257;116256;116253;116250;116249;116240;116237;116233;116219;116214;116212;116205;116204;116200;116198;116187;116184;116173;116172;116167;116162;116149;116142;116129/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":116504,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2025-05-19T21:46:48+00:00","raw_file":"raw/codex_api_v1/513f34509ea5b8cfd23e2c22ec69b0af899072a5df884318581dc59cdc06558f_1790824145019083900_0.json","raw_sha256":"e49bc4b696ee886e85729b5e43d509e97eb936a63dd33019b0855e8f32360f99","revision_guid":"D44E73EB-3129-4123-9A60-2751FE356B5C","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D44E73EB-3129-4123-9A60-2751FE356B5C/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Marcus Junius Brutus","author_url":"https://biology.stackexchange.com/users/5547/marcus-junius-brutus","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Marcus Junius Brutus","profile_url":"https://biology.stackexchange.com/users/5547/marcus-junius-brutus","user_type":"registered"},"created_at":"2025-05-19T14:41:08+00:00","raw_file":"raw/codex_api_v1/513f34509ea5b8cfd23e2c22ec69b0af899072a5df884318581dc59cdc06558f_1790824145019083900_0.json","raw_sha256":"e49bc4b696ee886e85729b5e43d509e97eb936a63dd33019b0855e8f32360f99","revision_guid":"5C93CA17-0191-4CE7-B80D-ECA864F703FA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5C93CA17-0191-4CE7-B80D-ECA864F703FA/view-source"}],"url":"https://biology.stackexchange.com/questions/116504/is-this-a-spiderling-or-something-nastier"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"116506","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2025-05-19T21:46:48+00:00","raw_file":"raw/codex_api_v1/513f34509ea5b8cfd23e2c22ec69b0af899072a5df884318581dc59cdc06558f_1790824145019083900_0.json","raw_sha256":"e49bc4b696ee886e85729b5e43d509e97eb936a63dd33019b0855e8f32360f99","revision_guid":"D44E73EB-3129-4123-9A60-2751FE356B5C","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D44E73EB-3129-4123-9A60-2751FE356B5C/view-source"}],"url":"https://biology.stackexchange.com/a/116506"}],"contexts":[{"context_id":"question","html":"<p>In Greece I recently (May, warm and dry weather) encountered lots and lots of these tiny creatures on a field / construction site. The ground was literally infested with them (I'd estimate 20 of them per square meter in some spots). Are these spiderlings or something more sinister? Size approximately 1-2 mm.<a href=\"https://i.sstatic.net/F0ee2J1V.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/F0ee2J1V.jpg\" alt=\"enter image description here\" /></a></p>\n","text":"In Greece I recently (May, warm and dry weather) encountered lots and lots of these tiny creatures on a field / construction site. The ground was literally infested with them (I'd estimate 20 of them per square meter in some spots). Are these spiderlings or something more sinister? Size approximately 1-2 mm.[image: enter image description here; source: https://i.sstatic.net/F0ee2J1V.jpg] (https://i.sstatic.net/F0ee2J1V.jpg)"},{"context_id":"116506","html":"<p>These are most likely Red Spider Mites (<em><a href=\"https://en.wikipedia.org/wiki/Tetranychus_urticae\" rel=\"nofollow noreferrer\">Tetranychus urticae</a></em>), which are found world-wide. They are <a href=\"https://en.wikipedia.org/wiki/Mite\" rel=\"nofollow noreferrer\">mites</a>, so arthropods within the arachnid family, but not spiders. They feed on plants and you can often see them scrambling over rocks or dirt in sunny spots, particularly where there is plant material for it to feed on.</p>\n<p>They are of no risk to you, but are a serious pest of crop and domestic plants.</p>\n","text":"These are most likely Red Spider Mites (Tetranychus urticae (https://en.wikipedia.org/wiki/Tetranychus_urticae)), which are found world-wide. They are mites (https://en.wikipedia.org/wiki/Mite), so arthropods within the arachnid family, but not spiders. They feed on plants and you can often see them scrambling over rocks or dirt in sunny spots, particularly where there is plant material for it to feed on.\n\n\n\n\nThey are of no risk to you, but are a serious pest of crop and domestic plants."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Mite","https://en.wikipedia.org/wiki/Tetranychus_urticae","https://i.sstatic.net/F0ee2J1V.jpg"],"ground_truth_type":"metadata_grounded","group_id":"47d623592279a898c68ad12fae3af92593aefba2ac1df6ee4b558924d0fcc76d","hard_case_family":["multiple_sources"],"id":"RHM-5e38d576cd3c3b83ecfdbbc0","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:02.598621+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/5d480e4bd1bd45ab525a4baf3227fba404f89b6af9dad33215fd9fa7c302a211_0.json","raw_sha256":"d723c7a62c8386d143891d26ae30b2234242ed3dac9599b11f141712ea994a96","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=3&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Marcus Junius Brutus","profile_url":"https://biology.stackexchange.com/users/5547/marcus-junius-brutus","user_type":"registered"},"created_at":"2025-05-19T14:41:08+00:00","raw_file":"raw/codex_api_v1/513f34509ea5b8cfd23e2c22ec69b0af899072a5df884318581dc59cdc06558f_1790824145019083900_0.json","raw_sha256":"e49bc4b696ee886e85729b5e43d509e97eb936a63dd33019b0855e8f32360f99","revision_guid":"5C93CA17-0191-4CE7-B80D-ECA864F703FA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5C93CA17-0191-4CE7-B80D-ECA864F703FA/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"116504","source_record_sha256":"6a224da83bc143caa6a3eaec2543032f74bdc2b1b39437ab7dc5e5285377cbef","source_url":"https://biology.stackexchange.com/questions/116504/is-this-a-spiderling-or-something-nastier","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"is this a spiderling or something nastier?\nIn Greece I recently (May, warm and dry weather) encountered lots and lots of these tiny creatures on a field / construction site. The ground was literally infested with them (I'd estimate 20 of them per square meter in some spots). Are these spiderlings or something more sinister? Size approximately 1-2 mm.[image: enter image description here; source: https://i.sstatic.net/F0ee2J1V.jpg] (https://i.sstatic.net/F0ee2J1V.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116506,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>It's difficult to tell without a higher resolution image, but one possibility is the sawtooth grain beetle (<em>Oryzaephilus surinamensis</em>), a common pest of stored food products (the bathroom is a strange place for it to be, so maybe you could look for more in the kitchen or pantry). The teeth running down the thorax are a characteristic feature. I'm pretty sure I can see these in your image (especially on the left side, behind the visible leg). However, this species only grows to about 2.5mm (1/10 of an inch), so if you can confirm the 1/4 in measurement I would reconsider my answer.</p>\n<p><a href=\"https://i.sstatic.net/FWzjZJVo.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/FWzjZJVo.png\" alt=\"O. surinamensis on a a blue background next to a tape-measure with mm markings\" /></a></p>\n<p><strong>Source:</strong> Iowa State University, <a href=\"https://yardandgarden.extension.iastate.edu/encyclopedia/sawtoothed-grain-beetle\" rel=\"nofollow noreferrer\">https://yardandgarden.extension.iastate.edu/encyclopedia/sawtoothed-grain-beetle</a></p>\n<p>It could also be the merchant grain beetle (<em>Oryzaephilus mercator</em>), which is largely identical. One difference is how far the temple continues behind the eyes, but this is difficult to see in your image.</p>\n<p><a href=\"https://i.sstatic.net/H3Cu78PO.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/H3Cu78PO.png\" alt=\"Comparison of the heads of  O suriamensis and O. mercator\" /></a></p>\n<p><strong>Source:</strong> <a href=\"https://www.ipmimages.org/browse/detail.cfm?imgnum=5489566\" rel=\"nofollow noreferrer\">https://www.ipmimages.org/browse/detail.cfm?imgnum=5489566</a> (credited to Bugwood.org, which is the website for the University of Georgia's Center for Invasive Species and Ecosystem Health)</p>\n","answer_id":117526,"answer_text":"It's difficult to tell without a higher resolution image, but one possibility is the sawtooth grain beetle (Oryzaephilus surinamensis), a common pest of stored food products (the bathroom is a strange place for it to be, so maybe you could look for more in the kitchen or pantry). The teeth running down the thorax are a characteristic feature. I'm pretty sure I can see these in your image (especially on the left side, behind the visible leg). However, this species only grows to about 2.5mm (1/10 of an inch), so if you can confirm the 1/4 in measurement I would reconsider my answer.\n\n\n\n\n[image: O. surinamensis on a a blue background next to a tape-measure with mm markings; source: https://i.sstatic.net/FWzjZJVo.png] (https://i.sstatic.net/FWzjZJVo.png)\n\n\n\n\nSource: Iowa State University, https://yardandgarden.extension.iastate.edu/encyclopedia/sawtoothed-grain-beetle (https://yardandgarden.extension.iastate.edu/encyclopedia/sawtoothed-grain-beetle)\n\n\n\n\nIt could also be the merchant grain beetle (Oryzaephilus mercator), which is largely identical. One difference is how far the temple continues behind the eyes, but this is difficult to see in your image.\n\n\n\n\n[image: Comparison of the heads of  O suriamensis and O. mercator; source: https://i.sstatic.net/H3Cu78PO.png] (https://i.sstatic.net/H3Cu78PO.png)\n\n\n\n\nSource: https://www.ipmimages.org/browse/detail.cfm?imgnum=5489566 (https://www.ipmimages.org/browse/detail.cfm?imgnum=5489566) (credited to Bugwood.org, which is the website for the University of Georgia's Center for Invasive Species and Ecosystem Health)","answer_url":"https://biology.stackexchange.com/a/117526","author":"Armin Taheri","author_url":"https://biology.stackexchange.com/users/107301/armin-taheri","content_license":"CC BY-SA 4.0","created_at":"2025-05-25T00:42:02+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:19.947691+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/df693642d727b738d2a533740632235c18a06cefec7a1e337c9589214a4ec91e_0.json","raw_sha256":"9df534f437f3b2f12d33db8536999ec4e6ffa10f2f59394799d9fe01c3c1ad16","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/117606;117602;117598;117594;117585;117579;117570;117568;117565;117559;117558;117555;117552;117548;117538;117524;117523;117522;117520;117515;117510;116509;116508;116504;116499;116491;116485;116483;116461;116454;116453;116445;116441;116435;116430;116426;116425;116414;116412;116406;116401;116399;116396;116395;116394;116392;116389;116384;116370;116367;116363;116361;116352;116351;116347;116345;116343;116338;116337;116332;116331;116324;116320;116316;116314;116312;116306;116292;116290;116284;116280;116277;116271;116270;116268;116267;116257;116256;116253;116250;116249;116240;116237;116233;116219;116214;116212;116205;116204;116200;116198;116187;116184;116173;116172;116167;116162;116149;116142;116129/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":117523,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Armin Taheri","profile_url":"https://biology.stackexchange.com/users/107301/armin-taheri","user_type":"registered"},"created_at":"2025-05-25T00:42:02+00:00","raw_file":"raw/codex_api_v1/513f34509ea5b8cfd23e2c22ec69b0af899072a5df884318581dc59cdc06558f_1790824145019083900_0.json","raw_sha256":"e49bc4b696ee886e85729b5e43d509e97eb936a63dd33019b0855e8f32360f99","revision_guid":"0EFB809E-BE2D-451F-ACD6-BA3B12C515B0","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0EFB809E-BE2D-451F-ACD6-BA3B12C515B0/view-source"}],"score":4}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Cheryl Wilkins","author_url":"https://biology.stackexchange.com/users/108724/cheryl-wilkins","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Cheryl Wilkins","profile_url":"https://biology.stackexchange.com/users/108724/cheryl-wilkins","user_type":"registered"},"created_at":"2025-05-24T16:04:27+00:00","raw_file":"raw/codex_api_v1/513f34509ea5b8cfd23e2c22ec69b0af899072a5df884318581dc59cdc06558f_1790824145019083900_0.json","raw_sha256":"e49bc4b696ee886e85729b5e43d509e97eb936a63dd33019b0855e8f32360f99","revision_guid":"AB6FD1C4-3C1A-4358-98F5-F306DC82B37D","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AB6FD1C4-3C1A-4358-98F5-F306DC82B37D/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2025-05-27T22:23:25+00:00","raw_file":"raw/codex_api_v1/513f34509ea5b8cfd23e2c22ec69b0af899072a5df884318581dc59cdc06558f_1790824145019083900_0.json","raw_sha256":"e49bc4b696ee886e85729b5e43d509e97eb936a63dd33019b0855e8f32360f99","revision_guid":"8C4495E5-72B2-405F-A051-3DACF4ABE942","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8C4495E5-72B2-405F-A051-3DACF4ABE942/view-source"}],"url":"https://biology.stackexchange.com/questions/117523/identification-of-insect-found-in-elgin-illinois"},{"author":"Armin Taheri","author_url":"https://biology.stackexchange.com/users/107301/armin-taheri","content_license":"CC BY-SA 4.0","context_id":"117526","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Armin Taheri","profile_url":"https://biology.stackexchange.com/users/107301/armin-taheri","user_type":"registered"},"created_at":"2025-05-25T00:42:02+00:00","raw_file":"raw/codex_api_v1/513f34509ea5b8cfd23e2c22ec69b0af899072a5df884318581dc59cdc06558f_1790824145019083900_0.json","raw_sha256":"e49bc4b696ee886e85729b5e43d509e97eb936a63dd33019b0855e8f32360f99","revision_guid":"0EFB809E-BE2D-451F-ACD6-BA3B12C515B0","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0EFB809E-BE2D-451F-ACD6-BA3B12C515B0/view-source"}],"url":"https://biology.stackexchange.com/a/117526"}],"contexts":[{"context_id":"question","html":"<p>What is this insect? An ant? A termite?</p>\n<p>Found in the bathroom Elgin, Illinois, USA. Maybe 1/4 inch long.  Brown.</p>\n<p><a href=\"https://i.sstatic.net/6HtWfifB.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/6HtWfifB.jpg\" alt=\"enter image description here\" /></a></p>\n","text":"What is this insect? An ant? A termite?\n\n\n\n\nFound in the bathroom Elgin, Illinois, USA. Maybe 1/4 inch long.  Brown.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/6HtWfifB.jpg] (https://i.sstatic.net/6HtWfifB.jpg)"},{"context_id":"117526","html":"<p>It's difficult to tell without a higher resolution image, but one possibility is the sawtooth grain beetle (<em>Oryzaephilus surinamensis</em>), a common pest of stored food products (the bathroom is a strange place for it to be, so maybe you could look for more in the kitchen or pantry). The teeth running down the thorax are a characteristic feature. I'm pretty sure I can see these in your image (especially on the left side, behind the visible leg). However, this species only grows to about 2.5mm (1/10 of an inch), so if you can confirm the 1/4 in measurement I would reconsider my answer.</p>\n<p><a href=\"https://i.sstatic.net/FWzjZJVo.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/FWzjZJVo.png\" alt=\"O. surinamensis on a a blue background next to a tape-measure with mm markings\" /></a></p>\n<p><strong>Source:</strong> Iowa State University, <a href=\"https://yardandgarden.extension.iastate.edu/encyclopedia/sawtoothed-grain-beetle\" rel=\"nofollow noreferrer\">https://yardandgarden.extension.iastate.edu/encyclopedia/sawtoothed-grain-beetle</a></p>\n<p>It could also be the merchant grain beetle (<em>Oryzaephilus mercator</em>), which is largely identical. One difference is how far the temple continues behind the eyes, but this is difficult to see in your image.</p>\n<p><a href=\"https://i.sstatic.net/H3Cu78PO.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/H3Cu78PO.png\" alt=\"Comparison of the heads of  O suriamensis and O. mercator\" /></a></p>\n<p><strong>Source:</strong> <a href=\"https://www.ipmimages.org/browse/detail.cfm?imgnum=5489566\" rel=\"nofollow noreferrer\">https://www.ipmimages.org/browse/detail.cfm?imgnum=5489566</a> (credited to Bugwood.org, which is the website for the University of Georgia's Center for Invasive Species and Ecosystem Health)</p>\n","text":"It's difficult to tell without a higher resolution image, but one possibility is the sawtooth grain beetle (Oryzaephilus surinamensis), a common pest of stored food products (the bathroom is a strange place for it to be, so maybe you could look for more in the kitchen or pantry). The teeth running down the thorax are a characteristic feature. I'm pretty sure I can see these in your image (especially on the left side, behind the visible leg). However, this species only grows to about 2.5mm (1/10 of an inch), so if you can confirm the 1/4 in measurement I would reconsider my answer.\n\n\n\n\n[image: O. surinamensis on a a blue background next to a tape-measure with mm markings; source: https://i.sstatic.net/FWzjZJVo.png] (https://i.sstatic.net/FWzjZJVo.png)\n\n\n\n\nSource: Iowa State University, https://yardandgarden.extension.iastate.edu/encyclopedia/sawtoothed-grain-beetle (https://yardandgarden.extension.iastate.edu/encyclopedia/sawtoothed-grain-beetle)\n\n\n\n\nIt could also be the merchant grain beetle (Oryzaephilus mercator), which is largely identical. One difference is how far the temple continues behind the eyes, but this is difficult to see in your image.\n\n\n\n\n[image: Comparison of the heads of  O suriamensis and O. mercator; source: https://i.sstatic.net/H3Cu78PO.png] (https://i.sstatic.net/H3Cu78PO.png)\n\n\n\n\nSource: https://www.ipmimages.org/browse/detail.cfm?imgnum=5489566 (https://www.ipmimages.org/browse/detail.cfm?imgnum=5489566) (credited to Bugwood.org, which is the website for the University of Georgia's Center for Invasive Species and Ecosystem Health)"}],"domain":"biology","external_citations":["https://i.sstatic.net/6HtWfifB.jpg","https://i.sstatic.net/FWzjZJVo.png","https://i.sstatic.net/H3Cu78PO.png","https://www.ipmimages.org/browse/detail.cfm?imgnum=5489566","https://yardandgarden.extension.iastate.edu/encyclopedia/sawtoothed-grain-beetle"],"ground_truth_type":"metadata_grounded","group_id":"8cb64e1c3fae109705e0640f5fe2376d84d3cdd4010b65220a64b5691999b6fb","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-b7995e39e88405a7c32c04d4","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:02.598621+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/5d480e4bd1bd45ab525a4baf3227fba404f89b6af9dad33215fd9fa7c302a211_0.json","raw_sha256":"d723c7a62c8386d143891d26ae30b2234242ed3dac9599b11f141712ea994a96","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=3&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Cheryl Wilkins","profile_url":"https://biology.stackexchange.com/users/108724/cheryl-wilkins","user_type":"registered"},"created_at":"2025-05-24T16:04:27+00:00","raw_file":"raw/codex_api_v1/513f34509ea5b8cfd23e2c22ec69b0af899072a5df884318581dc59cdc06558f_1790824145019083900_0.json","raw_sha256":"e49bc4b696ee886e85729b5e43d509e97eb936a63dd33019b0855e8f32360f99","revision_guid":"AB6FD1C4-3C1A-4358-98F5-F306DC82B37D","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AB6FD1C4-3C1A-4358-98F5-F306DC82B37D/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2025-05-27T22:23:25+00:00","raw_file":"raw/codex_api_v1/513f34509ea5b8cfd23e2c22ec69b0af899072a5df884318581dc59cdc06558f_1790824145019083900_0.json","raw_sha256":"e49bc4b696ee886e85729b5e43d509e97eb936a63dd33019b0855e8f32360f99","revision_guid":"8C4495E5-72B2-405F-A051-3DACF4ABE942","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8C4495E5-72B2-405F-A051-3DACF4ABE942/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"117523","source_record_sha256":"d61e113f59a3dab17f8bf9faa67e1a1f7e3253f51708be2a0cbe5afbfc59c166","source_url":"https://biology.stackexchange.com/questions/117523/identification-of-insect-found-in-elgin-illinois","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Identification of insect found in Elgin, Illinois\nWhat is this insect? An ant? A termite?\n\n\n\n\nFound in the bathroom Elgin, Illinois, USA. Maybe 1/4 inch long.  Brown.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/6HtWfifB.jpg] (https://i.sstatic.net/6HtWfifB.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":117526,"score":4}],"split":"test"}
{"accepted_status":{"accepted_answer_id":117727,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Gigantism in baleen whales is a trait that developed very recently in their evolutionary history, within the last 3 million years [<a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC5454272/\" rel=\"noreferrer\">1</a>]. Before that time period, many species of these whales rarely exceeded 10 metres. The size of a whale appears to be historically related to how big the bait balls of their prey get, and the amount of baleen they need to filter large quantities [<a href=\"https://ui.adsabs.harvard.edu/abs/2017ARMS....9..367G/abstract\" rel=\"noreferrer\">2</a>]. The informally named Plio-Pleistocene period changed the dynamics of ocean ecosystems, one of the side effects of which was the frequent formation of high-prey-density zones [<a href=\"https://ui.adsabs.harvard.edu/abs/2000Sci...290.2288M/abstract\" rel=\"noreferrer\">3</a>]. Their feeding strategy (ramming &amp; gulping) is significantly related to the impact of size on their fitness, and an increase in size developed multiple times independently in many whale species [<a href=\"https://royalsocietypublishing.org/doi/10.1098/rsbl.2019.0175\" rel=\"noreferrer\">4</a>][<a href=\"https://royalsocietypublishing.org/doi/10.1098/rspb.2017.0546\" rel=\"noreferrer\">5</a>].</p>\n<p>It is important to also understand that baleen whales are active animals and descended from active predators, so a slow, almost sessile filter-feeding strategy has a longer evolutionary path to stability than the gulping and ramming strategy, and were thus out-competed [<a href=\"https://ui.adsabs.harvard.edu/abs/2017ARMS....9..367G/abstract\" rel=\"noreferrer\">2</a>][<a href=\"https://books.google.com/books?id=sD3NBQAAQBAJ&amp;pg=PA111#v=onepage&amp;q&amp;f=false\" rel=\"noreferrer\">6</a>]. Also, baleen whales largely consume krill (especially the blue whale, which exclusively eats krill) and small filter-feeding fish largely consume plankton and nutrient particles [<a href=\"https://www.aoml.noaa.gov/general/lib/CREWS/Cleo/PuertoRico/prpdfs/randall-habits.pdf\" rel=\"noreferrer\">7</a>], so a diet difference does have an apparent influence on size.</p>\n<p>TLDR: Baleen whales feed by ramming and gulping, which requires being large enough to consume bait balls in droves. This strategy is evolutionarily stable and has seen no trends today towards filter-feedings strategies used by smaller organisms such as krill and forage fish. In fact, there is evidence that multiple baleen whale species are being sexually selected to be even larger, particularly the blue whale [<a href=\"https://www.int-res.com/abstracts/esr/v9/esr00217\" rel=\"noreferrer\">8</a>][<a href=\"https://www.popsci.com/baleen-whales-big/\" rel=\"noreferrer\">9</a>].</p>\n","answer_id":117727,"answer_text":"Gigantism in baleen whales is a trait that developed very recently in their evolutionary history, within the last 3 million years [1 (https://pmc.ncbi.nlm.nih.gov/articles/PMC5454272/)]. Before that time period, many species of these whales rarely exceeded 10 metres. The size of a whale appears to be historically related to how big the bait balls of their prey get, and the amount of baleen they need to filter large quantities [2 (https://ui.adsabs.harvard.edu/abs/2017ARMS....9..367G/abstract)]. The informally named Plio-Pleistocene period changed the dynamics of ocean ecosystems, one of the side effects of which was the frequent formation of high-prey-density zones [3 (https://ui.adsabs.harvard.edu/abs/2000Sci...290.2288M/abstract)]. Their feeding strategy (ramming & gulping) is significantly related to the impact of size on their fitness, and an increase in size developed multiple times independently in many whale species [4 (https://royalsocietypublishing.org/doi/10.1098/rsbl.2019.0175)][5 (https://royalsocietypublishing.org/doi/10.1098/rspb.2017.0546)].\n\n\n\n\nIt is important to also understand that baleen whales are active animals and descended from active predators, so a slow, almost sessile filter-feeding strategy has a longer evolutionary path to stability than the gulping and ramming strategy, and were thus out-competed [2 (https://ui.adsabs.harvard.edu/abs/2017ARMS....9..367G/abstract)][6 (https://books.google.com/books?id=sD3NBQAAQBAJ&pg=PA111#v=onepage&q&f=false)]. Also, baleen whales largely consume krill (especially the blue whale, which exclusively eats krill) and small filter-feeding fish largely consume plankton and nutrient particles [7 (https://www.aoml.noaa.gov/general/lib/CREWS/Cleo/PuertoRico/prpdfs/randall-habits.pdf)], so a diet difference does have an apparent influence on size.\n\n\n\n\nTLDR: Baleen whales feed by ramming and gulping, which requires being large enough to consume bait balls in droves. This strategy is evolutionarily stable and has seen no trends today towards filter-feedings strategies used by smaller organisms such as krill and forage fish. In fact, there is evidence that multiple baleen whale species are being sexually selected to be even larger, particularly the blue whale [8 (https://www.int-res.com/abstracts/esr/v9/esr00217)][9 (https://www.popsci.com/baleen-whales-big/)].","answer_url":"https://biology.stackexchange.com/a/117727","author":"Helichiral Catenoid","author_url":"https://biology.stackexchange.com/users/106437/helichiral-catenoid","content_license":"CC BY-SA 4.0","created_at":"2025-07-25T16:13:59+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:16.948131+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/46a41fae37d5c2c243f9abcbf6829a0045f46a51c624fbba2b897c320cdcba71_0.json","raw_sha256":"e039e310d0106dc61f992ee05bbb0b0b57ded1c5092f97df2c52989edd5eaf68","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/118153;118142;118137;118126;118122;118117;118113;118102;118099;118097;118094;118081;118076;118072;118069;118065;118059;118056;118043;118039;118036;118030;118029;118025;118022;118018;117994;117992;117990;117987;117983;117981;117975;117971;117956;117953;117951;117945;117943;117941;117934;117926;117924;117920;117916;117914;117907;117892;117889;117887;117883;117876;117872;117867;117861;117860;117856;117855;117850;117849;117844;117840;117833;117821;117819;117817;117815;117814;117805;117794;117782;117774;117771;117767;117766;117761;117759;117756;117747;117732;117726;117724;117709;117701;117694;117693;117681;117680;117677;117671;117668;117664;117662;117659;117651;117641;117632;117624;117623;117607/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":117724,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Helichiral Catenoid","profile_url":"https://biology.stackexchange.com/users/106437/helichiral-catenoid","user_type":"registered"},"created_at":"2025-07-25T16:13:59+00:00","raw_file":"raw/codex_api_v1/01815689c0e6362f8bdf7b8393d418437539b76345e52b5c663d1613602784aa_1790824154537857800_0.json","raw_sha256":"b2f446369df60a45c452a5be0d5e0c462ff7455589d79062d4d1f36a4c5e5880","revision_guid":"16F08644-1B54-4C39-94CA-BCD480D61B24","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/16F08644-1B54-4C39-94CA-BCD480D61B24/view-source"}],"score":10}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Ma Ye","author_url":"https://biology.stackexchange.com/users/93868/ma-ye","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Ma Ye","profile_url":"https://biology.stackexchange.com/users/93868/ma-ye","user_type":"registered"},"created_at":"2025-07-25T12:46:18+00:00","raw_file":"raw/codex_api_v1/01815689c0e6362f8bdf7b8393d418437539b76345e52b5c663d1613602784aa_1790824154537857800_0.json","raw_sha256":"b2f446369df60a45c452a5be0d5e0c462ff7455589d79062d4d1f36a4c5e5880","revision_guid":"CC1DC939-F285-48DB-9B38-04078691A68B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CC1DC939-F285-48DB-9B38-04078691A68B/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-07-25T20:58:38+00:00","raw_file":"raw/codex_api_v1/01815689c0e6362f8bdf7b8393d418437539b76345e52b5c663d1613602784aa_1790824154537857800_0.json","raw_sha256":"b2f446369df60a45c452a5be0d5e0c462ff7455589d79062d4d1f36a4c5e5880","revision_guid":"93D60822-3E7E-44EA-AE1F-88BBD390D1F6","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/93D60822-3E7E-44EA-AE1F-88BBD390D1F6/view-source"}],"url":"https://biology.stackexchange.com/questions/117724/why-arent-there-baleen-whales-at-about-the-size-of-a-dolphin"},{"author":"Helichiral Catenoid","author_url":"https://biology.stackexchange.com/users/106437/helichiral-catenoid","content_license":"CC BY-SA 4.0","context_id":"117727","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Helichiral Catenoid","profile_url":"https://biology.stackexchange.com/users/106437/helichiral-catenoid","user_type":"registered"},"created_at":"2025-07-25T16:13:59+00:00","raw_file":"raw/codex_api_v1/01815689c0e6362f8bdf7b8393d418437539b76345e52b5c663d1613602784aa_1790824154537857800_0.json","raw_sha256":"b2f446369df60a45c452a5be0d5e0c462ff7455589d79062d4d1f36a4c5e5880","revision_guid":"16F08644-1B54-4C39-94CA-BCD480D61B24","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/16F08644-1B54-4C39-94CA-BCD480D61B24/view-source"}],"url":"https://biology.stackexchange.com/a/117727"}],"contexts":[{"context_id":"question","html":"<p>The currently smallest baleen whale, pygmy right whale (<em>Caperea marginata</em>) under <em>Neobalaenidae</em>, is mature at about 6 meters, slightly smaller than an orca. However, I noticed that the length of different filter feeder fishes vary from ~10cm to ~9m. What would prevent baleen whales from developing species at the size of a common dolphin (<em>Delphinus delphis</em>,~2.5m) or even smaller?</p>\n","text":"The currently smallest baleen whale, pygmy right whale (Caperea marginata) under Neobalaenidae, is mature at about 6 meters, slightly smaller than an orca. However, I noticed that the length of different filter feeder fishes vary from ~10cm to ~9m. What would prevent baleen whales from developing species at the size of a common dolphin (Delphinus delphis,~2.5m) or even smaller?"},{"context_id":"117727","html":"<p>Gigantism in baleen whales is a trait that developed very recently in their evolutionary history, within the last 3 million years [<a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC5454272/\" rel=\"noreferrer\">1</a>]. Before that time period, many species of these whales rarely exceeded 10 metres. The size of a whale appears to be historically related to how big the bait balls of their prey get, and the amount of baleen they need to filter large quantities [<a href=\"https://ui.adsabs.harvard.edu/abs/2017ARMS....9..367G/abstract\" rel=\"noreferrer\">2</a>]. The informally named Plio-Pleistocene period changed the dynamics of ocean ecosystems, one of the side effects of which was the frequent formation of high-prey-density zones [<a href=\"https://ui.adsabs.harvard.edu/abs/2000Sci...290.2288M/abstract\" rel=\"noreferrer\">3</a>]. Their feeding strategy (ramming &amp; gulping) is significantly related to the impact of size on their fitness, and an increase in size developed multiple times independently in many whale species [<a href=\"https://royalsocietypublishing.org/doi/10.1098/rsbl.2019.0175\" rel=\"noreferrer\">4</a>][<a href=\"https://royalsocietypublishing.org/doi/10.1098/rspb.2017.0546\" rel=\"noreferrer\">5</a>].</p>\n<p>It is important to also understand that baleen whales are active animals and descended from active predators, so a slow, almost sessile filter-feeding strategy has a longer evolutionary path to stability than the gulping and ramming strategy, and were thus out-competed [<a href=\"https://ui.adsabs.harvard.edu/abs/2017ARMS....9..367G/abstract\" rel=\"noreferrer\">2</a>][<a href=\"https://books.google.com/books?id=sD3NBQAAQBAJ&amp;pg=PA111#v=onepage&amp;q&amp;f=false\" rel=\"noreferrer\">6</a>]. Also, baleen whales largely consume krill (especially the blue whale, which exclusively eats krill) and small filter-feeding fish largely consume plankton and nutrient particles [<a href=\"https://www.aoml.noaa.gov/general/lib/CREWS/Cleo/PuertoRico/prpdfs/randall-habits.pdf\" rel=\"noreferrer\">7</a>], so a diet difference does have an apparent influence on size.</p>\n<p>TLDR: Baleen whales feed by ramming and gulping, which requires being large enough to consume bait balls in droves. This strategy is evolutionarily stable and has seen no trends today towards filter-feedings strategies used by smaller organisms such as krill and forage fish. In fact, there is evidence that multiple baleen whale species are being sexually selected to be even larger, particularly the blue whale [<a href=\"https://www.int-res.com/abstracts/esr/v9/esr00217\" rel=\"noreferrer\">8</a>][<a href=\"https://www.popsci.com/baleen-whales-big/\" rel=\"noreferrer\">9</a>].</p>\n","text":"Gigantism in baleen whales is a trait that developed very recently in their evolutionary history, within the last 3 million years [1 (https://pmc.ncbi.nlm.nih.gov/articles/PMC5454272/)]. Before that time period, many species of these whales rarely exceeded 10 metres. The size of a whale appears to be historically related to how big the bait balls of their prey get, and the amount of baleen they need to filter large quantities [2 (https://ui.adsabs.harvard.edu/abs/2017ARMS....9..367G/abstract)]. The informally named Plio-Pleistocene period changed the dynamics of ocean ecosystems, one of the side effects of which was the frequent formation of high-prey-density zones [3 (https://ui.adsabs.harvard.edu/abs/2000Sci...290.2288M/abstract)]. Their feeding strategy (ramming & gulping) is significantly related to the impact of size on their fitness, and an increase in size developed multiple times independently in many whale species [4 (https://royalsocietypublishing.org/doi/10.1098/rsbl.2019.0175)][5 (https://royalsocietypublishing.org/doi/10.1098/rspb.2017.0546)].\n\n\n\n\nIt is important to also understand that baleen whales are active animals and descended from active predators, so a slow, almost sessile filter-feeding strategy has a longer evolutionary path to stability than the gulping and ramming strategy, and were thus out-competed [2 (https://ui.adsabs.harvard.edu/abs/2017ARMS....9..367G/abstract)][6 (https://books.google.com/books?id=sD3NBQAAQBAJ&pg=PA111#v=onepage&q&f=false)]. Also, baleen whales largely consume krill (especially the blue whale, which exclusively eats krill) and small filter-feeding fish largely consume plankton and nutrient particles [7 (https://www.aoml.noaa.gov/general/lib/CREWS/Cleo/PuertoRico/prpdfs/randall-habits.pdf)], so a diet difference does have an apparent influence on size.\n\n\n\n\nTLDR: Baleen whales feed by ramming and gulping, which requires being large enough to consume bait balls in droves. This strategy is evolutionarily stable and has seen no trends today towards filter-feedings strategies used by smaller organisms such as krill and forage fish. In fact, there is evidence that multiple baleen whale species are being sexually selected to be even larger, particularly the blue whale [8 (https://www.int-res.com/abstracts/esr/v9/esr00217)][9 (https://www.popsci.com/baleen-whales-big/)]."}],"domain":"biology","external_citations":["https://books.google.com/books?id=sD3NBQAAQBAJ&pg=PA111#v=onepage&q&f=false","https://pmc.ncbi.nlm.nih.gov/articles/PMC5454272/","https://royalsocietypublishing.org/doi/10.1098/rsbl.2019.0175","https://royalsocietypublishing.org/doi/10.1098/rspb.2017.0546","https://ui.adsabs.harvard.edu/abs/2000Sci...290.2288M/abstract","https://ui.adsabs.harvard.edu/abs/2017ARMS....9..367G/abstract","https://www.aoml.noaa.gov/general/lib/CREWS/Cleo/PuertoRico/prpdfs/randall-habits.pdf","https://www.int-res.com/abstracts/esr/v9/esr00217","https://www.popsci.com/baleen-whales-big/"],"ground_truth_type":"metadata_grounded","group_id":"81e2cd69c139cf13773c38daa67731e3f4bf5a43274875a2d6c3a62fec26794f","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-f683ef1a976a55f826206cef","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:01.208074+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f1b387b48f36041f506f18fa9796531023c7eae1e796ec622ad56833c02bea98_0.json","raw_sha256":"3f8214c87c0fe16dd016324597332ca392e0ba98600877cc746483ef492ce03d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Ma Ye","profile_url":"https://biology.stackexchange.com/users/93868/ma-ye","user_type":"registered"},"created_at":"2025-07-25T12:46:18+00:00","raw_file":"raw/codex_api_v1/01815689c0e6362f8bdf7b8393d418437539b76345e52b5c663d1613602784aa_1790824154537857800_0.json","raw_sha256":"b2f446369df60a45c452a5be0d5e0c462ff7455589d79062d4d1f36a4c5e5880","revision_guid":"CC1DC939-F285-48DB-9B38-04078691A68B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CC1DC939-F285-48DB-9B38-04078691A68B/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-07-25T20:58:38+00:00","raw_file":"raw/codex_api_v1/01815689c0e6362f8bdf7b8393d418437539b76345e52b5c663d1613602784aa_1790824154537857800_0.json","raw_sha256":"b2f446369df60a45c452a5be0d5e0c462ff7455589d79062d4d1f36a4c5e5880","revision_guid":"93D60822-3E7E-44EA-AE1F-88BBD390D1F6","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/93D60822-3E7E-44EA-AE1F-88BBD390D1F6/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"117724","source_record_sha256":"dd147f2df46a2e3b64c96eb0045fb55410eb6a08f96d214af42e23425c8764fc","source_url":"https://biology.stackexchange.com/questions/117724/why-arent-there-baleen-whales-at-about-the-size-of-a-dolphin","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Why aren't there baleen whales at about the size of a dolphin?\nThe currently smallest baleen whale, pygmy right whale (Caperea marginata) under Neobalaenidae, is mature at about 6 meters, slightly smaller than an orca. However, I noticed that the length of different filter feeder fishes vary from ~10cm to ~9m. What would prevent baleen whales from developing species at the size of a common dolphin (Delphinus delphis,~2.5m) or even smaller?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":117727,"score":10}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>This is Senna obtusifolia. It is more often considered a weed.</p>\n","answer_id":117812,"answer_text":"This is Senna obtusifolia. It is more often considered a weed.","answer_url":"https://biology.stackexchange.com/a/117812","author":"White Rabbit ","author_url":"https://biology.stackexchange.com/users/114680/white-rabbit","content_license":"CC BY-SA 4.0","created_at":"2025-08-20T18:59:51+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:16.948131+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/46a41fae37d5c2c243f9abcbf6829a0045f46a51c624fbba2b897c320cdcba71_0.json","raw_sha256":"e039e310d0106dc61f992ee05bbb0b0b57ded1c5092f97df2c52989edd5eaf68","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/118153;118142;118137;118126;118122;118117;118113;118102;118099;118097;118094;118081;118076;118072;118069;118065;118059;118056;118043;118039;118036;118030;118029;118025;118022;118018;117994;117992;117990;117987;117983;117981;117975;117971;117956;117953;117951;117945;117943;117941;117934;117926;117924;117920;117916;117914;117907;117892;117889;117887;117883;117876;117872;117867;117861;117860;117856;117855;117850;117849;117844;117840;117833;117821;117819;117817;117815;117814;117805;117794;117782;117774;117771;117767;117766;117761;117759;117756;117747;117732;117726;117724;117709;117701;117694;117693;117681;117680;117677;117671;117668;117664;117662;117659;117651;117641;117632;117624;117623;117607/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":117794,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"White Rabbit ","profile_url":"https://biology.stackexchange.com/users/114680/white-rabbit","user_type":"registered"},"created_at":"2025-08-20T18:59:51+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"517991A4-1CD5-476C-81C9-EC395FC70C28","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/517991A4-1CD5-476C-81C9-EC395FC70C28/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"anongoodnurse","profile_url":"https://biology.stackexchange.com/users/5198/anongoodnurse","user_type":"registered"},"created_at":"2025-08-21T17:07:20+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"672BB801-FC3F-41DE-B3E2-4CC511280CB8","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/672BB801-FC3F-41DE-B3E2-4CC511280CB8/view-source"}],"score":0},{"answer_html":"<p><em>Senna (or Cassia) Obtusifolia</em> or American Sicklepod.</p>\n<p>Usually grows to less than 2 meters, egg shaped leaves with 2-3 pairs on each branch.  Seedcases are long and curved, hence the name.  Foliage usually has an unpleasant smell, which I guess is why it's not usually cultivated in decorative gardens.</p>\n<p>Photo here which includes the seed pods:\n<a href=\"https://i.sstatic.net/9QR5iJ8K.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/9QR5iJ8K.jpg\" alt=\"Senna Obtusifolia\" /></a></p>\n<p>\n(photo source - <a href=\"https://keys.lucidcentral.org/keys/v3/eafrinet/weeds/key/weeds/Media/Html/Senna_obtusifolia_(Sicklepod).htm#\" rel=\"nofollow noreferrer\">link</a>)</p>\n<p>Interestingly, the leaves can be fermented to create a high-protein food product (<a href=\"https://www.jstor.org/stable/4254649\" rel=\"nofollow noreferrer\">Kawal</a>) and the leaves, seeds and roots are used in traditional medicine.</p>\n<p>Further reading:</p>\n<ul>\n<li><a href=\"https://www.healthbenefitstimes.com/sicklepod/\" rel=\"nofollow noreferrer\">Health Benefits</a></li>\n<li><a href=\"https://www.gardeningknowhow.com/plant-problems/weeds/sicklepod-control.htm\" rel=\"nofollow noreferrer\">Controlling as a weed</a></li>\n<li><a href=\"https://www.missouribotanicalgarden.org/PlantFinder/PlantFinderDetails.aspx?taxonid=369266\" rel=\"nofollow noreferrer\">Missouri Botanical Garden</a></li>\n</ul>\n<p><a href=\"https://keys.lucidcentral.org/keys/v3/eafrinet/weeds/key/weeds/Media/Html/Senna_obtusifolia_(Sicklepod).htm#\" rel=\"nofollow noreferrer\"></a></p>\n","answer_id":117940,"answer_text":"Senna (or Cassia) Obtusifolia or American Sicklepod.\n\n\n\n\nUsually grows to less than 2 meters, egg shaped leaves with 2-3 pairs on each branch.  Seedcases are long and curved, hence the name.  Foliage usually has an unpleasant smell, which I guess is why it's not usually cultivated in decorative gardens.\n\n\n\n\nPhoto here which includes the seed pods:\n[image: Senna Obtusifolia; source: https://i.sstatic.net/9QR5iJ8K.jpg] (https://i.sstatic.net/9QR5iJ8K.jpg)\n\n\n\n\n\n(photo source - link (https://keys.lucidcentral.org/keys/v3/eafrinet/weeds/key/weeds/Media/Html/Senna_obtusifolia_(Sicklepod).htm#))\n\n\n\n\nInterestingly, the leaves can be fermented to create a high-protein food product (Kawal (https://www.jstor.org/stable/4254649)) and the leaves, seeds and roots are used in traditional medicine.\n\n\n\n\nFurther reading:\n\n\n\n\n\nHealth Benefits (https://www.healthbenefitstimes.com/sicklepod/)\n\n\n\n\nControlling as a weed (https://www.gardeningknowhow.com/plant-problems/weeds/sicklepod-control.htm)\n\n\n\n\nMissouri Botanical Garden (https://www.missouribotanicalgarden.org/PlantFinder/PlantFinderDetails.aspx?taxonid=369266)\n\n\n\n\n\n (https://keys.lucidcentral.org/keys/v3/eafrinet/weeds/key/weeds/Media/Html/Senna_obtusifolia_(Sicklepod).htm#)","answer_url":"https://biology.stackexchange.com/a/117940","author":"Snow","author_url":"https://biology.stackexchange.com/users/116324/snow","content_license":"CC BY-SA 4.0","created_at":"2025-09-19T10:27:40+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:16.948131+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/46a41fae37d5c2c243f9abcbf6829a0045f46a51c624fbba2b897c320cdcba71_0.json","raw_sha256":"e039e310d0106dc61f992ee05bbb0b0b57ded1c5092f97df2c52989edd5eaf68","source_api":"Stack Exchange API 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4.0","contributor":{"display_name":"Snow","profile_url":"https://biology.stackexchange.com/users/116324/snow","user_type":"registered"},"created_at":"2025-09-19T10:27:40+00:00","raw_file":"raw/codex_api_v1/a76d8ab07f874a10eafefc315936b171795ddfe3f4ac47f247a19154460d4acc_1790824150220029700_0.json","raw_sha256":"d1e485076b0bfa0aed0ebdace356f1cab7a9d04a86bc0f38c43c8a253e51cebd","revision_guid":"BEBD8690-88F2-4B15-B676-301D305691F5","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/BEBD8690-88F2-4B15-B676-301D305691F5/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"LindaH","author_url":"https://biology.stackexchange.com/users/114238/lindah","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"LindaH","profile_url":"https://biology.stackexchange.com/users/114238/lindah","user_type":"registered"},"created_at":"2025-08-13T00:47:34+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"32C194A4-5F58-456F-8CC6-6C12C2D95674","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/32C194A4-5F58-456F-8CC6-6C12C2D95674/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"LindaH","profile_url":"https://biology.stackexchange.com/users/114238/lindah","user_type":"registered"},"created_at":"2025-08-14T16:19:01+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"0A7E5081-A3AC-42FC-9F1E-DA3403557EF1","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0A7E5081-A3AC-42FC-9F1E-DA3403557EF1/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"LindaH","profile_url":"https://biology.stackexchange.com/users/114238/lindah","user_type":"registered"},"created_at":"2025-08-14T16:22:03+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"47A22B32-FDE9-49EC-98D7-693394359678","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/47A22B32-FDE9-49EC-98D7-693394359678/view-source"}],"url":"https://biology.stackexchange.com/questions/117794/small-plant-identification"},{"author":"White Rabbit ","author_url":"https://biology.stackexchange.com/users/114680/white-rabbit","content_license":"CC BY-SA 4.0","context_id":"117812","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"White Rabbit ","profile_url":"https://biology.stackexchange.com/users/114680/white-rabbit","user_type":"registered"},"created_at":"2025-08-20T18:59:51+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"517991A4-1CD5-476C-81C9-EC395FC70C28","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/517991A4-1CD5-476C-81C9-EC395FC70C28/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"anongoodnurse","profile_url":"https://biology.stackexchange.com/users/5198/anongoodnurse","user_type":"registered"},"created_at":"2025-08-21T17:07:20+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"672BB801-FC3F-41DE-B3E2-4CC511280CB8","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/672BB801-FC3F-41DE-B3E2-4CC511280CB8/view-source"}],"url":"https://biology.stackexchange.com/a/117812"},{"author":"Snow","author_url":"https://biology.stackexchange.com/users/116324/snow","content_license":"CC BY-SA 4.0","context_id":"117940","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Snow","profile_url":"https://biology.stackexchange.com/users/116324/snow","user_type":"registered"},"created_at":"2025-09-19T10:27:40+00:00","raw_file":"raw/codex_api_v1/a76d8ab07f874a10eafefc315936b171795ddfe3f4ac47f247a19154460d4acc_1790824150220029700_0.json","raw_sha256":"d1e485076b0bfa0aed0ebdace356f1cab7a9d04a86bc0f38c43c8a253e51cebd","revision_guid":"BEBD8690-88F2-4B15-B676-301D305691F5","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/BEBD8690-88F2-4B15-B676-301D305691F5/view-source"}],"url":"https://biology.stackexchange.com/a/117940"}],"contexts":[{"context_id":"question","html":"<p><a href=\"https://i.sstatic.net/GPaLMzLQ.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/GPaLMzLQ.jpg\" alt=\"enter image description here\" /></a><a href=\"https://i.sstatic.net/IYuAi5BW.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/IYuAi5BW.jpg\" alt=\"enter image description here\" /></a>A small plant volunteered in my garden in North West Georgia (US) this year. I can’t identify it. It is about 2 ft high, yellow flowers, six opposite rounded laves on a stem. Yellow flowers produce long seed pods.</p>\n","text":"[image: enter image description here; source: https://i.sstatic.net/GPaLMzLQ.jpg] (https://i.sstatic.net/GPaLMzLQ.jpg)[image: enter image description here; source: https://i.sstatic.net/IYuAi5BW.jpg] (https://i.sstatic.net/IYuAi5BW.jpg)A small plant volunteered in my garden in North West Georgia (US) this year. I can’t identify it. It is about 2 ft high, yellow flowers, six opposite rounded laves on a stem. Yellow flowers produce long seed pods."},{"context_id":"117812","html":"<p>This is Senna obtusifolia. It is more often considered a weed.</p>\n","text":"This is Senna obtusifolia. It is more often considered a weed."},{"context_id":"117940","html":"<p><em>Senna (or Cassia) Obtusifolia</em> or American Sicklepod.</p>\n<p>Usually grows to less than 2 meters, egg shaped leaves with 2-3 pairs on each branch.  Seedcases are long and curved, hence the name.  Foliage usually has an unpleasant smell, which I guess is why it's not usually cultivated in decorative gardens.</p>\n<p>Photo here which includes the seed pods:\n<a href=\"https://i.sstatic.net/9QR5iJ8K.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/9QR5iJ8K.jpg\" alt=\"Senna Obtusifolia\" /></a></p>\n<p>\n(photo source - <a href=\"https://keys.lucidcentral.org/keys/v3/eafrinet/weeds/key/weeds/Media/Html/Senna_obtusifolia_(Sicklepod).htm#\" rel=\"nofollow noreferrer\">link</a>)</p>\n<p>Interestingly, the leaves can be fermented to create a high-protein food product (<a href=\"https://www.jstor.org/stable/4254649\" rel=\"nofollow noreferrer\">Kawal</a>) and the leaves, seeds and roots are used in traditional medicine.</p>\n<p>Further reading:</p>\n<ul>\n<li><a href=\"https://www.healthbenefitstimes.com/sicklepod/\" rel=\"nofollow noreferrer\">Health Benefits</a></li>\n<li><a href=\"https://www.gardeningknowhow.com/plant-problems/weeds/sicklepod-control.htm\" rel=\"nofollow noreferrer\">Controlling as a weed</a></li>\n<li><a href=\"https://www.missouribotanicalgarden.org/PlantFinder/PlantFinderDetails.aspx?taxonid=369266\" rel=\"nofollow noreferrer\">Missouri Botanical Garden</a></li>\n</ul>\n<p><a href=\"https://keys.lucidcentral.org/keys/v3/eafrinet/weeds/key/weeds/Media/Html/Senna_obtusifolia_(Sicklepod).htm#\" rel=\"nofollow noreferrer\"></a></p>\n","text":"Senna (or Cassia) Obtusifolia or American Sicklepod.\n\n\n\n\nUsually grows to less than 2 meters, egg shaped leaves with 2-3 pairs on each branch.  Seedcases are long and curved, hence the name.  Foliage usually has an unpleasant smell, which I guess is why it's not usually cultivated in decorative gardens.\n\n\n\n\nPhoto here which includes the seed pods:\n[image: Senna Obtusifolia; source: https://i.sstatic.net/9QR5iJ8K.jpg] (https://i.sstatic.net/9QR5iJ8K.jpg)\n\n\n\n\n\n(photo source - link (https://keys.lucidcentral.org/keys/v3/eafrinet/weeds/key/weeds/Media/Html/Senna_obtusifolia_(Sicklepod).htm#))\n\n\n\n\nInterestingly, the leaves can be fermented to create a high-protein food product (Kawal (https://www.jstor.org/stable/4254649)) and the leaves, seeds and roots are used in traditional medicine.\n\n\n\n\nFurther reading:\n\n\n\n\n\nHealth Benefits (https://www.healthbenefitstimes.com/sicklepod/)\n\n\n\n\nControlling as a weed (https://www.gardeningknowhow.com/plant-problems/weeds/sicklepod-control.htm)\n\n\n\n\nMissouri Botanical Garden (https://www.missouribotanicalgarden.org/PlantFinder/PlantFinderDetails.aspx?taxonid=369266)\n\n\n\n\n\n (https://keys.lucidcentral.org/keys/v3/eafrinet/weeds/key/weeds/Media/Html/Senna_obtusifolia_(Sicklepod).htm#)"}],"domain":"biology","external_citations":["https://i.sstatic.net/9QR5iJ8K.jpg","https://i.sstatic.net/GPaLMzLQ.jpg","https://i.sstatic.net/IYuAi5BW.jpg","https://keys.lucidcentral.org/keys/v3/eafrinet/weeds/key/weeds/Media/Html/Senna_obtusifolia_(Sicklepod).htm#","https://www.gardeningknowhow.com/plant-problems/weeds/sicklepod-control.htm","https://www.healthbenefitstimes.com/sicklepod/","https://www.jstor.org/stable/4254649","https://www.missouribotanicalgarden.org/PlantFinder/PlantFinderDetails.aspx?taxonid=369266"],"ground_truth_type":"metadata_grounded","group_id":"1b170a420868f0819317a66bf7d970a091c199003249d78732b0fd22287432b2","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-6c048cddf3ad53b93b75ab19","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:01.208074+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f1b387b48f36041f506f18fa9796531023c7eae1e796ec622ad56833c02bea98_0.json","raw_sha256":"3f8214c87c0fe16dd016324597332ca392e0ba98600877cc746483ef492ce03d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; 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no LLM truth labels"},"query":"Small plant identification\n[image: enter image description here; source: https://i.sstatic.net/GPaLMzLQ.jpg] (https://i.sstatic.net/GPaLMzLQ.jpg)[image: enter image description here; source: https://i.sstatic.net/IYuAi5BW.jpg] (https://i.sstatic.net/IYuAi5BW.jpg)A small plant volunteered in my garden in North West Georgia (US) this year. I can’t identify it. It is about 2 ft high, yellow flowers, six opposite rounded laves on a stem. Yellow flowers produce long seed pods.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":117812,"score":0},{"answer_id":117940,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":117845,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Actually, I found an answer to my question.\nHuman insulin doesn't have any methionine residues, so cyanogen bromide would not cleave insulin. Rather it would only cleave methionine residues in <span class=\"math-container\">$\\beta$</span>-galactosidase.</p>\n<p><a href=\"https://i.sstatic.net/iVRol8Xj.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/iVRol8Xj.png\" alt=\"Primary structure of human insulin, indicating position of B10 and B28-29 modifications. Also shown is the sequence of IGF-I homologous to the B25-30 portion of insulin\" /></a></p>\n<p>Primary structure of human insulin, indicating position of B10 and B28-29 modifications. Also shown is the sequence of IGF-I homologous to the B25-30 portion of insulin</p>\n<p><a href=\"https://i.sstatic.net/1SKrY83L.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/1SKrY83L.jpg\" alt=\"Human pro-insulin\" /></a>\nHere at 5th position there is met, however, in humulin production by rDNA technology, we do not need the signal peptide and the C - chain.</p>\n<p>In Eli - Lily's production we produce only the A and B chain seperately and form disulphide bonds between them. These genes are inserted into <span class=\"math-container\">$\\beta$</span>-galactoside gene of pBR322 and inserted into <em>E. coli</em>. When the peptide is produced some segments of <span class=\"math-container\">$\\beta$</span>-galactoside gene may be left which are cleaved using cyanogen bromide which cleaves selectively at methionine residues.</p>\n<hr/>\n<p><sup>Citations:</sup></p>\n<p><sup>1. Slieker, Lawrence &amp; Brooke, G. &amp; Dimarchi, Richard &amp; Flora, D. &amp; Green, Linda &amp; Hoffmann, JA &amp; Long, H. &amp; Shields, James &amp; Sundell, Karen &amp; Surface, Peggy &amp; Chance, R.. (1997). Modifications in the B10 and B26–30 regions of the B chain of human insulin alter affinity for the human IGF-I receptor more than for the insulin receptor. Diabetologia. 40. 10.1007/s001250051402.\n<a href=\"https://www.researchgate.net/figure/Primary-structure-of-human-insulin-indicating-position-of-B10-and-B28-29-modifications_fig1_245790866\" rel=\"nofollow noreferrer\">Link to the reference</a>\n</sup></p>\n<p><sup>2. Gerald Litwack,\nChapter 6 - Pancreatic hormones: insulin and glucagon,\nEditor(s): Gerald Litwack,\nHormones (Fourth Edition),\nAcademic Press,\n2022,\nPages 123-157,\nISBN 9780323902625,\n<a href=\"https://doi.org/10.1016/B978-0-323-90262-5.00022-6\" rel=\"nofollow noreferrer\">https://doi.org/10.1016/B978-0-323-90262-5.00022-6</a>.\n(<a href=\"https://www.sciencedirect.com/science/article/pii/B9780323902625000226\" rel=\"nofollow noreferrer\">https://www.sciencedirect.com/science/article/pii/B9780323902625000226</a>)\n</sup></p>\n","answer_id":117845,"answer_text":"Actually, I found an answer to my question.\nHuman insulin doesn't have any methionine residues, so cyanogen bromide would not cleave insulin. Rather it would only cleave methionine residues in $\\beta$-galactosidase.\n\n\n\n\n[image: Primary structure of human insulin, indicating position of B10 and B28-29 modifications. Also shown is the sequence of IGF-I homologous to the B25-30 portion of insulin; source: https://i.sstatic.net/iVRol8Xj.png] (https://i.sstatic.net/iVRol8Xj.png)\n\n\n\n\nPrimary structure of human insulin, indicating position of B10 and B28-29 modifications. Also shown is the sequence of IGF-I homologous to the B25-30 portion of insulin\n\n\n\n\n[image: Human pro-insulin; source: https://i.sstatic.net/1SKrY83L.jpg] (https://i.sstatic.net/1SKrY83L.jpg)\nHere at 5th position there is met, however, in humulin production by rDNA technology, we do not need the signal peptide and the C - chain.\n\n\n\n\nIn Eli - Lily's production we produce only the A and B chain seperately and form disulphide bonds between them. These genes are inserted into $\\beta$-galactoside gene of pBR322 and inserted into E. coli. When the peptide is produced some segments of $\\beta$-galactoside gene may be left which are cleaved using cyanogen bromide which cleaves selectively at methionine residues.\n\n\n\n\n\n\n\nCitations:\n\n\n\n\n1. Slieker, Lawrence & Brooke, G. & Dimarchi, Richard & Flora, D. & Green, Linda & Hoffmann, JA & Long, H. & Shields, James & Sundell, Karen & Surface, Peggy & Chance, R.. (1997). Modifications in the B10 and B26–30 regions of the B chain of human insulin alter affinity for the human IGF-I receptor more than for the insulin receptor. Diabetologia. 40. 10.1007/s001250051402.\nLink to the reference (https://www.researchgate.net/figure/Primary-structure-of-human-insulin-indicating-position-of-B10-and-B28-29-modifications_fig1_245790866)\n\n\n\n\n\n2. Gerald Litwack,\nChapter 6 - Pancreatic hormones: insulin and glucagon,\nEditor(s): Gerald Litwack,\nHormones (Fourth Edition),\nAcademic Press,\n2022,\nPages 123-157,\nISBN 9780323902625,\nhttps://doi.org/10.1016/B978-0-323-90262-5.00022-6 (https://doi.org/10.1016/B978-0-323-90262-5.00022-6).\n(https://www.sciencedirect.com/science/article/pii/B9780323902625000226 (https://www.sciencedirect.com/science/article/pii/B9780323902625000226))","answer_url":"https://biology.stackexchange.com/a/117845","author":"Shayan","author_url":"https://biology.stackexchange.com/users/114723/shayan","content_license":"CC BY-SA 4.0","created_at":"2025-08-27T15:59:07+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:16.948131+00:00","license":"CC BY-SA 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I thought it would be useful, therefore, to provide a brief referenced account of the original work, emphasizing the key strategy.</p>\n<p><strong>The Strategy Summarized</strong></p>\n<p>This is described in Figure 2 of the <a href=\"https://academic.oup.com/edrv/article/42/3/374/6042201\" rel=\"nofollow noreferrer\">2021 Review article</a> by Arthur D. Riggs, one of the original investigators:</p>\n<p><a href=\"https://i.sstatic.net/zOd3Nzo5.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/zOd3Nzo5.jpg\" alt=\"Strategy of Human Insulin production\" /></a></p>\n<p>The key points are:</p>\n<ol>\n<li><p>The ‘gene’ was actually two artificial oligonucleotides synthesized on the basis of the amino acid sequence of the mature A and B chains of human insulin.</p>\n</li>\n<li><p>In addition to encoding the actual amino acid sequence of the mature chains, each oligonucleotide included a methionine codon 5′ to the insulin-coding region.</p>\n</li>\n<li><p>The oligonucleotides included an <em>Eco</em>RI site at the extreme 5′-end and a <em>Bam</em>H1 site at the extreme 3′-end to allow insertion into the β-galactosidase gene of plasmid pBR322.</p>\n</li>\n<li><p>Expression of the genes encoded by the plasmid in <em>Escherichia coli</em> produced fusion proteins of  β-galactosidase and the respective insulin chain.</p>\n</li>\n<li><p>Cleavage of the chains from the β-galactosidase was achieved with cyanogen bromide attack on the artificially introduced methionine residue, mentioned above.</p>\n</li>\n<li><p>The insulin chains were not affected by the cyanogen bromide because they both lack methionine. (The methionine residue of pre-proinsulin is not present in the mature chains.)</p>\n</li>\n</ol>\n<p><strong>Synthesis and Cloning of Oligonucleotides</strong></p>\n<p>The design and synthesis of the oligonucleotides is described in the <a href=\"https://www.pnas.org/doi/10.1073/pnas.75.12.5765\" rel=\"nofollow noreferrer\">1978 paper of Crea <em>et al.</em></a>. Although rather small, I reproduce Figure 1 of this paper below, with the <em>Eco</em>R1 and <em>Bam</em>H1 sites outlined in red, and the additional methionine enlarged on a yellow background.</p>\n<p><a href=\"https://i.sstatic.net/IxtM5fnW.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/IxtM5fnW.png\" alt=\"Oligonucleotides for insulin synthesis\" /></a></p>\n<p>The cloning, expression and purification is described in the <a href=\"https://www.pnas.org/doi/abs/10.1073/pnas.76.1.106\" rel=\"nofollow noreferrer\">1979 paper of Goeddel <em>et al</em>.</a>. One of the recombinant plasmids described in that paper is illustrated below. The insulin ‘gene’ was actually inserted in two parts, BB and BH, as part of a strategy to ensure the correct orientation.</p>\n<p><a href=\"https://i.sstatic.net/MXPDUqpB.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/MXPDUqpB.png\" alt=\"Recombinant insulin plasmid pIB1\" /></a></p>\n","answer_id":117857,"answer_text":"Preamble\n\n\n\n\nThe answer provided by the poster is correct in essence, but the original construction of synthetic insulin is not actually described. I thought it would be useful, therefore, to provide a brief referenced account of the original work, emphasizing the key strategy.\n\n\n\n\nThe Strategy Summarized\n\n\n\n\nThis is described in Figure 2 of the 2021 Review article (https://academic.oup.com/edrv/article/42/3/374/6042201) by Arthur D. Riggs, one of the original investigators:\n\n\n\n\n[image: Strategy of Human Insulin production; source: https://i.sstatic.net/zOd3Nzo5.jpg] (https://i.sstatic.net/zOd3Nzo5.jpg)\n\n\n\n\nThe key points are:\n\n\n\n\n\n\n\nThe ‘gene’ was actually two artificial oligonucleotides synthesized on the basis of the amino acid sequence of the mature A and B chains of human insulin.\n\n\n\n\n\n\n\n\n\nIn addition to encoding the actual amino acid sequence of the mature chains, each oligonucleotide included a methionine codon 5′ to the insulin-coding region.\n\n\n\n\n\n\n\n\n\nThe oligonucleotides included an EcoRI site at the extreme 5′-end and a BamH1 site at the extreme 3′-end to allow insertion into the β-galactosidase gene of plasmid pBR322.\n\n\n\n\n\n\n\n\n\nExpression of the genes encoded by the plasmid in Escherichia coli produced fusion proteins of  β-galactosidase and the respective insulin chain.\n\n\n\n\n\n\n\n\n\nCleavage of the chains from the β-galactosidase was achieved with cyanogen bromide attack on the artificially introduced methionine residue, mentioned above.\n\n\n\n\n\n\n\n\n\nThe insulin chains were not affected by the cyanogen bromide because they both lack methionine. (The methionine residue of pre-proinsulin is not present in the mature chains.)\n\n\n\n\n\n\n\n\nSynthesis and Cloning of Oligonucleotides\n\n\n\n\nThe design and synthesis of the oligonucleotides is described in the 1978 paper of Crea et al. (https://www.pnas.org/doi/10.1073/pnas.75.12.5765). Although rather small, I reproduce Figure 1 of this paper below, with the EcoR1 and BamH1 sites outlined in red, and the additional methionine enlarged on a yellow background.\n\n\n\n\n[image: Oligonucleotides for insulin synthesis; source: https://i.sstatic.net/IxtM5fnW.png] (https://i.sstatic.net/IxtM5fnW.png)\n\n\n\n\nThe cloning, expression and purification is described in the 1979 paper of Goeddel et al. (https://www.pnas.org/doi/abs/10.1073/pnas.76.1.106). One of the recombinant plasmids described in that paper is illustrated below. The insulin ‘gene’ was actually inserted in two parts, BB and BH, as part of a strategy to ensure the correct orientation.\n\n\n\n\n[image: Recombinant insulin plasmid pIB1; source: https://i.sstatic.net/MXPDUqpB.png] (https://i.sstatic.net/MXPDUqpB.png)","answer_url":"https://biology.stackexchange.com/a/117857","author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","created_at":"2025-08-30T22:50:20+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:16.948131+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/46a41fae37d5c2c243f9abcbf6829a0045f46a51c624fbba2b897c320cdcba71_0.json","raw_sha256":"e039e310d0106dc61f992ee05bbb0b0b57ded1c5092f97df2c52989edd5eaf68","source_api":"Stack Exchange API 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It is well established that cyanogen bromide cleaves selectively at methionine residues<a href=\"https://www.sciencedirect.com/science/article/abs/pii/S007668796711029X\" rel=\"nofollow noreferrer\"><span class=\"math-container\">$^1$</span></a>. What prevents it cleaving these residue in insulin too?</p>\n","text":"For recombinant insulin production from E. coli (according to Eli Lilly), cyanogen bromide is used to cleave residues in residual $\\beta$-galactosidase. It is well established that cyanogen bromide cleaves selectively at methionine residues$^1$ (https://www.sciencedirect.com/science/article/abs/pii/S007668796711029X). What prevents it cleaving these residue in insulin too?"},{"context_id":"117845","html":"<p>Actually, I found an answer to my question.\nHuman insulin doesn't have any methionine residues, so cyanogen bromide would not cleave insulin. Rather it would only cleave methionine residues in <span class=\"math-container\">$\\beta$</span>-galactosidase.</p>\n<p><a href=\"https://i.sstatic.net/iVRol8Xj.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/iVRol8Xj.png\" alt=\"Primary structure of human insulin, indicating position of B10 and B28-29 modifications. Also shown is the sequence of IGF-I homologous to the B25-30 portion of insulin\" /></a></p>\n<p>Primary structure of human insulin, indicating position of B10 and B28-29 modifications. Also shown is the sequence of IGF-I homologous to the B25-30 portion of insulin</p>\n<p><a href=\"https://i.sstatic.net/1SKrY83L.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/1SKrY83L.jpg\" alt=\"Human pro-insulin\" /></a>\nHere at 5th position there is met, however, in humulin production by rDNA technology, we do not need the signal peptide and the C - chain.</p>\n<p>In Eli - Lily's production we produce only the A and B chain seperately and form disulphide bonds between them. These genes are inserted into <span class=\"math-container\">$\\beta$</span>-galactoside gene of pBR322 and inserted into <em>E. coli</em>. When the peptide is produced some segments of <span class=\"math-container\">$\\beta$</span>-galactoside gene may be left which are cleaved using cyanogen bromide which cleaves selectively at methionine residues.</p>\n<hr/>\n<p><sup>Citations:</sup></p>\n<p><sup>1. Slieker, Lawrence &amp; Brooke, G. &amp; Dimarchi, Richard &amp; Flora, D. &amp; Green, Linda &amp; Hoffmann, JA &amp; Long, H. &amp; Shields, James &amp; Sundell, Karen &amp; Surface, Peggy &amp; Chance, R.. (1997). Modifications in the B10 and B26–30 regions of the B chain of human insulin alter affinity for the human IGF-I receptor more than for the insulin receptor. Diabetologia. 40. 10.1007/s001250051402.\n<a href=\"https://www.researchgate.net/figure/Primary-structure-of-human-insulin-indicating-position-of-B10-and-B28-29-modifications_fig1_245790866\" rel=\"nofollow noreferrer\">Link to the reference</a>\n</sup></p>\n<p><sup>2. Gerald Litwack,\nChapter 6 - Pancreatic hormones: insulin and glucagon,\nEditor(s): Gerald Litwack,\nHormones (Fourth Edition),\nAcademic Press,\n2022,\nPages 123-157,\nISBN 9780323902625,\n<a href=\"https://doi.org/10.1016/B978-0-323-90262-5.00022-6\" rel=\"nofollow noreferrer\">https://doi.org/10.1016/B978-0-323-90262-5.00022-6</a>.\n(<a href=\"https://www.sciencedirect.com/science/article/pii/B9780323902625000226\" rel=\"nofollow noreferrer\">https://www.sciencedirect.com/science/article/pii/B9780323902625000226</a>)\n</sup></p>\n","text":"Actually, I found an answer to my question.\nHuman insulin doesn't have any methionine residues, so cyanogen bromide would not cleave insulin. Rather it would only cleave methionine residues in $\\beta$-galactosidase.\n\n\n\n\n[image: Primary structure of human insulin, indicating position of B10 and B28-29 modifications. Also shown is the sequence of IGF-I homologous to the B25-30 portion of insulin; source: https://i.sstatic.net/iVRol8Xj.png] (https://i.sstatic.net/iVRol8Xj.png)\n\n\n\n\nPrimary structure of human insulin, indicating position of B10 and B28-29 modifications. Also shown is the sequence of IGF-I homologous to the B25-30 portion of insulin\n\n\n\n\n[image: Human pro-insulin; source: https://i.sstatic.net/1SKrY83L.jpg] (https://i.sstatic.net/1SKrY83L.jpg)\nHere at 5th position there is met, however, in humulin production by rDNA technology, we do not need the signal peptide and the C - chain.\n\n\n\n\nIn Eli - Lily's production we produce only the A and B chain seperately and form disulphide bonds between them. These genes are inserted into $\\beta$-galactoside gene of pBR322 and inserted into E. coli. When the peptide is produced some segments of $\\beta$-galactoside gene may be left which are cleaved using cyanogen bromide which cleaves selectively at methionine residues.\n\n\n\n\n\n\n\nCitations:\n\n\n\n\n1. Slieker, Lawrence & Brooke, G. & Dimarchi, Richard & Flora, D. & Green, Linda & Hoffmann, JA & Long, H. & Shields, James & Sundell, Karen & Surface, Peggy & Chance, R.. (1997). Modifications in the B10 and B26–30 regions of the B chain of human insulin alter affinity for the human IGF-I receptor more than for the insulin receptor. Diabetologia. 40. 10.1007/s001250051402.\nLink to the reference (https://www.researchgate.net/figure/Primary-structure-of-human-insulin-indicating-position-of-B10-and-B28-29-modifications_fig1_245790866)\n\n\n\n\n\n2. Gerald Litwack,\nChapter 6 - Pancreatic hormones: insulin and glucagon,\nEditor(s): Gerald Litwack,\nHormones (Fourth Edition),\nAcademic Press,\n2022,\nPages 123-157,\nISBN 9780323902625,\nhttps://doi.org/10.1016/B978-0-323-90262-5.00022-6 (https://doi.org/10.1016/B978-0-323-90262-5.00022-6).\n(https://www.sciencedirect.com/science/article/pii/B9780323902625000226 (https://www.sciencedirect.com/science/article/pii/B9780323902625000226))"},{"context_id":"117857","html":"<p><strong>Preamble</strong></p>\n<p>The answer provided by the poster is correct in essence, but the original construction of synthetic insulin is not actually described. I thought it would be useful, therefore, to provide a brief referenced account of the original work, emphasizing the key strategy.</p>\n<p><strong>The Strategy Summarized</strong></p>\n<p>This is described in Figure 2 of the <a href=\"https://academic.oup.com/edrv/article/42/3/374/6042201\" rel=\"nofollow noreferrer\">2021 Review article</a> by Arthur D. Riggs, one of the original investigators:</p>\n<p><a href=\"https://i.sstatic.net/zOd3Nzo5.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/zOd3Nzo5.jpg\" alt=\"Strategy of Human Insulin production\" /></a></p>\n<p>The key points are:</p>\n<ol>\n<li><p>The ‘gene’ was actually two artificial oligonucleotides synthesized on the basis of the amino acid sequence of the mature A and B chains of human insulin.</p>\n</li>\n<li><p>In addition to encoding the actual amino acid sequence of the mature chains, each oligonucleotide included a methionine codon 5′ to the insulin-coding region.</p>\n</li>\n<li><p>The oligonucleotides included an <em>Eco</em>RI site at the extreme 5′-end and a <em>Bam</em>H1 site at the extreme 3′-end to allow insertion into the β-galactosidase gene of plasmid pBR322.</p>\n</li>\n<li><p>Expression of the genes encoded by the plasmid in <em>Escherichia coli</em> produced fusion proteins of  β-galactosidase and the respective insulin chain.</p>\n</li>\n<li><p>Cleavage of the chains from the β-galactosidase was achieved with cyanogen bromide attack on the artificially introduced methionine residue, mentioned above.</p>\n</li>\n<li><p>The insulin chains were not affected by the cyanogen bromide because they both lack methionine. (The methionine residue of pre-proinsulin is not present in the mature chains.)</p>\n</li>\n</ol>\n<p><strong>Synthesis and Cloning of Oligonucleotides</strong></p>\n<p>The design and synthesis of the oligonucleotides is described in the <a href=\"https://www.pnas.org/doi/10.1073/pnas.75.12.5765\" rel=\"nofollow noreferrer\">1978 paper of Crea <em>et al.</em></a>. Although rather small, I reproduce Figure 1 of this paper below, with the <em>Eco</em>R1 and <em>Bam</em>H1 sites outlined in red, and the additional methionine enlarged on a yellow background.</p>\n<p><a href=\"https://i.sstatic.net/IxtM5fnW.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/IxtM5fnW.png\" alt=\"Oligonucleotides for insulin synthesis\" /></a></p>\n<p>The cloning, expression and purification is described in the <a href=\"https://www.pnas.org/doi/abs/10.1073/pnas.76.1.106\" rel=\"nofollow noreferrer\">1979 paper of Goeddel <em>et al</em>.</a>. One of the recombinant plasmids described in that paper is illustrated below. The insulin ‘gene’ was actually inserted in two parts, BB and BH, as part of a strategy to ensure the correct orientation.</p>\n<p><a href=\"https://i.sstatic.net/MXPDUqpB.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/MXPDUqpB.png\" alt=\"Recombinant insulin plasmid pIB1\" /></a></p>\n","text":"Preamble\n\n\n\n\nThe answer provided by the poster is correct in essence, but the original construction of synthetic insulin is not actually described. I thought it would be useful, therefore, to provide a brief referenced account of the original work, emphasizing the key strategy.\n\n\n\n\nThe Strategy Summarized\n\n\n\n\nThis is described in Figure 2 of the 2021 Review article (https://academic.oup.com/edrv/article/42/3/374/6042201) by Arthur D. Riggs, one of the original investigators:\n\n\n\n\n[image: Strategy of Human Insulin production; source: https://i.sstatic.net/zOd3Nzo5.jpg] (https://i.sstatic.net/zOd3Nzo5.jpg)\n\n\n\n\nThe key points are:\n\n\n\n\n\n\n\nThe ‘gene’ was actually two artificial oligonucleotides synthesized on the basis of the amino acid sequence of the mature A and B chains of human insulin.\n\n\n\n\n\n\n\n\n\nIn addition to encoding the actual amino acid sequence of the mature chains, each oligonucleotide included a methionine codon 5′ to the insulin-coding region.\n\n\n\n\n\n\n\n\n\nThe oligonucleotides included an EcoRI site at the extreme 5′-end and a BamH1 site at the extreme 3′-end to allow insertion into the β-galactosidase gene of plasmid pBR322.\n\n\n\n\n\n\n\n\n\nExpression of the genes encoded by the plasmid in Escherichia coli produced fusion proteins of  β-galactosidase and the respective insulin chain.\n\n\n\n\n\n\n\n\n\nCleavage of the chains from the β-galactosidase was achieved with cyanogen bromide attack on the artificially introduced methionine residue, mentioned above.\n\n\n\n\n\n\n\n\n\nThe insulin chains were not affected by the cyanogen bromide because they both lack methionine. (The methionine residue of pre-proinsulin is not present in the mature chains.)\n\n\n\n\n\n\n\n\nSynthesis and Cloning of Oligonucleotides\n\n\n\n\nThe design and synthesis of the oligonucleotides is described in the 1978 paper of Crea et al. (https://www.pnas.org/doi/10.1073/pnas.75.12.5765). Although rather small, I reproduce Figure 1 of this paper below, with the EcoR1 and BamH1 sites outlined in red, and the additional methionine enlarged on a yellow background.\n\n\n\n\n[image: Oligonucleotides for insulin synthesis; source: https://i.sstatic.net/IxtM5fnW.png] (https://i.sstatic.net/IxtM5fnW.png)\n\n\n\n\nThe cloning, expression and purification is described in the 1979 paper of Goeddel et al. (https://www.pnas.org/doi/abs/10.1073/pnas.76.1.106). One of the recombinant plasmids described in that paper is illustrated below. The insulin ‘gene’ was actually inserted in two parts, BB and BH, as part of a strategy to ensure the correct orientation.\n\n\n\n\n[image: Recombinant insulin plasmid pIB1; source: https://i.sstatic.net/MXPDUqpB.png] (https://i.sstatic.net/MXPDUqpB.png)"}],"domain":"biology","external_citations":["https://academic.oup.com/edrv/article/42/3/374/6042201","https://doi.org/10.1016/B978-0-323-90262-5.00022-6","https://i.sstatic.net/1SKrY83L.jpg","https://i.sstatic.net/IxtM5fnW.png","https://i.sstatic.net/MXPDUqpB.png","https://i.sstatic.net/iVRol8Xj.png","https://i.sstatic.net/zOd3Nzo5.jpg","https://www.pnas.org/doi/10.1073/pnas.75.12.5765","https://www.pnas.org/doi/abs/10.1073/pnas.76.1.106","https://www.researchgate.net/figure/Primary-structure-of-human-insulin-indicating-position-of-B10-and-B28-29-modifications_fig1_245790866","https://www.sciencedirect.com/science/article/abs/pii/S007668796711029X","https://www.sciencedirect.com/science/article/pii/B9780323902625000226"],"ground_truth_type":"metadata_grounded","group_id":"e86ddce3f1d409ae37da0f6aaf740e6575139e1dcb93ec48eb331662eb22d076","hard_case_family":["accepted_vs_highest_score_disagreement","multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-6b6489e482eed4838bd5001b","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:01.208074+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f1b387b48f36041f506f18fa9796531023c7eae1e796ec622ad56833c02bea98_0.json","raw_sha256":"3f8214c87c0fe16dd016324597332ca392e0ba98600877cc746483ef492ce03d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Shayan","profile_url":"https://biology.stackexchange.com/users/114723/shayan","user_type":"registered"},"created_at":"2025-08-27T15:29:15+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"26AD7149-3E85-473C-BED6-EE3D46A1C5C2","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/26AD7149-3E85-473C-BED6-EE3D46A1C5C2/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-08-27T23:43:34+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"037F4440-7B51-4806-8AEB-718F5F219F08","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/037F4440-7B51-4806-8AEB-718F5F219F08/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2025-08-30T22:29:10+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"0C39BDF1-B68C-4CFF-A2FE-082813ECEB9D","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0C39BDF1-B68C-4CFF-A2FE-082813ECEB9D/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"117844","source_record_sha256":"9dfba2dd7935b71440829e335e5cf4e6101f63a1455d82c58056e594962c71ee","source_url":"https://biology.stackexchange.com/questions/117844/recombinant-insulin-production-and-cyanogen-bromide-action","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Recombinant insulin production and cyanogen bromide action\nFor recombinant insulin production from E. coli (according to Eli Lilly), cyanogen bromide is used to cleave residues in residual $\\beta$-galactosidase. It is well established that cyanogen bromide cleaves selectively at methionine residues$^1$ (https://www.sciencedirect.com/science/article/abs/pii/S007668796711029X). What prevents it cleaving these residue in insulin too?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":117845,"score":3},{"answer_id":117857,"score":4}],"split":"test"}
{"accepted_status":{"accepted_answer_id":117875,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p><em>Katamenes arbustorum</em>\n<a href=\"https://i.sstatic.net/jtzmevhF.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/jtzmevhF.jpg\" alt=\"File:Katamenes arbustorum01.jpg\" /></a>\n<a href=\"https://en.m.wikipedia.org/wiki/File:Katamenes_arbustorum01.jpg\" rel=\"nofollow noreferrer\">Image source Wikipedia</a></p>\n<p>The distinctive feature which helps in identification is that the body has a black and yellow pattern. <a href=\"https://en.m.wikipedia.org/wiki/Petiole_(insect_anatomy)\" rel=\"nofollow noreferrer\">Petiole</a> and postpetiole are strongly divided.</p>\n<p><a href=\"https://uk.inaturalist.org/taxa/631004-Katamenes-arbustorum\" rel=\"nofollow noreferrer\">iNaturalist link</a></p>\n<p>However, these species are found in Northern Africa and Europe so might not be this.</p>\n<p>Some species from genus <em>Katamanes</em> were moved to <a href=\"https://en.m.wikipedia.org/wiki/Eumenes_(wasp)\" rel=\"nofollow noreferrer\"><em>Eumenes</em></a>\n<a href=\"https://i.sstatic.net/JpSoMnC2.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/JpSoMnC2.jpg\" alt=\"Eumenes\" /></a></p>\n<blockquote>\n<p><a href=\"https://en.m.wikipedia.org/wiki/Eumenes_(wasp)\" rel=\"nofollow noreferrer\">Wikipedia</a>: It is a large and widespread genus, with over 100 species and subspecies occurring worldwide</p>\n</blockquote>\n","answer_id":117863,"answer_text":"Katamenes arbustorum\n[image: File:Katamenes arbustorum01.jpg; source: https://i.sstatic.net/jtzmevhF.jpg] (https://i.sstatic.net/jtzmevhF.jpg)\nImage source Wikipedia (https://en.m.wikipedia.org/wiki/File:Katamenes_arbustorum01.jpg)\n\n\n\n\nThe distinctive feature which helps in identification is that the body has a black and yellow pattern. Petiole (https://en.m.wikipedia.org/wiki/Petiole_(insect_anatomy)) and postpetiole are strongly divided.\n\n\n\n\niNaturalist link (https://uk.inaturalist.org/taxa/631004-Katamenes-arbustorum)\n\n\n\n\nHowever, these species are found in Northern Africa and Europe so might not be this.\n\n\n\n\nSome species from genus Katamanes were moved to Eumenes (https://en.m.wikipedia.org/wiki/Eumenes_(wasp))\n[image: Eumenes; source: https://i.sstatic.net/JpSoMnC2.jpg] (https://i.sstatic.net/JpSoMnC2.jpg)\n\n\n\n\n\n\n\nWikipedia (https://en.m.wikipedia.org/wiki/Eumenes_(wasp)): It is a large and widespread genus, with over 100 species and subspecies occurring worldwide","answer_url":"https://biology.stackexchange.com/a/117863","author":"Shayan","author_url":"https://biology.stackexchange.com/users/114723/shayan","content_license":"CC BY-SA 4.0","created_at":"2025-08-31T13:55:11+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:16.948131+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/46a41fae37d5c2c243f9abcbf6829a0045f46a51c624fbba2b897c320cdcba71_0.json","raw_sha256":"e039e310d0106dc61f992ee05bbb0b0b57ded1c5092f97df2c52989edd5eaf68","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/118153;118142;118137;118126;118122;118117;118113;118102;118099;118097;118094;118081;118076;118072;118069;118065;118059;118056;118043;118039;118036;118030;118029;118025;118022;118018;117994;117992;117990;117987;117983;117981;117975;117971;117956;117953;117951;117945;117943;117941;117934;117926;117924;117920;117916;117914;117907;117892;117889;117887;117883;117876;117872;117867;117861;117860;117856;117855;117850;117849;117844;117840;117833;117821;117819;117817;117815;117814;117805;117794;117782;117774;117771;117767;117766;117761;117759;117756;117747;117732;117726;117724;117709;117701;117694;117693;117681;117680;117677;117671;117668;117664;117662;117659;117651;117641;117632;117624;117623;117607/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":117861,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Shayan","profile_url":"https://biology.stackexchange.com/users/114723/shayan","user_type":"registered"},"created_at":"2025-08-31T13:55:11+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"6F378600-F65C-40E9-A0CA-8B5DA8728806","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/6F378600-F65C-40E9-A0CA-8B5DA8728806/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Shayan","profile_url":"https://biology.stackexchange.com/users/114723/shayan","user_type":"registered"},"created_at":"2025-08-31T14:04:07+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"5D003885-4A38-41A0-9E89-A48EC34C87DF","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5D003885-4A38-41A0-9E89-A48EC34C87DF/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Shayan","profile_url":"https://biology.stackexchange.com/users/114723/shayan","user_type":"registered"},"created_at":"2025-08-31T18:21:32+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"989E78E8-077E-4F87-8725-8EA50A5405EB","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/989E78E8-077E-4F87-8725-8EA50A5405EB/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Shayan","profile_url":"https://biology.stackexchange.com/users/114723/shayan","user_type":"registered"},"created_at":"2025-08-31T18:36:26+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"BEFBD40E-7622-4550-B94C-91E6A89456A3","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/BEFBD40E-7622-4550-B94C-91E6A89456A3/view-source"}],"score":4},{"answer_html":"<p><em>Phimenes flavopictus subspecies formosanus!</em></p>\n<p>Thanks to the <a href=\"https://www.tfri.gov.tw/en/\" rel=\"nofollow noreferrer\">Taiwan Forestry Research Institute</a> for the identification.</p>\n<p>The species <a href=\"https://www.inaturalist.org/taxa/371705-Phimenes-flavopictus\" rel=\"nofollow noreferrer\"><em>Phimenes flavopictus</em></a> is found throughout India, Southeast Asia, Pacific Islands and southern China, and the subspecies <em>formosanus</em> throughout the lower elevations of the island of Taiwan according to the iNaturalist maps.</p>\n<p>Of course, <a href=\"https://www.inaturalist.org/observations/308729934\" rel=\"nofollow noreferrer\">this observation</a> in Hong Kong looks exactly like <em>formosanus</em> (I'm looking at the detailed markings on the top of the thorax and the skinny part of the abdomen for example).</p>\n<p>Anyway, although <a href=\"https://biology.stackexchange.com/a/117863/27918\">@ShayanBiswas's</a> find of <em>Katamenes arbustorum</em> is a close match in appearance (but not region) the distinctive detailed markings on the thorax are so similar between the image of subspecies <em>formosanus</em> and my photos that I think the identification has been resolved.</p>\n<p><a href=\"https://i.sstatic.net/8z1y5BTK.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/8z1y5BTK.jpg\" alt=\"Phimenes flavopictus Kolkata https://www.inaturalist.org/observations/308178166\" /></a></p>\n<p><a href=\"https://www.inaturalist.org/observations/308178166\" rel=\"nofollow noreferrer\"><em>Phimenes flavopictus</em> Kolkata, India</a></p>\n<p><a href=\"https://i.sstatic.net/kkAQlSb8.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/kkAQlSb8.jpg\" alt=\"Phimenes flavopictus ssp. formosanus, Taitung, Taiwan, https://www.inaturalist.org/observations/74324022\" /></a></p>\n<p><a href=\"https://www.inaturalist.org/observations/74324022\" rel=\"nofollow noreferrer\"><em>Phimenes flavopictus ssp. formosanus</em> Taitung, Taiwan</a></p>\n<p><a href=\"https://i.sstatic.net/yrfmOgW0.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/yrfmOgW0.jpg\" alt=\"Wasp in northern Taiwan in August\" /></a></p>\n<p>Photo from the question (Northern Taiwan)</p>\n","answer_id":117875,"answer_text":"Phimenes flavopictus subspecies formosanus!\n\n\n\n\nThanks to the Taiwan Forestry Research Institute (https://www.tfri.gov.tw/en/) for the identification.\n\n\n\n\nThe species Phimenes flavopictus (https://www.inaturalist.org/taxa/371705-Phimenes-flavopictus) is found throughout India, Southeast Asia, Pacific Islands and southern China, and the subspecies formosanus throughout the lower elevations of the island of Taiwan according to the iNaturalist maps.\n\n\n\n\nOf course, this observation (https://www.inaturalist.org/observations/308729934) in Hong Kong looks exactly like formosanus (I'm looking at the detailed markings on the top of the thorax and the skinny part of the abdomen for example).\n\n\n\n\nAnyway, although @ShayanBiswas's (https://biology.stackexchange.com/a/117863/27918) find of Katamenes arbustorum is a close match in appearance (but not region) the distinctive detailed markings on the thorax are so similar between the image of subspecies formosanus and my photos that I think the identification has been resolved.\n\n\n\n\n[image: Phimenes flavopictus Kolkata https://www.inaturalist.org/observations/308178166; source: https://i.sstatic.net/8z1y5BTK.jpg] (https://i.sstatic.net/8z1y5BTK.jpg)\n\n\n\n\nPhimenes flavopictus Kolkata, India (https://www.inaturalist.org/observations/308178166)\n\n\n\n\n[image: Phimenes flavopictus ssp. formosanus, Taitung, Taiwan, https://www.inaturalist.org/observations/74324022; source: https://i.sstatic.net/kkAQlSb8.jpg] (https://i.sstatic.net/kkAQlSb8.jpg)\n\n\n\n\nPhimenes flavopictus ssp. formosanus Taitung, Taiwan (https://www.inaturalist.org/observations/74324022)\n\n\n\n\n[image: Wasp in northern Taiwan in August; source: https://i.sstatic.net/yrfmOgW0.jpg] (https://i.sstatic.net/yrfmOgW0.jpg)\n\n\n\n\nPhoto from the question (Northern Taiwan)","answer_url":"https://biology.stackexchange.com/a/117875","author":"uhoh","author_url":"https://biology.stackexchange.com/users/27918/uhoh","content_license":"CC BY-SA 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4.0","contributor":{"display_name":"uhoh","profile_url":"https://biology.stackexchange.com/users/27918/uhoh","user_type":"registered"},"created_at":"2025-09-03T16:39:06+00:00","raw_file":"raw/codex_api_v1/a76d8ab07f874a10eafefc315936b171795ddfe3f4ac47f247a19154460d4acc_1790824150220029700_0.json","raw_sha256":"d1e485076b0bfa0aed0ebdace356f1cab7a9d04a86bc0f38c43c8a253e51cebd","revision_guid":"16D4F03E-D4B1-46B8-992F-27CF7F98DCD3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/16D4F03E-D4B1-46B8-992F-27CF7F98DCD3/view-source"}],"url":"https://biology.stackexchange.com/a/117875"}],"contexts":[{"context_id":"question","html":"<p>I noticed this wasp showing an interested in this ~12 cm open pipe end, on a warm August day in northern Taiwan.</p>\n<p>Based on these photos I esitmate that it's about 4 cm long. It's certainly the longest one I've ever seen.</p>\n<p>Besides the size, I am surprised that nearly 1/3 of the total length is that very thin waist, separating the thorax and the bulbous part of the abdomen where most of the abdomen's volume resides. It's more extreme than the specimen shown in <a href=\"https://biology.stackexchange.com/q/113738/27918\">Why do wasps have &quot;wasp waists&quot;? What&#39;s been optimized?</a></p>\n<p><strong>Question:</strong> Is it possible to identify this wasp? And &quot;bonus points&quot; for a more extreme example of &quot;wasp-waistedness&quot; than this, i.e. with a longer &quot;skinny part&quot; relative to total length.</p>\n<hr />\n<p><a href=\"https://i.sstatic.net/zeCbem5n.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/zeCbem5n.jpg\" alt=\"4 cm wasp in northern Taiwan in August\" /></a></p>\n<p><a href=\"https://i.sstatic.net/bZOWXpcU.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/bZOWXpcUm.jpg\" alt=\"4 cm wasp in northern Taiwan in August\" /></a> <a href=\"https://i.sstatic.net/yrfmOgW0.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/yrfmOgW0m.jpg\" alt=\"4 cm wasp in northern Taiwan in August\" /></a></p>\n<p><a href=\"https://i.sstatic.net/2fZCsTaM.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/2fZCsTaMm.jpg\" alt=\"4 cm wasp in northern Taiwan in August\" /></a> <a href=\"https://i.sstatic.net/2Oe63zM6.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/2Oe63zM6m.jpg\" alt=\"4 cm wasp in northern Taiwan in August\" /></a></p>\n","text":"I noticed this wasp showing an interested in this ~12 cm open pipe end, on a warm August day in northern Taiwan.\n\n\n\n\nBased on these photos I esitmate that it's about 4 cm long. It's certainly the longest one I've ever seen.\n\n\n\n\nBesides the size, I am surprised that nearly 1/3 of the total length is that very thin waist, separating the thorax and the bulbous part of the abdomen where most of the abdomen's volume resides. It's more extreme than the specimen shown in Why do wasps have \"wasp waists\"? What's been optimized? (https://biology.stackexchange.com/q/113738/27918)\n\n\n\n\nQuestion: Is it possible to identify this wasp? And \"bonus points\" for a more extreme example of \"wasp-waistedness\" than this, i.e. with a longer \"skinny part\" relative to total length.\n\n\n\n\n\n\n\n[image: 4 cm wasp in northern Taiwan in August; source: https://i.sstatic.net/zeCbem5n.jpg] (https://i.sstatic.net/zeCbem5n.jpg)\n\n\n\n\n[image: 4 cm wasp in northern Taiwan in August; source: https://i.sstatic.net/bZOWXpcUm.jpg] (https://i.sstatic.net/bZOWXpcU.jpg) [image: 4 cm wasp in northern Taiwan in August; source: https://i.sstatic.net/yrfmOgW0m.jpg] (https://i.sstatic.net/yrfmOgW0.jpg)\n\n\n\n\n[image: 4 cm wasp in northern Taiwan in August; source: https://i.sstatic.net/2fZCsTaMm.jpg] (https://i.sstatic.net/2fZCsTaM.jpg) [image: 4 cm wasp in northern Taiwan in August; source: https://i.sstatic.net/2Oe63zM6m.jpg] (https://i.sstatic.net/2Oe63zM6.jpg)"},{"context_id":"117863","html":"<p><em>Katamenes arbustorum</em>\n<a href=\"https://i.sstatic.net/jtzmevhF.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/jtzmevhF.jpg\" alt=\"File:Katamenes arbustorum01.jpg\" /></a>\n<a href=\"https://en.m.wikipedia.org/wiki/File:Katamenes_arbustorum01.jpg\" rel=\"nofollow noreferrer\">Image source Wikipedia</a></p>\n<p>The distinctive feature which helps in identification is that the body has a black and yellow pattern. <a href=\"https://en.m.wikipedia.org/wiki/Petiole_(insect_anatomy)\" rel=\"nofollow noreferrer\">Petiole</a> and postpetiole are strongly divided.</p>\n<p><a href=\"https://uk.inaturalist.org/taxa/631004-Katamenes-arbustorum\" rel=\"nofollow noreferrer\">iNaturalist link</a></p>\n<p>However, these species are found in Northern Africa and Europe so might not be this.</p>\n<p>Some species from genus <em>Katamanes</em> were moved to <a href=\"https://en.m.wikipedia.org/wiki/Eumenes_(wasp)\" rel=\"nofollow noreferrer\"><em>Eumenes</em></a>\n<a href=\"https://i.sstatic.net/JpSoMnC2.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/JpSoMnC2.jpg\" alt=\"Eumenes\" /></a></p>\n<blockquote>\n<p><a href=\"https://en.m.wikipedia.org/wiki/Eumenes_(wasp)\" rel=\"nofollow noreferrer\">Wikipedia</a>: It is a large and widespread genus, with over 100 species and subspecies occurring worldwide</p>\n</blockquote>\n","text":"Katamenes arbustorum\n[image: File:Katamenes arbustorum01.jpg; source: https://i.sstatic.net/jtzmevhF.jpg] (https://i.sstatic.net/jtzmevhF.jpg)\nImage source Wikipedia (https://en.m.wikipedia.org/wiki/File:Katamenes_arbustorum01.jpg)\n\n\n\n\nThe distinctive feature which helps in identification is that the body has a black and yellow pattern. Petiole (https://en.m.wikipedia.org/wiki/Petiole_(insect_anatomy)) and postpetiole are strongly divided.\n\n\n\n\niNaturalist link (https://uk.inaturalist.org/taxa/631004-Katamenes-arbustorum)\n\n\n\n\nHowever, these species are found in Northern Africa and Europe so might not be this.\n\n\n\n\nSome species from genus Katamanes were moved to Eumenes (https://en.m.wikipedia.org/wiki/Eumenes_(wasp))\n[image: Eumenes; source: https://i.sstatic.net/JpSoMnC2.jpg] (https://i.sstatic.net/JpSoMnC2.jpg)\n\n\n\n\n\n\n\nWikipedia (https://en.m.wikipedia.org/wiki/Eumenes_(wasp)): It is a large and widespread genus, with over 100 species and subspecies occurring worldwide"},{"context_id":"117875","html":"<p><em>Phimenes flavopictus subspecies formosanus!</em></p>\n<p>Thanks to the <a href=\"https://www.tfri.gov.tw/en/\" rel=\"nofollow noreferrer\">Taiwan Forestry Research Institute</a> for the identification.</p>\n<p>The species <a href=\"https://www.inaturalist.org/taxa/371705-Phimenes-flavopictus\" rel=\"nofollow noreferrer\"><em>Phimenes flavopictus</em></a> is found throughout India, Southeast Asia, Pacific Islands and southern China, and the subspecies <em>formosanus</em> throughout the lower elevations of the island of Taiwan according to the iNaturalist maps.</p>\n<p>Of course, <a href=\"https://www.inaturalist.org/observations/308729934\" rel=\"nofollow noreferrer\">this observation</a> in Hong Kong looks exactly like <em>formosanus</em> (I'm looking at the detailed markings on the top of the thorax and the skinny part of the abdomen for example).</p>\n<p>Anyway, although <a href=\"https://biology.stackexchange.com/a/117863/27918\">@ShayanBiswas's</a> find of <em>Katamenes arbustorum</em> is a close match in appearance (but not region) the distinctive detailed markings on the thorax are so similar between the image of subspecies <em>formosanus</em> and my photos that I think the identification has been resolved.</p>\n<p><a href=\"https://i.sstatic.net/8z1y5BTK.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/8z1y5BTK.jpg\" alt=\"Phimenes flavopictus Kolkata https://www.inaturalist.org/observations/308178166\" /></a></p>\n<p><a href=\"https://www.inaturalist.org/observations/308178166\" rel=\"nofollow noreferrer\"><em>Phimenes flavopictus</em> Kolkata, India</a></p>\n<p><a href=\"https://i.sstatic.net/kkAQlSb8.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/kkAQlSb8.jpg\" alt=\"Phimenes flavopictus ssp. formosanus, Taitung, Taiwan, https://www.inaturalist.org/observations/74324022\" /></a></p>\n<p><a href=\"https://www.inaturalist.org/observations/74324022\" rel=\"nofollow noreferrer\"><em>Phimenes flavopictus ssp. formosanus</em> Taitung, Taiwan</a></p>\n<p><a href=\"https://i.sstatic.net/yrfmOgW0.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/yrfmOgW0.jpg\" alt=\"Wasp in northern Taiwan in August\" /></a></p>\n<p>Photo from the question (Northern Taiwan)</p>\n","text":"Phimenes flavopictus subspecies formosanus!\n\n\n\n\nThanks to the Taiwan Forestry Research Institute (https://www.tfri.gov.tw/en/) for the identification.\n\n\n\n\nThe species Phimenes flavopictus (https://www.inaturalist.org/taxa/371705-Phimenes-flavopictus) is found throughout India, Southeast Asia, Pacific Islands and southern China, and the subspecies formosanus throughout the lower elevations of the island of Taiwan according to the iNaturalist maps.\n\n\n\n\nOf course, this observation (https://www.inaturalist.org/observations/308729934) in Hong Kong looks exactly like formosanus (I'm looking at the detailed markings on the top of the thorax and the skinny part of the abdomen for example).\n\n\n\n\nAnyway, although @ShayanBiswas's (https://biology.stackexchange.com/a/117863/27918) find of Katamenes arbustorum is a close match in appearance (but not region) the distinctive detailed markings on the thorax are so similar between the image of subspecies formosanus and my photos that I think the identification has been resolved.\n\n\n\n\n[image: Phimenes flavopictus Kolkata https://www.inaturalist.org/observations/308178166; source: https://i.sstatic.net/8z1y5BTK.jpg] (https://i.sstatic.net/8z1y5BTK.jpg)\n\n\n\n\nPhimenes flavopictus Kolkata, India (https://www.inaturalist.org/observations/308178166)\n\n\n\n\n[image: Phimenes flavopictus ssp. formosanus, Taitung, Taiwan, https://www.inaturalist.org/observations/74324022; source: https://i.sstatic.net/kkAQlSb8.jpg] (https://i.sstatic.net/kkAQlSb8.jpg)\n\n\n\n\nPhimenes flavopictus ssp. formosanus Taitung, Taiwan (https://www.inaturalist.org/observations/74324022)\n\n\n\n\n[image: Wasp in northern Taiwan in August; source: https://i.sstatic.net/yrfmOgW0.jpg] (https://i.sstatic.net/yrfmOgW0.jpg)\n\n\n\n\nPhoto from the question (Northern Taiwan)"}],"domain":"biology","external_citations":["https://biology.stackexchange.com/a/117863/27918","https://biology.stackexchange.com/q/113738/27918","https://en.m.wikipedia.org/wiki/Eumenes_(wasp)","https://en.m.wikipedia.org/wiki/File:Katamenes_arbustorum01.jpg","https://en.m.wikipedia.org/wiki/Petiole_(insect_anatomy)","https://i.sstatic.net/2Oe63zM6.jpg","https://i.sstatic.net/2fZCsTaM.jpg","https://i.sstatic.net/8z1y5BTK.jpg","https://i.sstatic.net/JpSoMnC2.jpg","https://i.sstatic.net/bZOWXpcU.jpg","https://i.sstatic.net/jtzmevhF.jpg","https://i.sstatic.net/kkAQlSb8.jpg","https://i.sstatic.net/yrfmOgW0.jpg","https://i.sstatic.net/zeCbem5n.jpg","https://uk.inaturalist.org/taxa/631004-Katamenes-arbustorum","https://www.inaturalist.org/observations/308178166","https://www.inaturalist.org/observations/308729934","https://www.inaturalist.org/observations/74324022","https://www.inaturalist.org/taxa/371705-Phimenes-flavopictus","https://www.tfri.gov.tw/en/"],"ground_truth_type":"metadata_grounded","group_id":"cd019b5aae296e0f6e9cebb7db5455c416026f7e1a77a22347c99d0b583b969e","hard_case_family":["multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-9a509dbf1177276c361cee47","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:01.208074+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f1b387b48f36041f506f18fa9796531023c7eae1e796ec622ad56833c02bea98_0.json","raw_sha256":"3f8214c87c0fe16dd016324597332ca392e0ba98600877cc746483ef492ce03d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"uhoh","profile_url":"https://biology.stackexchange.com/users/27918/uhoh","user_type":"registered"},"created_at":"2025-08-31T08:20:42+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"8D698FBC-91AE-4912-93C3-EBE7281D02F6","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8D698FBC-91AE-4912-93C3-EBE7281D02F6/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-08-31T16:31:56+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"D980E130-FDCB-4227-B3E4-7CF1B0405FB4","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/D980E130-FDCB-4227-B3E4-7CF1B0405FB4/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"AccidentalTaylorExpansion","profile_url":"https://biology.stackexchange.com/users/62338/accidentaltaylorexpansion","user_type":"registered"},"created_at":"2025-08-31T20:47:29+00:00","raw_file":"raw/codex_api_v1/d8f60fae1c998cc8c158494f81f9d96078105a2ba0c494044a17f0f0183714e8_1790824152377234600_0.json","raw_sha256":"271777c6d25c770388803b7ee2725f9a2ad11be7bd2802305c1c50f6e43933bb","revision_guid":"BFF2A3F9-F0F3-4A1E-8A2D-AF023609DF93","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/BFF2A3F9-F0F3-4A1E-8A2D-AF023609DF93/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"117861","source_record_sha256":"e46f36286c258e56eba38c089e576083d0b58f0d9f74ebed817c38a00fbf8f68","source_url":"https://biology.stackexchange.com/questions/117861/identify-this-very-wasp-waisted-wasp-and-are-there-even-more-extreme-examples","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Identify this very \"wasp-waisted\" wasp, and are there even more extreme examples?\nI noticed this wasp showing an interested in this ~12 cm open pipe end, on a warm August day in northern Taiwan.\n\n\n\n\nBased on these photos I esitmate that it's about 4 cm long. It's certainly the longest one I've ever seen.\n\n\n\n\nBesides the size, I am surprised that nearly 1/3 of the total length is that very thin waist, separating the thorax and the bulbous part of the abdomen where most of the abdomen's volume resides. It's more extreme than the specimen shown in Why do wasps have \"wasp waists\"? What's been optimized? (https://biology.stackexchange.com/q/113738/27918)\n\n\n\n\nQuestion: Is it possible to identify this wasp? And \"bonus points\" for a more extreme example of \"wasp-waistedness\" than this, i.e. with a longer \"skinny part\" relative to total length.\n\n\n\n\n\n\n\n[image: 4 cm wasp in northern Taiwan in August; source: https://i.sstatic.net/zeCbem5n.jpg] (https://i.sstatic.net/zeCbem5n.jpg)\n\n\n\n\n[image: 4 cm wasp in northern Taiwan in August; source: https://i.sstatic.net/bZOWXpcUm.jpg] (https://i.sstatic.net/bZOWXpcU.jpg) [image: 4 cm wasp in northern Taiwan in August; source: https://i.sstatic.net/yrfmOgW0m.jpg] (https://i.sstatic.net/yrfmOgW0.jpg)\n\n\n\n\n[image: 4 cm wasp in northern Taiwan in August; source: https://i.sstatic.net/2fZCsTaMm.jpg] (https://i.sstatic.net/2fZCsTaM.jpg) [image: 4 cm wasp in northern Taiwan in August; source: https://i.sstatic.net/2Oe63zM6m.jpg] (https://i.sstatic.net/2Oe63zM6.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":117863,"score":4},{"answer_id":117875,"score":4}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Given the response in comment - the answer is easy.</p>\n<p>You generate 3 primers - two are common to both isoforms and one is for the longer isoform. The longer isoform primer is composed entirely of the 15 bp sequence that makes up this isoform. As this is the only difference in the sequences, you are forced to use these bases and only these bases. The longer isoform primer must be a reverse, and you use this with the common forward primer in the PCR</p>\n<p>I'd recommend that you make the products from both short so that you can distinguish the 15 bp difference in size on a gel, which might help troubleshoot if you get contamination problems. However, this isn't entirely necessary.</p>\n<p>For every detection, you run two separate PCRs, one is with the common primers together and the other with the longer isoform reverse and the common forward. The first PCR is to detect that you have something there and the second tells you if it is the longer isoform or not.</p>\n<p>It will take careful optimization to ensure that you can consistently amplify the longer isoform with the short primer and to ensure that you aren't amplifying things that aren't the intended target. You will of course need to BLAST the isoform primer against the <em>Bos taurus</em> genome to ensure that it will only bind to the gene you are looking at, as 15 bp is short for specificity.</p>\n","answer_id":117877,"answer_text":"Given the response in comment - the answer is easy.\n\n\n\n\nYou generate 3 primers - two are common to both isoforms and one is for the longer isoform. The longer isoform primer is composed entirely of the 15 bp sequence that makes up this isoform. As this is the only difference in the sequences, you are forced to use these bases and only these bases. The longer isoform primer must be a reverse, and you use this with the common forward primer in the PCR\n\n\n\n\nI'd recommend that you make the products from both short so that you can distinguish the 15 bp difference in size on a gel, which might help troubleshoot if you get contamination problems. However, this isn't entirely necessary.\n\n\n\n\nFor every detection, you run two separate PCRs, one is with the common primers together and the other with the longer isoform reverse and the common forward. The first PCR is to detect that you have something there and the second tells you if it is the longer isoform or not.\n\n\n\n\nIt will take careful optimization to ensure that you can consistently amplify the longer isoform with the short primer and to ensure that you aren't amplifying things that aren't the intended target. You will of course need to BLAST the isoform primer against the Bos taurus genome to ensure that it will only bind to the gene you are looking at, as 15 bp is short for specificity.","answer_url":"https://biology.stackexchange.com/a/117877","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2025-09-04T10:21:10+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:16.948131+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/46a41fae37d5c2c243f9abcbf6829a0045f46a51c624fbba2b897c320cdcba71_0.json","raw_sha256":"e039e310d0106dc61f992ee05bbb0b0b57ded1c5092f97df2c52989edd5eaf68","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/118153;118142;118137;118126;118122;118117;118113;118102;118099;118097;118094;118081;118076;118072;118069;118065;118059;118056;118043;118039;118036;118030;118029;118025;118022;118018;117994;117992;117990;117987;117983;117981;117975;117971;117956;117953;117951;117945;117943;117941;117934;117926;117924;117920;117916;117914;117907;117892;117889;117887;117883;117876;117872;117867;117861;117860;117856;117855;117850;117849;117844;117840;117833;117821;117819;117817;117815;117814;117805;117794;117782;117774;117771;117767;117766;117761;117759;117756;117747;117732;117726;117724;117709;117701;117694;117693;117681;117680;117677;117671;117668;117664;117662;117659;117651;117641;117632;117624;117623;117607/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":117876,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2025-09-04T10:21:10+00:00","raw_file":"raw/codex_api_v1/a76d8ab07f874a10eafefc315936b171795ddfe3f4ac47f247a19154460d4acc_1790824150220029700_0.json","raw_sha256":"d1e485076b0bfa0aed0ebdace356f1cab7a9d04a86bc0f38c43c8a253e51cebd","revision_guid":"67153053-52D8-4280-B518-E4AF2F986CF7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/67153053-52D8-4280-B518-E4AF2F986CF7/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"taiwo bello","author_url":"https://biology.stackexchange.com/users/115446/taiwo-bello","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"taiwo bello","profile_url":"https://biology.stackexchange.com/users/115446/taiwo-bello","user_type":"registered"},"created_at":"2025-09-04T06:22:14+00:00","raw_file":"raw/codex_api_v1/a76d8ab07f874a10eafefc315936b171795ddfe3f4ac47f247a19154460d4acc_1790824150220029700_0.json","raw_sha256":"d1e485076b0bfa0aed0ebdace356f1cab7a9d04a86bc0f38c43c8a253e51cebd","revision_guid":"C1B0E25B-ED28-4FC8-BD5A-6FF7C88ECF86","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C1B0E25B-ED28-4FC8-BD5A-6FF7C88ECF86/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-09-04T14:35:20+00:00","raw_file":"raw/codex_api_v1/a76d8ab07f874a10eafefc315936b171795ddfe3f4ac47f247a19154460d4acc_1790824150220029700_0.json","raw_sha256":"d1e485076b0bfa0aed0ebdace356f1cab7a9d04a86bc0f38c43c8a253e51cebd","revision_guid":"ED97838C-2368-431F-858B-BF327B42EF4C","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/ED97838C-2368-431F-858B-BF327B42EF4C/view-source"}],"url":"https://biology.stackexchange.com/questions/117876/primer-design-for-an-isoform"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"117877","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2025-09-04T10:21:10+00:00","raw_file":"raw/codex_api_v1/a76d8ab07f874a10eafefc315936b171795ddfe3f4ac47f247a19154460d4acc_1790824150220029700_0.json","raw_sha256":"d1e485076b0bfa0aed0ebdace356f1cab7a9d04a86bc0f38c43c8a253e51cebd","revision_guid":"67153053-52D8-4280-B518-E4AF2F986CF7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/67153053-52D8-4280-B518-E4AF2F986CF7/view-source"}],"url":"https://biology.stackexchange.com/a/117877"}],"contexts":[{"context_id":"question","html":"<p>I am trying to design a primer for leptin receptor isoform (short form). The region that differentiates it from the long form is just after exon 18. Every other sequence before then are completely similar. I have tried primer BLAST on NCBI, but the region the primer binds is the region that is similar to both isoform. My question is how to I design a primer specific to that region post 18 axon. The bp length is not more than 15. NB: The species is bos Taurus</p>\n","text":"I am trying to design a primer for leptin receptor isoform (short form). The region that differentiates it from the long form is just after exon 18. Every other sequence before then are completely similar. I have tried primer BLAST on NCBI, but the region the primer binds is the region that is similar to both isoform. My question is how to I design a primer specific to that region post 18 axon. The bp length is not more than 15. NB: The species is bos Taurus"},{"context_id":"117877","html":"<p>Given the response in comment - the answer is easy.</p>\n<p>You generate 3 primers - two are common to both isoforms and one is for the longer isoform. The longer isoform primer is composed entirely of the 15 bp sequence that makes up this isoform. As this is the only difference in the sequences, you are forced to use these bases and only these bases. The longer isoform primer must be a reverse, and you use this with the common forward primer in the PCR</p>\n<p>I'd recommend that you make the products from both short so that you can distinguish the 15 bp difference in size on a gel, which might help troubleshoot if you get contamination problems. However, this isn't entirely necessary.</p>\n<p>For every detection, you run two separate PCRs, one is with the common primers together and the other with the longer isoform reverse and the common forward. The first PCR is to detect that you have something there and the second tells you if it is the longer isoform or not.</p>\n<p>It will take careful optimization to ensure that you can consistently amplify the longer isoform with the short primer and to ensure that you aren't amplifying things that aren't the intended target. You will of course need to BLAST the isoform primer against the <em>Bos taurus</em> genome to ensure that it will only bind to the gene you are looking at, as 15 bp is short for specificity.</p>\n","text":"Given the response in comment - the answer is easy.\n\n\n\n\nYou generate 3 primers - two are common to both isoforms and one is for the longer isoform. The longer isoform primer is composed entirely of the 15 bp sequence that makes up this isoform. As this is the only difference in the sequences, you are forced to use these bases and only these bases. The longer isoform primer must be a reverse, and you use this with the common forward primer in the PCR\n\n\n\n\nI'd recommend that you make the products from both short so that you can distinguish the 15 bp difference in size on a gel, which might help troubleshoot if you get contamination problems. However, this isn't entirely necessary.\n\n\n\n\nFor every detection, you run two separate PCRs, one is with the common primers together and the other with the longer isoform reverse and the common forward. The first PCR is to detect that you have something there and the second tells you if it is the longer isoform or not.\n\n\n\n\nIt will take careful optimization to ensure that you can consistently amplify the longer isoform with the short primer and to ensure that you aren't amplifying things that aren't the intended target. You will of course need to BLAST the isoform primer against the Bos taurus genome to ensure that it will only bind to the gene you are looking at, as 15 bp is short for specificity."}],"domain":"biology","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"0d211e6dd9c64521b9ccef9c1eecf5a938a292c5a4c7606135d66ad5994ec01c","hard_case_family":["no_accepted_answer"],"id":"RHM-53c0be871376e622c0ce02fe","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:01.208074+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f1b387b48f36041f506f18fa9796531023c7eae1e796ec622ad56833c02bea98_0.json","raw_sha256":"3f8214c87c0fe16dd016324597332ca392e0ba98600877cc746483ef492ce03d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"taiwo bello","profile_url":"https://biology.stackexchange.com/users/115446/taiwo-bello","user_type":"registered"},"created_at":"2025-09-04T06:22:14+00:00","raw_file":"raw/codex_api_v1/a76d8ab07f874a10eafefc315936b171795ddfe3f4ac47f247a19154460d4acc_1790824150220029700_0.json","raw_sha256":"d1e485076b0bfa0aed0ebdace356f1cab7a9d04a86bc0f38c43c8a253e51cebd","revision_guid":"C1B0E25B-ED28-4FC8-BD5A-6FF7C88ECF86","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C1B0E25B-ED28-4FC8-BD5A-6FF7C88ECF86/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-09-04T14:35:20+00:00","raw_file":"raw/codex_api_v1/a76d8ab07f874a10eafefc315936b171795ddfe3f4ac47f247a19154460d4acc_1790824150220029700_0.json","raw_sha256":"d1e485076b0bfa0aed0ebdace356f1cab7a9d04a86bc0f38c43c8a253e51cebd","revision_guid":"ED97838C-2368-431F-858B-BF327B42EF4C","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/ED97838C-2368-431F-858B-BF327B42EF4C/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"117876","source_record_sha256":"da70fba14b8d88a4e1c2a313862d333e7bd13e13834e891190509d7e070cc93d","source_url":"https://biology.stackexchange.com/questions/117876/primer-design-for-an-isoform","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Primer design for an isoform\nI am trying to design a primer for leptin receptor isoform (short form). The region that differentiates it from the long form is just after exon 18. Every other sequence before then are completely similar. I have tried primer BLAST on NCBI, but the region the primer binds is the region that is similar to both isoform. My question is how to I design a primer specific to that region post 18 axon. The bp length is not more than 15. NB: The species is bos Taurus","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":117877,"score":1}],"split":"test"}
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The type and extent of injury depends entirely on the nature of contact.","answer_url":"https://biology.stackexchange.com/a/117888","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2025-09-05T19:19:29+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:16.948131+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/46a41fae37d5c2c243f9abcbf6829a0045f46a51c624fbba2b897c320cdcba71_0.json","raw_sha256":"e039e310d0106dc61f992ee05bbb0b0b57ded1c5092f97df2c52989edd5eaf68","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/118153;118142;118137;118126;118122;118117;118113;118102;118099;118097;118094;118081;118076;118072;118069;118065;118059;118056;118043;118039;118036;118030;118029;118025;118022;118018;117994;117992;117990;117987;117983;117981;117975;117971;117956;117953;117951;117945;117943;117941;117934;117926;117924;117920;117916;117914;117907;117892;117889;117887;117883;117876;117872;117867;117861;117860;117856;117855;117850;117849;117844;117840;117833;117821;117819;117817;117815;117814;117805;117794;117782;117774;117771;117767;117766;117761;117759;117756;117747;117732;117726;117724;117709;117701;117694;117693;117681;117680;117677;117671;117668;117664;117662;117659;117651;117641;117632;117624;117623;117607/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; 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But what if the current does not flow through the heart? For example, we can place two electrodes at the palm and the back of one hand. Even if the hand sustains a lethal amount of current, there will be little current flowing through the heart. So what kinds of injuries will it cause?</p>\n","text":"Electric shocks can be fatal because a large amount of currents flowing through the heart can stop its beating. But what if the current does not flow through the heart? For example, we can place two electrodes at the palm and the back of one hand. Even if the hand sustains a lethal amount of current, there will be little current flowing through the heart. So what kinds of injuries will it cause?"},{"context_id":"117888","html":"<p><a href=\"https://en.m.wikipedia.org/wiki/Electrical_burn\" rel=\"nofollow noreferrer\">Electrical burns</a> are rather common effects of contact with substantial currents. The type and extent of injury depends entirely on the nature of contact.</p>\n","text":"Electrical burns (https://en.m.wikipedia.org/wiki/Electrical_burn) are rather common effects of contact with substantial currents. The type and extent of injury depends entirely on the nature of contact."}],"domain":"biology","external_citations":["https://en.m.wikipedia.org/wiki/Electrical_burn"],"ground_truth_type":"metadata_grounded","group_id":"5ed26b1f75425ab2eaadabb5260a773be543f32fcbc94bba9441bd2ac9450170","hard_case_family":["no_accepted_answer"],"id":"RHM-30fee48e4f362eec48d416f9","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:01.208074+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f1b387b48f36041f506f18fa9796531023c7eae1e796ec622ad56833c02bea98_0.json","raw_sha256":"3f8214c87c0fe16dd016324597332ca392e0ba98600877cc746483ef492ce03d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"哲煜黄","profile_url":"https://biology.stackexchange.com/users/67047/%e5%93%b2%e7%85%9c%e9%bb%84","user_type":"registered"},"created_at":"2025-09-05T18:18:46+00:00","raw_file":"raw/codex_api_v1/a76d8ab07f874a10eafefc315936b171795ddfe3f4ac47f247a19154460d4acc_1790824150220029700_0.json","raw_sha256":"d1e485076b0bfa0aed0ebdace356f1cab7a9d04a86bc0f38c43c8a253e51cebd","revision_guid":"F4ED8FF1-0BBC-480B-AF9C-E90E9AD0C8E6","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F4ED8FF1-0BBC-480B-AF9C-E90E9AD0C8E6/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2025-10-05T20:04:00+00:00","raw_file":"raw/codex_api_v1/a76d8ab07f874a10eafefc315936b171795ddfe3f4ac47f247a19154460d4acc_1790824150220029700_0.json","raw_sha256":"d1e485076b0bfa0aed0ebdace356f1cab7a9d04a86bc0f38c43c8a253e51cebd","revision_guid":"F1F2D16C-28DB-4692-BA4A-94A8932C5620","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/F1F2D16C-28DB-4692-BA4A-94A8932C5620/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"117887","source_record_sha256":"ca154b547c7789a7b1ce4f67ab8b86f85e0a7750114da32813209c272292104b","source_url":"https://biology.stackexchange.com/questions/117887/what-will-happen-if-a-large-amount-of-electric-currents-flows-through-a-small-pa","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What will happen if a large amount of electric currents flows through a small part of human body?\nElectric shocks can be fatal because a large amount of currents flowing through the heart can stop its beating. But what if the current does not flow through the heart? For example, we can place two electrodes at the palm and the back of one hand. Even if the hand sustains a lethal amount of current, there will be little current flowing through the heart. So what kinds of injuries will it cause?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":117888,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Most moulds in nature are actually soft and fluffy as they are not compositey made of cells like us rather they are made of hyphae and mycelium which are rather loosely coiled. <br><br>\nAs to <a href=\"https://en.m.wikipedia.org/wiki/Mold\" rel=\"nofollow noreferrer\">Wikipedia</a> says about this:</p>\n<blockquote>\n<p>The hyphae are generally transparent, so the mycelium appears like very fine, <strong>fluffy</strong> white threads over the surface.</p>\n</blockquote>\n<hr />\n<p>&quot;White fluffy fungus&quot; is a mention here as an example to your fluffy fungus. Here is <a href=\"https://www.bustmold.com/resources/about-mold/types-of-mold/white-mold/#:%7E:text=What%20is%20white%20fuzzy%20mold,of%20indoor%20and%20outdoor%20houseplants.\" rel=\"nofollow noreferrer\">Bustmould website's</a> description of it:</p>\n<blockquote>\n<p>Most of the time, you can identify white mold by examining its colour, texture, and odour. If it is <strong>fluffy</strong>, white, slimy and carries a specific musty odour, it’s likely white mold. Meanwhile, black or olive green discoloration will most likely be black mold.&quot;</p>\n</blockquote>\n<hr />\n<p>Other sources mentioning about this white fluffy fungus:</p>\n<ol>\n<li><a href=\"https://www.icecleaning.co.uk/blog/what-causes-white-fluffy-mould-on-interior-walls\" rel=\"nofollow noreferrer\">https://www.icecleaning.co.uk/blog/what-causes-white-fluffy-mould-on-interior-walls</a>\n<Br></li>\n<li><a href=\"https://www.instructables.com/How-to-Kill-Fluffy-White-Mould-on-Plants/\" rel=\"nofollow noreferrer\">https://www.instructables.com/How-to-Kill-Fluffy-White-Mould-on-Plants/</a></li>\n</ol>\n<hr />\n<p>Species of this white fluffy fungus <em>might</em> include Aspergillus, Penicillium, Cladosporium, and Geotrichum found in homes, and Sclerotinia on plants. <a href=\"https://jenkinsenvironmentalservices.com/what-is-white-mold/#:%7E:text=Mold%20Remediation%20Professionals-,So%20What%20is%20White%20Mold?,a%20fuzzy%20or%20powdery%20texture.\" rel=\"nofollow noreferrer\">Source</a> <Br><br>\n<a href=\"https://en.m.wikipedia.org/wiki/Sclerotinia_sclerotiorum\" rel=\"nofollow noreferrer\"><em>Sclerotinia sclerotiorum</em></a>\n<a href=\"https://i.sstatic.net/f5PLb8t6.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/f5PLb8t6.jpg\" alt=\"Sclerotinia\" /></a></p>\n","answer_id":117900,"answer_text":"Most moulds in nature are actually soft and fluffy as they are not compositey made of cells like us rather they are made of hyphae and mycelium which are rather loosely coiled. \n\n\nAs to Wikipedia (https://en.m.wikipedia.org/wiki/Mold) says about this:\n\n\n\n\n\n\n\nThe hyphae are generally transparent, so the mycelium appears like very fine, fluffy white threads over the surface.\n\n\n\n\n\n\n\n\n\n\n\"White fluffy fungus\" is a mention here as an example to your fluffy fungus. Here is Bustmould website's (https://www.bustmold.com/resources/about-mold/types-of-mold/white-mold/#:%7E:text=What%20is%20white%20fuzzy%20mold,of%20indoor%20and%20outdoor%20houseplants.) description of it:\n\n\n\n\n\n\n\nMost of the time, you can identify white mold by examining its colour, texture, and odour. If it is fluffy, white, slimy and carries a specific musty odour, it’s likely white mold. Meanwhile, black or olive green discoloration will most likely be black mold.\"\n\n\n\n\n\n\n\n\n\n\nOther sources mentioning about this white fluffy fungus:\n\n\n\n\n\nhttps://www.icecleaning.co.uk/blog/what-causes-white-fluffy-mould-on-interior-walls (https://www.icecleaning.co.uk/blog/what-causes-white-fluffy-mould-on-interior-walls)\n\n\n\n\n\n\nhttps://www.instructables.com/How-to-Kill-Fluffy-White-Mould-on-Plants/ (https://www.instructables.com/How-to-Kill-Fluffy-White-Mould-on-Plants/)\n\n\n\n\n\n\n\n\nSpecies of this white fluffy fungus might include Aspergillus, Penicillium, Cladosporium, and Geotrichum found in homes, and Sclerotinia on plants. Source (https://jenkinsenvironmentalservices.com/what-is-white-mold/#:%7E:text=Mold%20Remediation%20Professionals-,So%20What%20is%20White%20Mold?,a%20fuzzy%20or%20powdery%20texture.) \n\n\nSclerotinia sclerotiorum (https://en.m.wikipedia.org/wiki/Sclerotinia_sclerotiorum)\n[image: Sclerotinia; source: https://i.sstatic.net/f5PLb8t6.jpg] (https://i.sstatic.net/f5PLb8t6.jpg)","answer_url":"https://biology.stackexchange.com/a/117900","author":"Shayan","author_url":"https://biology.stackexchange.com/users/114723/shayan","content_license":"CC BY-SA 4.0","created_at":"2025-09-06T15:55:33+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:16.948131+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/46a41fae37d5c2c243f9abcbf6829a0045f46a51c624fbba2b897c320cdcba71_0.json","raw_sha256":"e039e310d0106dc61f992ee05bbb0b0b57ded1c5092f97df2c52989edd5eaf68","source_api":"Stack 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This includes using mould as a material when you want things to be fluffy like blankets and pillows. However, all the mould I know only looks fluffy, but collapses when touched. As I am not a connoisseur of mould, I am thus wondering: <strong>Does mould ever have a fluffy consistency?</strong></p>\n<p>Naturally, a few clarifications or definitions are in order (for the purposes of this question):</p>\n<ul>\n<li><p>By <em>fluffy,</em> I mean an elastic surface of protruding fibres (or similar). Since every material is elastic on some scale, some rough bounds: The mould should not collapse under forces of 0.1 N (roughly the force of a finger tap) or displacements of 5 mm. Instead it should continuously build up a counter-force and it should relax back to roughly its original size when the force is released. (And just to be very clear: I am not looking for a quantitative biomechanical analysis; I just use numbers to specify what I am talking about because they are the best way to do this.)</p>\n</li>\n<li><p>By <em>mould,</em> I mean fungal growths that look fluffy and would colloquially be called <em>mould</em> without further specifiers (as, e.g., in <em>slime mould)</em>.</p>\n</li>\n<li><p>Also, I am only interested in close-to-standard conditions, in particular the mould should not even partially be frozen.</p>\n</li>\n</ul>\n<p>My understanding so far is that moulds primarily consist of hypha that – at least for typical moulds – are not sufficiently long, robust, or interconnected to yield the elasticity on the relevant scales here.</p>\n","text":"I have been reading the fungal-punk novel Mushroom Blues by Adrian Gibson, which features a lot of fungi-based technology. This includes using mould as a material when you want things to be fluffy like blankets and pillows. However, all the mould I know only looks fluffy, but collapses when touched. As I am not a connoisseur of mould, I am thus wondering: Does mould ever have a fluffy consistency?\n\n\n\n\nNaturally, a few clarifications or definitions are in order (for the purposes of this question):\n\n\n\n\n\n\n\nBy fluffy, I mean an elastic surface of protruding fibres (or similar). Since every material is elastic on some scale, some rough bounds: The mould should not collapse under forces of 0.1 N (roughly the force of a finger tap) or displacements of 5 mm. Instead it should continuously build up a counter-force and it should relax back to roughly its original size when the force is released. (And just to be very clear: I am not looking for a quantitative biomechanical analysis; I just use numbers to specify what I am talking about because they are the best way to do this.)\n\n\n\n\n\n\n\n\n\nBy mould, I mean fungal growths that look fluffy and would colloquially be called mould without further specifiers (as, e.g., in slime mould).\n\n\n\n\n\n\n\n\n\nAlso, I am only interested in close-to-standard conditions, in particular the mould should not even partially be frozen.\n\n\n\n\n\n\n\n\nMy understanding so far is that moulds primarily consist of hypha that – at least for typical moulds – are not sufficiently long, robust, or interconnected to yield the elasticity on the relevant scales here."},{"context_id":"117900","html":"<p>Most moulds in nature are actually soft and fluffy as they are not compositey made of cells like us rather they are made of hyphae and mycelium which are rather loosely coiled. <br><br>\nAs to <a href=\"https://en.m.wikipedia.org/wiki/Mold\" rel=\"nofollow noreferrer\">Wikipedia</a> says about this:</p>\n<blockquote>\n<p>The hyphae are generally transparent, so the mycelium appears like very fine, <strong>fluffy</strong> white threads over the surface.</p>\n</blockquote>\n<hr />\n<p>&quot;White fluffy fungus&quot; is a mention here as an example to your fluffy fungus. Here is <a href=\"https://www.bustmold.com/resources/about-mold/types-of-mold/white-mold/#:%7E:text=What%20is%20white%20fuzzy%20mold,of%20indoor%20and%20outdoor%20houseplants.\" rel=\"nofollow noreferrer\">Bustmould website's</a> description of it:</p>\n<blockquote>\n<p>Most of the time, you can identify white mold by examining its colour, texture, and odour. If it is <strong>fluffy</strong>, white, slimy and carries a specific musty odour, it’s likely white mold. Meanwhile, black or olive green discoloration will most likely be black mold.&quot;</p>\n</blockquote>\n<hr />\n<p>Other sources mentioning about this white fluffy fungus:</p>\n<ol>\n<li><a href=\"https://www.icecleaning.co.uk/blog/what-causes-white-fluffy-mould-on-interior-walls\" rel=\"nofollow noreferrer\">https://www.icecleaning.co.uk/blog/what-causes-white-fluffy-mould-on-interior-walls</a>\n<Br></li>\n<li><a href=\"https://www.instructables.com/How-to-Kill-Fluffy-White-Mould-on-Plants/\" rel=\"nofollow noreferrer\">https://www.instructables.com/How-to-Kill-Fluffy-White-Mould-on-Plants/</a></li>\n</ol>\n<hr />\n<p>Species of this white fluffy fungus <em>might</em> include Aspergillus, Penicillium, Cladosporium, and Geotrichum found in homes, and Sclerotinia on plants. <a href=\"https://jenkinsenvironmentalservices.com/what-is-white-mold/#:%7E:text=Mold%20Remediation%20Professionals-,So%20What%20is%20White%20Mold?,a%20fuzzy%20or%20powdery%20texture.\" rel=\"nofollow noreferrer\">Source</a> <Br><br>\n<a href=\"https://en.m.wikipedia.org/wiki/Sclerotinia_sclerotiorum\" rel=\"nofollow noreferrer\"><em>Sclerotinia sclerotiorum</em></a>\n<a href=\"https://i.sstatic.net/f5PLb8t6.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/f5PLb8t6.jpg\" alt=\"Sclerotinia\" /></a></p>\n","text":"Most moulds in nature are actually soft and fluffy as they are not compositey made of cells like us rather they are made of hyphae and mycelium which are rather loosely coiled. \n\n\nAs to Wikipedia (https://en.m.wikipedia.org/wiki/Mold) says about this:\n\n\n\n\n\n\n\nThe hyphae are generally transparent, so the mycelium appears like very fine, fluffy white threads over the surface.\n\n\n\n\n\n\n\n\n\n\n\"White fluffy fungus\" is a mention here as an example to your fluffy fungus. Here is Bustmould website's (https://www.bustmold.com/resources/about-mold/types-of-mold/white-mold/#:%7E:text=What%20is%20white%20fuzzy%20mold,of%20indoor%20and%20outdoor%20houseplants.) description of it:\n\n\n\n\n\n\n\nMost of the time, you can identify white mold by examining its colour, texture, and odour. If it is fluffy, white, slimy and carries a specific musty odour, it’s likely white mold. Meanwhile, black or olive green discoloration will most likely be black mold.\"\n\n\n\n\n\n\n\n\n\n\nOther sources mentioning about this white fluffy fungus:\n\n\n\n\n\nhttps://www.icecleaning.co.uk/blog/what-causes-white-fluffy-mould-on-interior-walls (https://www.icecleaning.co.uk/blog/what-causes-white-fluffy-mould-on-interior-walls)\n\n\n\n\n\n\nhttps://www.instructables.com/How-to-Kill-Fluffy-White-Mould-on-Plants/ (https://www.instructables.com/How-to-Kill-Fluffy-White-Mould-on-Plants/)\n\n\n\n\n\n\n\n\nSpecies of this white fluffy fungus might include Aspergillus, Penicillium, Cladosporium, and Geotrichum found in homes, and Sclerotinia on plants. Source (https://jenkinsenvironmentalservices.com/what-is-white-mold/#:%7E:text=Mold%20Remediation%20Professionals-,So%20What%20is%20White%20Mold?,a%20fuzzy%20or%20powdery%20texture.) \n\n\nSclerotinia sclerotiorum (https://en.m.wikipedia.org/wiki/Sclerotinia_sclerotiorum)\n[image: Sclerotinia; source: https://i.sstatic.net/f5PLb8t6.jpg] (https://i.sstatic.net/f5PLb8t6.jpg)"}],"domain":"biology","external_citations":["https://en.m.wikipedia.org/wiki/Mold","https://en.m.wikipedia.org/wiki/Sclerotinia_sclerotiorum","https://i.sstatic.net/f5PLb8t6.jpg","https://jenkinsenvironmentalservices.com/what-is-white-mold/#:%7E:text=Mold%20Remediation%20Professionals-,So%20What%20is%20White%20Mold?,a%20fuzzy%20or%20powdery%20texture.","https://www.bustmold.com/resources/about-mold/types-of-mold/white-mold/#:%7E:text=What%20is%20white%20fuzzy%20mold,of%20indoor%20and%20outdoor%20houseplants.","https://www.icecleaning.co.uk/blog/what-causes-white-fluffy-mould-on-interior-walls","https://www.instructables.com/How-to-Kill-Fluffy-White-Mould-on-Plants/"],"ground_truth_type":"metadata_grounded","group_id":"8604a3ad437d35717d98db4c33d1fae9f405505e0460f5d705567aa9c60da5c7","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-717613f0409844b89720e849","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:01.208074+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f1b387b48f36041f506f18fa9796531023c7eae1e796ec622ad56833c02bea98_0.json","raw_sha256":"3f8214c87c0fe16dd016324597332ca392e0ba98600877cc746483ef492ce03d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; 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no LLM truth labels"},"query":"Is mould ever fluffy?\nI have been reading the fungal-punk novel Mushroom Blues by Adrian Gibson, which features a lot of fungi-based technology. This includes using mould as a material when you want things to be fluffy like blankets and pillows. However, all the mould I know only looks fluffy, but collapses when touched. As I am not a connoisseur of mould, I am thus wondering: Does mould ever have a fluffy consistency?\n\n\n\n\nNaturally, a few clarifications or definitions are in order (for the purposes of this question):\n\n\n\n\n\n\n\nBy fluffy, I mean an elastic surface of protruding fibres (or similar). Since every material is elastic on some scale, some rough bounds: The mould should not collapse under forces of 0.1 N (roughly the force of a finger tap) or displacements of 5 mm. Instead it should continuously build up a counter-force and it should relax back to roughly its original size when the force is released. (And just to be very clear: I am not looking for a quantitative biomechanical analysis; I just use numbers to specify what I am talking about because they are the best way to do this.)\n\n\n\n\n\n\n\n\n\nBy mould, I mean fungal growths that look fluffy and would colloquially be called mould without further specifiers (as, e.g., in slime mould).\n\n\n\n\n\n\n\n\n\nAlso, I am only interested in close-to-standard conditions, in particular the mould should not even partially be frozen.\n\n\n\n\n\n\n\n\nMy understanding so far is that moulds primarily consist of hypha that – at least for typical moulds – are not sufficiently long, robust, or interconnected to yield the elasticity on the relevant scales here.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":117900,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>It's difficult for this to be a bedbug's moulted exoskeleton (probably what you call &quot;shell&quot;). Bedbugs are typically 4-5 mm long and this is a similar size to a nymph's mould. But the colour doesn't match.\n<a href=\"https://i.sstatic.net/oT2HTVuA.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/oT2HTVuA.jpg\" alt=\"bedbug size\" /></a>\n<a href=\"https://i.sstatic.net/YjmP2wIx.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/YjmP2wIx.jpg\" alt=\"bedbug moulted exoskeleton\" /></a>\nSources:\n<a href=\"https://en.m.wikipedia.org/wiki/Bed_bug\" rel=\"nofollow noreferrer\">https://en.m.wikipedia.org/wiki/Bed_bug</a>\n<a href=\"https://burninbugs.com/2020/10/12/bed-bug-skins/\" rel=\"nofollow noreferrer\">https://burninbugs.com/2020/10/12/bed-bug-skins/</a></p>\n","answer_id":117980,"answer_text":"It's difficult for this to be a bedbug's moulted exoskeleton (probably what you call \"shell\"). Bedbugs are typically 4-5 mm long and this is a similar size to a nymph's mould. But the colour doesn't match.\n[image: bedbug size; source: https://i.sstatic.net/oT2HTVuA.jpg] (https://i.sstatic.net/oT2HTVuA.jpg)\n[image: bedbug moulted exoskeleton; source: https://i.sstatic.net/YjmP2wIx.jpg] (https://i.sstatic.net/YjmP2wIx.jpg)\nSources:\nhttps://en.m.wikipedia.org/wiki/Bed_bug (https://en.m.wikipedia.org/wiki/Bed_bug)\nhttps://burninbugs.com/2020/10/12/bed-bug-skins/ (https://burninbugs.com/2020/10/12/bed-bug-skins/)","answer_url":"https://biology.stackexchange.com/a/117980","author":"Shayan","author_url":"https://biology.stackexchange.com/users/114723/shayan","content_license":"CC BY-SA 4.0","created_at":"2025-09-25T06:07:30+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:16.948131+00:00","license":"CC BY-SA 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BY-SA 4.0","context_id":"117980","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Shayan","profile_url":"https://biology.stackexchange.com/users/114723/shayan","user_type":"registered"},"created_at":"2025-09-25T06:07:30+00:00","raw_file":"raw/codex_api_v1/e6c4101e2e357aa8c5379bd547ec537e2ae9d3a66d32b72c727e9d2ad82690d6_1790824162028580600_0.json","raw_sha256":"cba09186cd183cf1116bbe2f874d16b08a8bc537baa01c33e34f5c3821229cc5","revision_guid":"55A00704-C7FF-46B8-B89C-16F2B65F2150","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/55A00704-C7FF-46B8-B89C-16F2B65F2150/view-source"},{"content_license":"CC BY-SA 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4.0","contributor":{"display_name":"Shayan","profile_url":"https://biology.stackexchange.com/users/114723/shayan","user_type":"registered"},"created_at":"2025-09-28T10:12:19+00:00","raw_file":"raw/codex_api_v1/e6c4101e2e357aa8c5379bd547ec537e2ae9d3a66d32b72c727e9d2ad82690d6_1790824162028580600_0.json","raw_sha256":"cba09186cd183cf1116bbe2f874d16b08a8bc537baa01c33e34f5c3821229cc5","revision_guid":"DBC36D2B-43CC-4E8B-AD66-3969E9D48F32","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DBC36D2B-43CC-4E8B-AD66-3969E9D48F32/view-source"}],"url":"https://biology.stackexchange.com/a/117980"}],"contexts":[{"context_id":"question","html":"<p>I found this on the carpet, with other fragments like this next to it.</p>\n<p>I live in Poland, Europe. The shell is approximately 2-3 mm.</p>\n<p><a href=\"https://i.sstatic.net/1gMZJ63L.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/1gMZJ63L.png\" alt=\"enter image description here\" /></a></p>\n","text":"I found this on the carpet, with other fragments like this next to it.\n\n\n\n\nI live in Poland, Europe. The shell is approximately 2-3 mm.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/1gMZJ63L.png] (https://i.sstatic.net/1gMZJ63L.png)"},{"context_id":"117980","html":"<p>It's difficult for this to be a bedbug's moulted exoskeleton (probably what you call &quot;shell&quot;). Bedbugs are typically 4-5 mm long and this is a similar size to a nymph's mould. But the colour doesn't match.\n<a href=\"https://i.sstatic.net/oT2HTVuA.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/oT2HTVuA.jpg\" alt=\"bedbug size\" /></a>\n<a href=\"https://i.sstatic.net/YjmP2wIx.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/YjmP2wIx.jpg\" alt=\"bedbug moulted exoskeleton\" /></a>\nSources:\n<a href=\"https://en.m.wikipedia.org/wiki/Bed_bug\" rel=\"nofollow noreferrer\">https://en.m.wikipedia.org/wiki/Bed_bug</a>\n<a href=\"https://burninbugs.com/2020/10/12/bed-bug-skins/\" rel=\"nofollow noreferrer\">https://burninbugs.com/2020/10/12/bed-bug-skins/</a></p>\n","text":"It's difficult for this to be a bedbug's moulted exoskeleton (probably what you call \"shell\"). Bedbugs are typically 4-5 mm long and this is a similar size to a nymph's mould. But the colour doesn't match.\n[image: bedbug size; source: https://i.sstatic.net/oT2HTVuA.jpg] (https://i.sstatic.net/oT2HTVuA.jpg)\n[image: bedbug moulted exoskeleton; source: https://i.sstatic.net/YjmP2wIx.jpg] (https://i.sstatic.net/YjmP2wIx.jpg)\nSources:\nhttps://en.m.wikipedia.org/wiki/Bed_bug (https://en.m.wikipedia.org/wiki/Bed_bug)\nhttps://burninbugs.com/2020/10/12/bed-bug-skins/ (https://burninbugs.com/2020/10/12/bed-bug-skins/)"}],"domain":"biology","external_citations":["https://burninbugs.com/2020/10/12/bed-bug-skins/","https://en.m.wikipedia.org/wiki/Bed_bug","https://i.sstatic.net/1gMZJ63L.png","https://i.sstatic.net/YjmP2wIx.jpg","https://i.sstatic.net/oT2HTVuA.jpg"],"ground_truth_type":"metadata_grounded","group_id":"cab231031202484a6f6d1c09a6861bbb6db5d4a9cf99fd547576ab05382212cb","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-ae00d6490e910477c4f9d8eb","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:01.208074+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f1b387b48f36041f506f18fa9796531023c7eae1e796ec622ad56833c02bea98_0.json","raw_sha256":"3f8214c87c0fe16dd016324597332ca392e0ba98600877cc746483ef492ce03d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; 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no LLM truth labels"},"query":"is this a bedbug's shell?\nI found this on the carpet, with other fragments like this next to it.\n\n\n\n\nI live in Poland, Europe. The shell is approximately 2-3 mm.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/1gMZJ63L.png] (https://i.sstatic.net/1gMZJ63L.png)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":117980,"score":0}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p><strong>The plasma proteins ARE dissolved in blood plasma—you're correct about that. However, they don't participate in equilibration across the capillary wall because they cannot freely cross the capillary membrane due to their large molecular size.</strong></p>\n<p>Capillary endothelium acts as a size-selective barrier. Water and small ions (like Na⁺, K⁺, Cl⁻) cross freely, but plasma proteins (albumin at 66 kDa, globulins at 150+ kDa) are too large to pass through capillary pores <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC2878124/\" rel=\"nofollow noreferrer\"></a><a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC2482911/\" rel=\"nofollow noreferrer\"></a>. The reflection coefficient for albumin is approximately 0.9-0.95, meaning 90-95% of protein molecules are retained in plasma <a href=\"https://cvphysiology.com/microcirculation/m012\" rel=\"nofollow noreferrer\"></a>.[1][2][3]</p>\n<p>Because proteins cannot cross, they remain confined to the vascular compartment and don't equilibrate with interstitial fluid <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC2878124/\" rel=\"nofollow noreferrer\"></a>. When measuring ion concentrations relevant to cells bathed in interstitial fluid, you need concentrations expressed per liter of water <strong>that can actually reach those cells</strong>—the protein-free plasma water <a href=\"https://philippelefevre.com/downloads/gibbs_donnan/whole-body-gibbs-donnan.pdf\" rel=\"nofollow noreferrer\"></a><a href=\"https://pubmed.ncbi.nlm.nih.gov/3414807/\" rel=\"nofollow noreferrer\"></a>.[4][5][1]</p>\n<p><strong>Addressing Your Chemistry Question</strong></p>\n<p>Yes, your reasoning is correct. If solute B cannot permeate the membrane but solute A can, you should calculate equilibrium concentrations of A using only the volume available for equilibration—essentially the solvent volume minus the space occupied by B <a href=\"https://philippelefevre.com/downloads/gibbs_donnan/whole-body-gibbs-donnan.pdf\" rel=\"nofollow noreferrer\"></a>.[4]</p>\n<p>Plasma proteins do maintain colloid osmotic pressure, as you noted, but this is separate from ion equilibration <a href=\"https://cvphysiology.com/microcirculation/m012\" rel=\"nofollow noreferrer\"></a>. The proteins create osmotic gradients and influence ion distribution via the Gibbs-Donnan effect (since proteins carry negative charges), but they themselves don't cross the capillary barrier and therefore don't participate in the equilibrium between plasma and interstitial fluid <a href=\"https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/gibbs-donnan-effect\" rel=\"nofollow noreferrer\"></a><a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC3118367/\" rel=\"nofollow noreferrer\"></a><a href=\"https://pubmed.ncbi.nlm.nih.gov/3414807/\" rel=\"nofollow noreferrer\"></a>.[3][5][6][7]</p>\n<p><strong>Permeability determines participation in equilibrium. Dissolved status doesn't matter if the molecule is physically excluded from crossing the membrane.</strong></p>\n<p><a href=\"https://cvphysiology.com/microcirculation/m012\" rel=\"nofollow noreferrer\">1</a>\n<a href=\"https://pubmed.ncbi.nlm.nih.gov/842368/\" rel=\"nofollow noreferrer\">2</a>\n<a href=\"https://www.jci.org/articles/view/100445/version/1/pdf/render.pdf\" rel=\"nofollow noreferrer\">3</a>\n<a href=\"https://www.ncbi.nlm.nih.gov/books/NBK541059/\" rel=\"nofollow noreferrer\">4</a>\n<a href=\"https://www.sciencedirect.com/topics/immunology-and-microbiology/capillary-wall\" rel=\"nofollow noreferrer\">5</a>\n<a href=\"https://en.wikipedia.org/wiki/Extracellular_fluid\" rel=\"nofollow noreferrer\">6</a>\n<a href=\"https://en.wikipedia.org/wiki/Oncotic_pressure\" rel=\"nofollow noreferrer\">7</a></p>\n","answer_id":118067,"answer_text":"The plasma proteins ARE dissolved in blood plasma—you're correct about that. However, they don't participate in equilibration across the capillary wall because they cannot freely cross the capillary membrane due to their large molecular size.\n\n\n\n\nCapillary endothelium acts as a size-selective barrier. Water and small ions (like Na⁺, K⁺, Cl⁻) cross freely, but plasma proteins (albumin at 66 kDa, globulins at 150+ kDa) are too large to pass through capillary pores  (https://pmc.ncbi.nlm.nih.gov/articles/PMC2878124/) (https://pmc.ncbi.nlm.nih.gov/articles/PMC2482911/). The reflection coefficient for albumin is approximately 0.9-0.95, meaning 90-95% of protein molecules are retained in plasma  (https://cvphysiology.com/microcirculation/m012).[1][2][3]\n\n\n\n\nBecause proteins cannot cross, they remain confined to the vascular compartment and don't equilibrate with interstitial fluid  (https://pmc.ncbi.nlm.nih.gov/articles/PMC2878124/). When measuring ion concentrations relevant to cells bathed in interstitial fluid, you need concentrations expressed per liter of water that can actually reach those cells—the protein-free plasma water  (https://philippelefevre.com/downloads/gibbs_donnan/whole-body-gibbs-donnan.pdf) (https://pubmed.ncbi.nlm.nih.gov/3414807/).[4][5][1]\n\n\n\n\nAddressing Your Chemistry Question\n\n\n\n\nYes, your reasoning is correct. If solute B cannot permeate the membrane but solute A can, you should calculate equilibrium concentrations of A using only the volume available for equilibration—essentially the solvent volume minus the space occupied by B  (https://philippelefevre.com/downloads/gibbs_donnan/whole-body-gibbs-donnan.pdf).[4]\n\n\n\n\nPlasma proteins do maintain colloid osmotic pressure, as you noted, but this is separate from ion equilibration  (https://cvphysiology.com/microcirculation/m012). The proteins create osmotic gradients and influence ion distribution via the Gibbs-Donnan effect (since proteins carry negative charges), but they themselves don't cross the capillary barrier and therefore don't participate in the equilibrium between plasma and interstitial fluid  (https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/gibbs-donnan-effect) (https://pmc.ncbi.nlm.nih.gov/articles/PMC3118367/) (https://pubmed.ncbi.nlm.nih.gov/3414807/).[3][5][6][7]\n\n\n\n\nPermeability determines participation in equilibrium. Dissolved status doesn't matter if the molecule is physically excluded from crossing the membrane.\n\n\n\n\n1 (https://cvphysiology.com/microcirculation/m012)\n2 (https://pubmed.ncbi.nlm.nih.gov/842368/)\n3 (https://www.jci.org/articles/view/100445/version/1/pdf/render.pdf)\n4 (https://www.ncbi.nlm.nih.gov/books/NBK541059/)\n5 (https://www.sciencedirect.com/topics/immunology-and-microbiology/capillary-wall)\n6 (https://en.wikipedia.org/wiki/Extracellular_fluid)\n7 (https://en.wikipedia.org/wiki/Oncotic_pressure)","answer_url":"https://biology.stackexchange.com/a/118067","author":"Ansh Tandon","author_url":"https://biology.stackexchange.com/users/68056/ansh-tandon","content_license":"CC BY-SA 4.0","created_at":"2025-11-02T01:30:13+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:16.948131+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/46a41fae37d5c2c243f9abcbf6829a0045f46a51c624fbba2b897c320cdcba71_0.json","raw_sha256":"e039e310d0106dc61f992ee05bbb0b0b57ded1c5092f97df2c52989edd5eaf68","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/118153;118142;118137;118126;118122;118117;118113;118102;118099;118097;118094;118081;118076;118072;118069;118065;118059;118056;118043;118039;118036;118030;118029;118025;118022;118018;117994;117992;117990;117987;117983;117981;117975;117971;117956;117953;117951;117945;117943;117941;117934;117926;117924;117920;117916;117914;117907;117892;117889;117887;117883;117876;117872;117867;117861;117860;117856;117855;117850;117849;117844;117840;117833;117821;117819;117817;117815;117814;117805;117794;117782;117774;117771;117767;117766;117761;117759;117756;117747;117732;117726;117724;117709;117701;117694;117693;117681;117680;117677;117671;117668;117664;117662;117659;117651;117641;117632;117624;117623;117607/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":118065,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Ansh Tandon","profile_url":"https://biology.stackexchange.com/users/68056/ansh-tandon","user_type":"registered"},"created_at":"2025-11-02T01:30:13+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"A3853A0A-E2FF-470E-A979-F027171C1B67","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A3853A0A-E2FF-470E-A979-F027171C1B67/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Aurelius","author_url":"https://biology.stackexchange.com/users/68545/aurelius","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Aurelius","profile_url":"https://biology.stackexchange.com/users/68545/aurelius","user_type":"registered"},"created_at":"2025-11-01T00:37:17+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"3E67EB0C-EAB4-4F75-B17E-027DD30419F3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3E67EB0C-EAB4-4F75-B17E-027DD30419F3/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Aurelius","profile_url":"https://biology.stackexchange.com/users/68545/aurelius","user_type":"registered"},"created_at":"2025-11-01T01:31:13+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"FAE57945-9D8F-437E-B5B7-97BD6091C76F","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FAE57945-9D8F-437E-B5B7-97BD6091C76F/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Aurelius","profile_url":"https://biology.stackexchange.com/users/68545/aurelius","user_type":"registered"},"created_at":"2025-11-01T08:40:47+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"7696BD47-478C-4402-B5D0-E587272FD009","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7696BD47-478C-4402-B5D0-E587272FD009/view-source"}],"url":"https://biology.stackexchange.com/questions/118065/what-is-the-contribution-of-plasma-proteins-to-osmosis-if-semi-permeable-cell-me"},{"author":"Ansh Tandon","author_url":"https://biology.stackexchange.com/users/68056/ansh-tandon","content_license":"CC BY-SA 4.0","context_id":"118067","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Ansh Tandon","profile_url":"https://biology.stackexchange.com/users/68056/ansh-tandon","user_type":"registered"},"created_at":"2025-11-02T01:30:13+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"A3853A0A-E2FF-470E-A979-F027171C1B67","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A3853A0A-E2FF-470E-A979-F027171C1B67/view-source"}],"url":"https://biology.stackexchange.com/a/118067"}],"contexts":[{"context_id":"question","html":"<blockquote>\n<p>Clinical laboratories report the plasma composition of ions (e.g., Na, K&quot;) in units of milliequivalents (meq) per liter of plasma solution. However, for cells bathed by interstitial fluid, a more meaningful unit would be milliequivalents per liter of protein-free plasma solution because it is only the protein-free portion of plasma-and not the proteins dissolved in this water that can equilibrate across capillary wall.</p>\n</blockquote>\n<p>From Medical Physiology book.</p>\n<p><em><strong>What  I don't understand is why plasma with proteins doesn't take part in equilibrium? Why only protein free plasma does so??</strong></em></p>\n<p>My guess was that plasma proteins are floating in the blood plasma somewhat like a suspension/pebbles in water so don't cobtribute to concentration.<br> But I remember reading that plasma proteins are dissolved in blood plasma. <br><strong>Also plasma proteins maintain the blood colloidal osmotic pressure so I don't know why the book says it doesn't participate in the equilibrium?</strong></p>\n<p>So if there is a higher conc. of both solutes A and B on one side of semi permeable membrane and membrane only allows solute A and solvent to pass through, will B have no effect on movement/equilibrium we should use volume of solvent minus B for calculation?- <em>This chemistry doesn't seem right</em></p>\n","text":"Clinical laboratories report the plasma composition of ions (e.g., Na, K\") in units of milliequivalents (meq) per liter of plasma solution. However, for cells bathed by interstitial fluid, a more meaningful unit would be milliequivalents per liter of protein-free plasma solution because it is only the protein-free portion of plasma-and not the proteins dissolved in this water that can equilibrate across capillary wall.\n\n\n\n\n\n\n\nFrom Medical Physiology book.\n\n\n\n\nWhat  I don't understand is why plasma with proteins doesn't take part in equilibrium? Why only protein free plasma does so??\n\n\n\n\nMy guess was that plasma proteins are floating in the blood plasma somewhat like a suspension/pebbles in water so don't cobtribute to concentration.\n But I remember reading that plasma proteins are dissolved in blood plasma. \nAlso plasma proteins maintain the blood colloidal osmotic pressure so I don't know why the book says it doesn't participate in the equilibrium?\n\n\n\n\nSo if there is a higher conc. of both solutes A and B on one side of semi permeable membrane and membrane only allows solute A and solvent to pass through, will B have no effect on movement/equilibrium we should use volume of solvent minus B for calculation?- This chemistry doesn't seem right"},{"context_id":"118067","html":"<p><strong>The plasma proteins ARE dissolved in blood plasma—you're correct about that. However, they don't participate in equilibration across the capillary wall because they cannot freely cross the capillary membrane due to their large molecular size.</strong></p>\n<p>Capillary endothelium acts as a size-selective barrier. Water and small ions (like Na⁺, K⁺, Cl⁻) cross freely, but plasma proteins (albumin at 66 kDa, globulins at 150+ kDa) are too large to pass through capillary pores <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC2878124/\" rel=\"nofollow noreferrer\"></a><a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC2482911/\" rel=\"nofollow noreferrer\"></a>. The reflection coefficient for albumin is approximately 0.9-0.95, meaning 90-95% of protein molecules are retained in plasma <a href=\"https://cvphysiology.com/microcirculation/m012\" rel=\"nofollow noreferrer\"></a>.[1][2][3]</p>\n<p>Because proteins cannot cross, they remain confined to the vascular compartment and don't equilibrate with interstitial fluid <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC2878124/\" rel=\"nofollow noreferrer\"></a>. When measuring ion concentrations relevant to cells bathed in interstitial fluid, you need concentrations expressed per liter of water <strong>that can actually reach those cells</strong>—the protein-free plasma water <a href=\"https://philippelefevre.com/downloads/gibbs_donnan/whole-body-gibbs-donnan.pdf\" rel=\"nofollow noreferrer\"></a><a href=\"https://pubmed.ncbi.nlm.nih.gov/3414807/\" rel=\"nofollow noreferrer\"></a>.[4][5][1]</p>\n<p><strong>Addressing Your Chemistry Question</strong></p>\n<p>Yes, your reasoning is correct. If solute B cannot permeate the membrane but solute A can, you should calculate equilibrium concentrations of A using only the volume available for equilibration—essentially the solvent volume minus the space occupied by B <a href=\"https://philippelefevre.com/downloads/gibbs_donnan/whole-body-gibbs-donnan.pdf\" rel=\"nofollow noreferrer\"></a>.[4]</p>\n<p>Plasma proteins do maintain colloid osmotic pressure, as you noted, but this is separate from ion equilibration <a href=\"https://cvphysiology.com/microcirculation/m012\" rel=\"nofollow noreferrer\"></a>. The proteins create osmotic gradients and influence ion distribution via the Gibbs-Donnan effect (since proteins carry negative charges), but they themselves don't cross the capillary barrier and therefore don't participate in the equilibrium between plasma and interstitial fluid <a href=\"https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/gibbs-donnan-effect\" rel=\"nofollow noreferrer\"></a><a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC3118367/\" rel=\"nofollow noreferrer\"></a><a href=\"https://pubmed.ncbi.nlm.nih.gov/3414807/\" rel=\"nofollow noreferrer\"></a>.[3][5][6][7]</p>\n<p><strong>Permeability determines participation in equilibrium. Dissolved status doesn't matter if the molecule is physically excluded from crossing the membrane.</strong></p>\n<p><a href=\"https://cvphysiology.com/microcirculation/m012\" rel=\"nofollow noreferrer\">1</a>\n<a href=\"https://pubmed.ncbi.nlm.nih.gov/842368/\" rel=\"nofollow noreferrer\">2</a>\n<a href=\"https://www.jci.org/articles/view/100445/version/1/pdf/render.pdf\" rel=\"nofollow noreferrer\">3</a>\n<a href=\"https://www.ncbi.nlm.nih.gov/books/NBK541059/\" rel=\"nofollow noreferrer\">4</a>\n<a href=\"https://www.sciencedirect.com/topics/immunology-and-microbiology/capillary-wall\" rel=\"nofollow noreferrer\">5</a>\n<a href=\"https://en.wikipedia.org/wiki/Extracellular_fluid\" rel=\"nofollow noreferrer\">6</a>\n<a href=\"https://en.wikipedia.org/wiki/Oncotic_pressure\" rel=\"nofollow noreferrer\">7</a></p>\n","text":"The plasma proteins ARE dissolved in blood plasma—you're correct about that. However, they don't participate in equilibration across the capillary wall because they cannot freely cross the capillary membrane due to their large molecular size.\n\n\n\n\nCapillary endothelium acts as a size-selective barrier. Water and small ions (like Na⁺, K⁺, Cl⁻) cross freely, but plasma proteins (albumin at 66 kDa, globulins at 150+ kDa) are too large to pass through capillary pores  (https://pmc.ncbi.nlm.nih.gov/articles/PMC2878124/) (https://pmc.ncbi.nlm.nih.gov/articles/PMC2482911/). The reflection coefficient for albumin is approximately 0.9-0.95, meaning 90-95% of protein molecules are retained in plasma  (https://cvphysiology.com/microcirculation/m012).[1][2][3]\n\n\n\n\nBecause proteins cannot cross, they remain confined to the vascular compartment and don't equilibrate with interstitial fluid  (https://pmc.ncbi.nlm.nih.gov/articles/PMC2878124/). When measuring ion concentrations relevant to cells bathed in interstitial fluid, you need concentrations expressed per liter of water that can actually reach those cells—the protein-free plasma water  (https://philippelefevre.com/downloads/gibbs_donnan/whole-body-gibbs-donnan.pdf) (https://pubmed.ncbi.nlm.nih.gov/3414807/).[4][5][1]\n\n\n\n\nAddressing Your Chemistry Question\n\n\n\n\nYes, your reasoning is correct. If solute B cannot permeate the membrane but solute A can, you should calculate equilibrium concentrations of A using only the volume available for equilibration—essentially the solvent volume minus the space occupied by B  (https://philippelefevre.com/downloads/gibbs_donnan/whole-body-gibbs-donnan.pdf).[4]\n\n\n\n\nPlasma proteins do maintain colloid osmotic pressure, as you noted, but this is separate from ion equilibration  (https://cvphysiology.com/microcirculation/m012). The proteins create osmotic gradients and influence ion distribution via the Gibbs-Donnan effect (since proteins carry negative charges), but they themselves don't cross the capillary barrier and therefore don't participate in the equilibrium between plasma and interstitial fluid  (https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/gibbs-donnan-effect) (https://pmc.ncbi.nlm.nih.gov/articles/PMC3118367/) (https://pubmed.ncbi.nlm.nih.gov/3414807/).[3][5][6][7]\n\n\n\n\nPermeability determines participation in equilibrium. Dissolved status doesn't matter if the molecule is physically excluded from crossing the membrane.\n\n\n\n\n1 (https://cvphysiology.com/microcirculation/m012)\n2 (https://pubmed.ncbi.nlm.nih.gov/842368/)\n3 (https://www.jci.org/articles/view/100445/version/1/pdf/render.pdf)\n4 (https://www.ncbi.nlm.nih.gov/books/NBK541059/)\n5 (https://www.sciencedirect.com/topics/immunology-and-microbiology/capillary-wall)\n6 (https://en.wikipedia.org/wiki/Extracellular_fluid)\n7 (https://en.wikipedia.org/wiki/Oncotic_pressure)"}],"domain":"biology","external_citations":["https://cvphysiology.com/microcirculation/m012","https://en.wikipedia.org/wiki/Extracellular_fluid","https://en.wikipedia.org/wiki/Oncotic_pressure","https://philippelefevre.com/downloads/gibbs_donnan/whole-body-gibbs-donnan.pdf","https://pmc.ncbi.nlm.nih.gov/articles/PMC2482911/","https://pmc.ncbi.nlm.nih.gov/articles/PMC2878124/","https://pmc.ncbi.nlm.nih.gov/articles/PMC3118367/","https://pubmed.ncbi.nlm.nih.gov/3414807/","https://pubmed.ncbi.nlm.nih.gov/842368/","https://www.jci.org/articles/view/100445/version/1/pdf/render.pdf","https://www.ncbi.nlm.nih.gov/books/NBK541059/","https://www.sciencedirect.com/topics/immunology-and-microbiology/capillary-wall","https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/gibbs-donnan-effect"],"ground_truth_type":"metadata_grounded","group_id":"c41d9346ecf8b2ef1f8d61090182832c3c183373b338294fe1354d89659eb7f2","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-ea04634d463e9a5698c352df","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:01.208074+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/f1b387b48f36041f506f18fa9796531023c7eae1e796ec622ad56833c02bea98_0.json","raw_sha256":"3f8214c87c0fe16dd016324597332ca392e0ba98600877cc746483ef492ce03d","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Aurelius","profile_url":"https://biology.stackexchange.com/users/68545/aurelius","user_type":"registered"},"created_at":"2025-11-01T00:37:17+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"3E67EB0C-EAB4-4F75-B17E-027DD30419F3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3E67EB0C-EAB4-4F75-B17E-027DD30419F3/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Aurelius","profile_url":"https://biology.stackexchange.com/users/68545/aurelius","user_type":"registered"},"created_at":"2025-11-01T01:31:13+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"FAE57945-9D8F-437E-B5B7-97BD6091C76F","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FAE57945-9D8F-437E-B5B7-97BD6091C76F/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Aurelius","profile_url":"https://biology.stackexchange.com/users/68545/aurelius","user_type":"registered"},"created_at":"2025-11-01T08:40:47+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"7696BD47-478C-4402-B5D0-E587272FD009","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7696BD47-478C-4402-B5D0-E587272FD009/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"118065","source_record_sha256":"609a2c13a32cd568d2be66cd8373591f7879f76c6e18a75d91a3d6714599384c","source_url":"https://biology.stackexchange.com/questions/118065/what-is-the-contribution-of-plasma-proteins-to-osmosis-if-semi-permeable-cell-me","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What is the contribution of plasma proteins to osmosis if semi-permeable/cell membrane is impermeable to it?\nClinical laboratories report the plasma composition of ions (e.g., Na, K\") in units of milliequivalents (meq) per liter of plasma solution. However, for cells bathed by interstitial fluid, a more meaningful unit would be milliequivalents per liter of protein-free plasma solution because it is only the protein-free portion of plasma-and not the proteins dissolved in this water that can equilibrate across capillary wall.\n\n\n\n\n\n\n\nFrom Medical Physiology book.\n\n\n\n\nWhat  I don't understand is why plasma with proteins doesn't take part in equilibrium? Why only protein free plasma does so??\n\n\n\n\nMy guess was that plasma proteins are floating in the blood plasma somewhat like a suspension/pebbles in water so don't cobtribute to concentration.\n But I remember reading that plasma proteins are dissolved in blood plasma. \nAlso plasma proteins maintain the blood colloidal osmotic pressure so I don't know why the book says it doesn't participate in the equilibrium?\n\n\n\n\nSo if there is a higher conc. of both solutes A and B on one side of semi permeable membrane and membrane only allows solute A and solvent to pass through, will B have no effect on movement/equilibrium we should use volume of solvent minus B for calculation?- This chemistry doesn't seem right","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":118067,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":119196,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<blockquote>\n<p>unless enzymes have a common evolution origin</p>\n</blockquote>\n<p>Many enzymes do in fact have a common origin.</p>\n<p>For example, from: <a href=\"https://link.springer.com/article/10.1007/BF00762534\" rel=\"nofollow noreferrer\">Kibak, H., Taiz, L., Starke, T., Bernasconi, P., &amp; Gogarten, J. P. (1992). Evolution of structure and function of V-ATPases. Journal of bioenergetics and biomembranes, 24(4), 415-424.</a></p>\n<blockquote>\n<p>Proton pumping ATPases/ATPsynthases are found in all groups of present-day organisms. The structure of V- and F-type ATPases/ATP synthases is very conserved throughout evolution. Sequence analysis shows that the V- and F-type ATPases evolved from the same enzyme already present in the last common ancestor of all known extant life forms.</p>\n</blockquote>\n<p>Further, the <em>ATP-consuming</em> and <em>ATP-synthesizing</em> enzymes from this class all likely evolved from the same protein: <a href=\"https://www.sciencedirect.com/science/article/pii/S0014579304010841\" rel=\"nofollow noreferrer\">Cross, R. L., &amp; Müller, V. (2004). The evolution of A-, F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+/ATP coupling ratio. FEBS letters, 576(1-2), 1-4.</a></p>\n<p>Another category are the <a href=\"https://www.tcdb.org/search/result.php?tc=3.A.3\" rel=\"nofollow noreferrer\">P-type ATPases</a>, which are all related.</p>\n<p>Protein kinases are grouped into &quot;tyrosine kinases&quot; and &quot;serine/threonine kinases&quot;, but <a href=\"https://www.nature.com/articles/s41467-024-50812-0\" rel=\"nofollow noreferrer\">they are also actually all related</a>: serine/threonine kinases are much older, with tyrosine kinases evolving from them more recently and creating their own branch.</p>\n<p>Mutations are random, but selection is not, and biology frequently re-uses the things it has to work with. For example, you'll find signaling molecules in a multicellular organism that are exactly the same molecule yet do completely different functions in different tissues.</p>\n<p>ATP is an available, energetic molecule, so it's sensible that new functionality will be based on a molecule that's already present, rather than evolving a separate energy source which would need to also evolve alongside enzymes to synthesize that energy source. Other NTPs may be candidates and <em>are</em> used as energy sources in some reactions, but there is a lot of inertia towards using ATP. See also: <a href=\"https://biology.stackexchange.com/questions/11286/why-is-atp-the-preferred-choice-for-energy-carriers\">Why is ATP the preferred choice for energy carriers?</a></p>\n","answer_id":119196,"answer_text":"unless enzymes have a common evolution origin\n\n\n\n\n\n\n\nMany enzymes do in fact have a common origin.\n\n\n\n\nFor example, from: Kibak, H., Taiz, L., Starke, T., Bernasconi, P., & Gogarten, J. P. (1992). Evolution of structure and function of V-ATPases. Journal of bioenergetics and biomembranes, 24(4), 415-424. (https://link.springer.com/article/10.1007/BF00762534)\n\n\n\n\n\n\n\nProton pumping ATPases/ATPsynthases are found in all groups of present-day organisms. The structure of V- and F-type ATPases/ATP synthases is very conserved throughout evolution. Sequence analysis shows that the V- and F-type ATPases evolved from the same enzyme already present in the last common ancestor of all known extant life forms.\n\n\n\n\n\n\n\nFurther, the ATP-consuming and ATP-synthesizing enzymes from this class all likely evolved from the same protein: Cross, R. L., & Müller, V. (2004). The evolution of A-, F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+/ATP coupling ratio. FEBS letters, 576(1-2), 1-4. (https://www.sciencedirect.com/science/article/pii/S0014579304010841)\n\n\n\n\nAnother category are the P-type ATPases (https://www.tcdb.org/search/result.php?tc=3.A.3), which are all related.\n\n\n\n\nProtein kinases are grouped into \"tyrosine kinases\" and \"serine/threonine kinases\", but they are also actually all related (https://www.nature.com/articles/s41467-024-50812-0): serine/threonine kinases are much older, with tyrosine kinases evolving from them more recently and creating their own branch.\n\n\n\n\nMutations are random, but selection is not, and biology frequently re-uses the things it has to work with. For example, you'll find signaling molecules in a multicellular organism that are exactly the same molecule yet do completely different functions in different tissues.\n\n\n\n\nATP is an available, energetic molecule, so it's sensible that new functionality will be based on a molecule that's already present, rather than evolving a separate energy source which would need to also evolve alongside enzymes to synthesize that energy source. Other NTPs may be candidates and are used as energy sources in some reactions, but there is a lot of inertia towards using ATP. See also: Why is ATP the preferred choice for energy carriers? (https://biology.stackexchange.com/questions/11286/why-is-atp-the-preferred-choice-for-energy-carriers)","answer_url":"https://biology.stackexchange.com/a/119196","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2025-12-23T16:38:27+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:14.203473+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/bc31fe4e1e84f43ae95f846a38e90acc9e22beb08e25c5d964f94cb8f2d4bfcb_0.json","raw_sha256":"d7cf716376a9764909548809f10c8760f535f0ca4093eb29d910aae44edf1878","source_api":"Stack Exchange API 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Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2025-12-23T16:38:27+00:00","raw_file":"raw/codex_api_v1/758108496d7e56a3cf6614dffa5104a8870c129dcf518abbe860f55a089c6a12_1790824171594894000_0.json","raw_sha256":"5e5d792a6c484fda48193064d730da32774df13fc12222582feb4605d4472664","revision_guid":"526C9DDD-20A2-4E73-98C9-A584F6FD8F9B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/526C9DDD-20A2-4E73-98C9-A584F6FD8F9B/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2025-12-23T16:50:17+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"81F9EBC1-8664-49D3-B307-EDA2A5D0F89A","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/81F9EBC1-8664-49D3-B307-EDA2A5D0F89A/view-source"}],"url":"https://biology.stackexchange.com/a/119196"}],"contexts":[{"context_id":"question","html":"<p>Other than a few processes like protein translation, most energy consuming processes use the energy from ATP. I just don’t quite understand because unless enzymes have a common evolution origin (which is extremely unlikely considering the sheer diversity of enzymes), enzymes using other nucleoside triphosphates (NTPs) should  be equally likely. The reason is that other NTPs carry just as much energy as ATP, and because of NDPK, the chemical potential of the 4 NTPs should be similar. So why is ATP favored over other NTPs?</p>\n","text":"Other than a few processes like protein translation, most energy consuming processes use the energy from ATP. I just don’t quite understand because unless enzymes have a common evolution origin (which is extremely unlikely considering the sheer diversity of enzymes), enzymes using other nucleoside triphosphates (NTPs) should  be equally likely. The reason is that other NTPs carry just as much energy as ATP, and because of NDPK, the chemical potential of the 4 NTPs should be similar. So why is ATP favored over other NTPs?"},{"context_id":"119196","html":"<blockquote>\n<p>unless enzymes have a common evolution origin</p>\n</blockquote>\n<p>Many enzymes do in fact have a common origin.</p>\n<p>For example, from: <a href=\"https://link.springer.com/article/10.1007/BF00762534\" rel=\"nofollow noreferrer\">Kibak, H., Taiz, L., Starke, T., Bernasconi, P., &amp; Gogarten, J. P. (1992). Evolution of structure and function of V-ATPases. Journal of bioenergetics and biomembranes, 24(4), 415-424.</a></p>\n<blockquote>\n<p>Proton pumping ATPases/ATPsynthases are found in all groups of present-day organisms. The structure of V- and F-type ATPases/ATP synthases is very conserved throughout evolution. Sequence analysis shows that the V- and F-type ATPases evolved from the same enzyme already present in the last common ancestor of all known extant life forms.</p>\n</blockquote>\n<p>Further, the <em>ATP-consuming</em> and <em>ATP-synthesizing</em> enzymes from this class all likely evolved from the same protein: <a href=\"https://www.sciencedirect.com/science/article/pii/S0014579304010841\" rel=\"nofollow noreferrer\">Cross, R. L., &amp; Müller, V. (2004). The evolution of A-, F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+/ATP coupling ratio. FEBS letters, 576(1-2), 1-4.</a></p>\n<p>Another category are the <a href=\"https://www.tcdb.org/search/result.php?tc=3.A.3\" rel=\"nofollow noreferrer\">P-type ATPases</a>, which are all related.</p>\n<p>Protein kinases are grouped into &quot;tyrosine kinases&quot; and &quot;serine/threonine kinases&quot;, but <a href=\"https://www.nature.com/articles/s41467-024-50812-0\" rel=\"nofollow noreferrer\">they are also actually all related</a>: serine/threonine kinases are much older, with tyrosine kinases evolving from them more recently and creating their own branch.</p>\n<p>Mutations are random, but selection is not, and biology frequently re-uses the things it has to work with. For example, you'll find signaling molecules in a multicellular organism that are exactly the same molecule yet do completely different functions in different tissues.</p>\n<p>ATP is an available, energetic molecule, so it's sensible that new functionality will be based on a molecule that's already present, rather than evolving a separate energy source which would need to also evolve alongside enzymes to synthesize that energy source. Other NTPs may be candidates and <em>are</em> used as energy sources in some reactions, but there is a lot of inertia towards using ATP. See also: <a href=\"https://biology.stackexchange.com/questions/11286/why-is-atp-the-preferred-choice-for-energy-carriers\">Why is ATP the preferred choice for energy carriers?</a></p>\n","text":"unless enzymes have a common evolution origin\n\n\n\n\n\n\n\nMany enzymes do in fact have a common origin.\n\n\n\n\nFor example, from: Kibak, H., Taiz, L., Starke, T., Bernasconi, P., & Gogarten, J. P. (1992). Evolution of structure and function of V-ATPases. Journal of bioenergetics and biomembranes, 24(4), 415-424. (https://link.springer.com/article/10.1007/BF00762534)\n\n\n\n\n\n\n\nProton pumping ATPases/ATPsynthases are found in all groups of present-day organisms. The structure of V- and F-type ATPases/ATP synthases is very conserved throughout evolution. Sequence analysis shows that the V- and F-type ATPases evolved from the same enzyme already present in the last common ancestor of all known extant life forms.\n\n\n\n\n\n\n\nFurther, the ATP-consuming and ATP-synthesizing enzymes from this class all likely evolved from the same protein: Cross, R. L., & Müller, V. (2004). The evolution of A-, F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+/ATP coupling ratio. FEBS letters, 576(1-2), 1-4. (https://www.sciencedirect.com/science/article/pii/S0014579304010841)\n\n\n\n\nAnother category are the P-type ATPases (https://www.tcdb.org/search/result.php?tc=3.A.3), which are all related.\n\n\n\n\nProtein kinases are grouped into \"tyrosine kinases\" and \"serine/threonine kinases\", but they are also actually all related (https://www.nature.com/articles/s41467-024-50812-0): serine/threonine kinases are much older, with tyrosine kinases evolving from them more recently and creating their own branch.\n\n\n\n\nMutations are random, but selection is not, and biology frequently re-uses the things it has to work with. For example, you'll find signaling molecules in a multicellular organism that are exactly the same molecule yet do completely different functions in different tissues.\n\n\n\n\nATP is an available, energetic molecule, so it's sensible that new functionality will be based on a molecule that's already present, rather than evolving a separate energy source which would need to also evolve alongside enzymes to synthesize that energy source. Other NTPs may be candidates and are used as energy sources in some reactions, but there is a lot of inertia towards using ATP. See also: Why is ATP the preferred choice for energy carriers? (https://biology.stackexchange.com/questions/11286/why-is-atp-the-preferred-choice-for-energy-carriers)"}],"domain":"biology","external_citations":["https://biology.stackexchange.com/questions/11286/why-is-atp-the-preferred-choice-for-energy-carriers","https://link.springer.com/article/10.1007/BF00762534","https://www.nature.com/articles/s41467-024-50812-0","https://www.sciencedirect.com/science/article/pii/S0014579304010841","https://www.tcdb.org/search/result.php?tc=3.A.3"],"ground_truth_type":"metadata_grounded","group_id":"74ad5e89e6f291f0453099101d5ae0e51eb6e6784cd5d4f0a1f3cefe7d32bba7","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-4e4200aaba738fbff3515440","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:02:59.816967+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/55bbc2350ddd64077cfc2cba10ad5323a3aabdbe06356ba63f9b4f2161e7b47f_0.json","raw_sha256":"816eaaa302266f8cc647e663e24b4d7ecdb9f8cc125751c689d3329286131873","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"哲煜黄","profile_url":"https://biology.stackexchange.com/users/67047/%e5%93%b2%e7%85%9c%e9%bb%84","user_type":"registered"},"created_at":"2025-12-23T16:04:49+00:00","raw_file":"raw/codex_api_v1/758108496d7e56a3cf6614dffa5104a8870c129dcf518abbe860f55a089c6a12_1790824171594894000_0.json","raw_sha256":"5e5d792a6c484fda48193064d730da32774df13fc12222582feb4605d4472664","revision_guid":"02020145-6EE0-4426-8388-BA4D8E887E65","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/02020145-6EE0-4426-8388-BA4D8E887E65/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"哲煜黄","profile_url":"https://biology.stackexchange.com/users/67047/%e5%93%b2%e7%85%9c%e9%bb%84","user_type":"registered"},"created_at":"2025-12-23T16:13:10+00:00","raw_file":"raw/codex_api_v1/758108496d7e56a3cf6614dffa5104a8870c129dcf518abbe860f55a089c6a12_1790824171594894000_0.json","raw_sha256":"5e5d792a6c484fda48193064d730da32774df13fc12222582feb4605d4472664","revision_guid":"4C9C8CAE-BE47-4C9A-BEB8-2C6554742DAA","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4C9C8CAE-BE47-4C9A-BEB8-2C6554742DAA/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"哲煜黄","profile_url":"https://biology.stackexchange.com/users/67047/%e5%93%b2%e7%85%9c%e9%bb%84","user_type":"registered"},"created_at":"2025-12-23T16:39:59+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"5D6B6183-159D-41EE-A1F8-654832DB3A96","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5D6B6183-159D-41EE-A1F8-654832DB3A96/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"119195","source_record_sha256":"d0e8f8e30aa4f61dc4fbf36e09deed9ed35fe68ec6a4c15ea5dd51ce0d79c5bf","source_url":"https://biology.stackexchange.com/questions/119195/if-mutations-are-random-why-did-most-enzymes-evolve-to-use-atp-as-fuel","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"If mutations are random, why did most enzymes evolve to use ATP as fuel?\nOther than a few processes like protein translation, most energy consuming processes use the energy from ATP. I just don’t quite understand because unless enzymes have a common evolution origin (which is extremely unlikely considering the sheer diversity of enzymes), enzymes using other nucleoside triphosphates (NTPs) should  be equally likely. The reason is that other NTPs carry just as much energy as ATP, and because of NDPK, the chemical potential of the 4 NTPs should be similar. So why is ATP favored over other NTPs?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":119196,"score":4}],"split":"test"}
{"accepted_status":{"accepted_answer_id":119239,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I suspect that this is <em><a href=\"https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:110661-1/general-information\" rel=\"noreferrer\">Spathodea campanulata</a></em>, the African Tulip Tree or Flame Tree. This is a common introduced species, planted as an ornamental in many tropical countries. It is a medium to large tree (7 m - 25 m) with bright red flowers and heart-shaped seeds with a papery transparent wing (<a href=\"https://en.wikipedia.org/wiki/Samara_(fruit)\" rel=\"noreferrer\">samara</a>).</p>\n<p><a href=\"https://i.sstatic.net/XQ4aeHcg.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/XQ4aeHcg.png\" alt=\"Spathodea campanulata seed\" /></a></p>\n<p><sup>Image credit: JMK, CC BY-SA 3.0 <a href=\"https://creativecommons.org/licenses/by-sa/3.0\" rel=\"noreferrer\">https://creativecommons.org/licenses/by-sa/3.0</a>, via Wikimedia Commons</sup></p>\n","answer_id":119239,"answer_text":"I suspect that this is Spathodea campanulata (https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:110661-1/general-information), the African Tulip Tree or Flame Tree. This is a common introduced species, planted as an ornamental in many tropical countries. It is a medium to large tree (7 m - 25 m) with bright red flowers and heart-shaped seeds with a papery transparent wing (samara (https://en.wikipedia.org/wiki/Samara_(fruit))).\n\n\n\n\n[image: Spathodea campanulata seed; source: https://i.sstatic.net/XQ4aeHcg.png] (https://i.sstatic.net/XQ4aeHcg.png)\n\n\n\n\nImage credit: JMK, CC BY-SA 3.0 https://creativecommons.org/licenses/by-sa/3.0 (https://creativecommons.org/licenses/by-sa/3.0), via Wikimedia Commons","answer_url":"https://biology.stackexchange.com/a/119239","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2026-01-11T22:17:37+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:14.203473+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/bc31fe4e1e84f43ae95f846a38e90acc9e22beb08e25c5d964f94cb8f2d4bfcb_0.json","raw_sha256":"d7cf716376a9764909548809f10c8760f535f0ca4093eb29d910aae44edf1878","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/119725;119721;119720;119695;119675;119670;119661;119648;119640;119639;119635;119631;119628;119607;119605;119601;119598;119586;119582;119579;119577;119565;119561;119560;119542;119539;119529;119527;119522;119518;119506;119501;119497;119489;119487;119479;119465;119455;119453;119450;119444;119439;119434;119430;119421;119416;119404;119399;119398;119377;119376;119369;119362;119361;119355;119353;119350;119342;119340;119328;119326;119321;119317;119313;119312;119311;119306;119304;119287;119275;119273;119270;119268;119267;119260;119256;119251;119248;119238;119237;119235;119231;119227;119221;119212;119211;119209;119207;119201;119195;119193;119190;119185;119180;118180;118175;118172;118168;118158;118155/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":119238,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2026-01-11T22:17:37+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"FE63A43D-C99B-499E-8C9B-5C998F3ECAD5","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FE63A43D-C99B-499E-8C9B-5C998F3ECAD5/view-source"}],"score":16}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Ongky Denny Wijaya","author_url":"https://biology.stackexchange.com/users/123958/ongky-denny-wijaya","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Ongky Denny Wijaya","profile_url":"https://biology.stackexchange.com/users/123958/ongky-denny-wijaya","user_type":"registered"},"created_at":"2026-01-11T06:50:41+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"4DBB1DA6-F468-4EC3-9F9A-E041FB604399","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4DBB1DA6-F468-4EC3-9F9A-E041FB604399/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2026-01-11T11:32:23+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"57D9A5CD-8EF2-4926-BB8E-2417A9302070","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/57D9A5CD-8EF2-4926-BB8E-2417A9302070/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-01-12T00:03:53+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"CF993238-4BB6-4DB1-BEF7-189C07051CBA","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/CF993238-4BB6-4DB1-BEF7-189C07051CBA/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"terdon","profile_url":"https://biology.stackexchange.com/users/1306/terdon","user_type":"moderator"},"created_at":"2026-01-12T10:29:39+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"7DFE3302-395E-49DF-96F0-1D7BE1FDB9C7","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7DFE3302-395E-49DF-96F0-1D7BE1FDB9C7/view-source"}],"url":"https://biology.stackexchange.com/questions/119238/what-is-the-species-of-this-seed"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"119239","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2026-01-11T22:17:37+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"FE63A43D-C99B-499E-8C9B-5C998F3ECAD5","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FE63A43D-C99B-499E-8C9B-5C998F3ECAD5/view-source"}],"url":"https://biology.stackexchange.com/a/119239"}],"contexts":[{"context_id":"question","html":"<p>I found this seed at my home in East Java, Indonesia, and I have also often seen it on the street.\nThe seed is like a heart in the center and the side is like plastic. What kind of plant does it come from?</p>\n<p>(A Google image search yielded no results.)</p>\n<p><a href=\"https://i.sstatic.net/C9WjFFrk.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/C9WjFFrk.jpg\" alt=\"enter image description here\" /></a></p>\n","text":"I found this seed at my home in East Java, Indonesia, and I have also often seen it on the street.\nThe seed is like a heart in the center and the side is like plastic. What kind of plant does it come from?\n\n\n\n\n(A Google image search yielded no results.)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/C9WjFFrk.jpg] (https://i.sstatic.net/C9WjFFrk.jpg)"},{"context_id":"119239","html":"<p>I suspect that this is <em><a href=\"https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:110661-1/general-information\" rel=\"noreferrer\">Spathodea campanulata</a></em>, the African Tulip Tree or Flame Tree. This is a common introduced species, planted as an ornamental in many tropical countries. It is a medium to large tree (7 m - 25 m) with bright red flowers and heart-shaped seeds with a papery transparent wing (<a href=\"https://en.wikipedia.org/wiki/Samara_(fruit)\" rel=\"noreferrer\">samara</a>).</p>\n<p><a href=\"https://i.sstatic.net/XQ4aeHcg.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/XQ4aeHcg.png\" alt=\"Spathodea campanulata seed\" /></a></p>\n<p><sup>Image credit: JMK, CC BY-SA 3.0 <a href=\"https://creativecommons.org/licenses/by-sa/3.0\" rel=\"noreferrer\">https://creativecommons.org/licenses/by-sa/3.0</a>, via Wikimedia Commons</sup></p>\n","text":"I suspect that this is Spathodea campanulata (https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:110661-1/general-information), the African Tulip Tree or Flame Tree. This is a common introduced species, planted as an ornamental in many tropical countries. It is a medium to large tree (7 m - 25 m) with bright red flowers and heart-shaped seeds with a papery transparent wing (samara (https://en.wikipedia.org/wiki/Samara_(fruit))).\n\n\n\n\n[image: Spathodea campanulata seed; source: https://i.sstatic.net/XQ4aeHcg.png] (https://i.sstatic.net/XQ4aeHcg.png)\n\n\n\n\nImage credit: JMK, CC BY-SA 3.0 https://creativecommons.org/licenses/by-sa/3.0 (https://creativecommons.org/licenses/by-sa/3.0), via Wikimedia Commons"}],"domain":"biology","external_citations":["https://creativecommons.org/licenses/by-sa/3.0","https://en.wikipedia.org/wiki/Samara_(fruit)","https://i.sstatic.net/C9WjFFrk.jpg","https://i.sstatic.net/XQ4aeHcg.png","https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:110661-1/general-information"],"ground_truth_type":"metadata_grounded","group_id":"75aa81aa6f2a520e87de19b1a47bf2b8ce066d1550180d2854e46bfdbac8a689","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-09e37337df9853d85316f1d6","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:02:59.816967+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/55bbc2350ddd64077cfc2cba10ad5323a3aabdbe06356ba63f9b4f2161e7b47f_0.json","raw_sha256":"816eaaa302266f8cc647e663e24b4d7ecdb9f8cc125751c689d3329286131873","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Ongky Denny Wijaya","profile_url":"https://biology.stackexchange.com/users/123958/ongky-denny-wijaya","user_type":"registered"},"created_at":"2026-01-11T06:50:41+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"4DBB1DA6-F468-4EC3-9F9A-E041FB604399","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4DBB1DA6-F468-4EC3-9F9A-E041FB604399/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2026-01-11T11:32:23+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"57D9A5CD-8EF2-4926-BB8E-2417A9302070","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/57D9A5CD-8EF2-4926-BB8E-2417A9302070/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-01-12T00:03:53+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"CF993238-4BB6-4DB1-BEF7-189C07051CBA","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/CF993238-4BB6-4DB1-BEF7-189C07051CBA/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"terdon","profile_url":"https://biology.stackexchange.com/users/1306/terdon","user_type":"moderator"},"created_at":"2026-01-12T10:29:39+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"7DFE3302-395E-49DF-96F0-1D7BE1FDB9C7","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7DFE3302-395E-49DF-96F0-1D7BE1FDB9C7/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"119238","source_record_sha256":"fe12c5a6cf925c6d6f2ca0d97e4b2a7b051eca78838fd03d962b9ca802200493","source_url":"https://biology.stackexchange.com/questions/119238/what-is-the-species-of-this-seed","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What is the species of this seed?\nI found this seed at my home in East Java, Indonesia, and I have also often seen it on the street.\nThe seed is like a heart in the center and the side is like plastic. What kind of plant does it come from?\n\n\n\n\n(A Google image search yielded no results.)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/C9WjFFrk.jpg] (https://i.sstatic.net/C9WjFFrk.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":119239,"score":16}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>It obviously depends a lot on the model and its purpose, my experience is only with evolutionary algorithms in machine learning, but may be relevant.</p>\n<p>As with biological evolution, it is not only the individuals crude measurements such as direct descendants of the individual agent that define its fitness. Often, you will also measure its effect on the rest of the simulation, for example its niche members (other agents in its cluster). A good example of this is collateral descent, where one agents genetics may survive through relatives despite the main carrier having no descendants.</p>\n<p>As a parallel between this example and biological evolution, you can think of human groups, where one member may not directly have many descendants, but still makes major contributions to its own group regarding its total reproduction rates.</p>\n<p>In the end, it all depends on what the model is trying to achieve. Like you said, the success across time of certain clusters may also be taken into account, however, especially in computational evolutionary simulations, it usually does not matter if some cluster did better than another for longer, if another scored better fitness scores based on other parameters at the end of the simulation.</p>\n<p>Other examples of parameters that may be taken into account for fitness evaluation are generation time, reproductive variance, social network position, environmental resilience, extinction risk reduction, mutation rates and more.</p>\n","answer_id":119367,"answer_text":"It obviously depends a lot on the model and its purpose, my experience is only with evolutionary algorithms in machine learning, but may be relevant.\n\n\n\n\nAs with biological evolution, it is not only the individuals crude measurements such as direct descendants of the individual agent that define its fitness. Often, you will also measure its effect on the rest of the simulation, for example its niche members (other agents in its cluster). A good example of this is collateral descent, where one agents genetics may survive through relatives despite the main carrier having no descendants.\n\n\n\n\nAs a parallel between this example and biological evolution, you can think of human groups, where one member may not directly have many descendants, but still makes major contributions to its own group regarding its total reproduction rates.\n\n\n\n\nIn the end, it all depends on what the model is trying to achieve. Like you said, the success across time of certain clusters may also be taken into account, however, especially in computational evolutionary simulations, it usually does not matter if some cluster did better than another for longer, if another scored better fitness scores based on other parameters at the end of the simulation.\n\n\n\n\nOther examples of parameters that may be taken into account for fitness evaluation are generation time, reproductive variance, social network position, environmental resilience, extinction risk reduction, mutation rates and more.","answer_url":"https://biology.stackexchange.com/a/119367","author":"realhealth","author_url":"https://biology.stackexchange.com/users/125048/realhealth","content_license":"CC BY-SA 4.0","created_at":"2026-03-10T16:28:32+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:14.203473+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/bc31fe4e1e84f43ae95f846a38e90acc9e22beb08e25c5d964f94cb8f2d4bfcb_0.json","raw_sha256":"d7cf716376a9764909548809f10c8760f535f0ca4093eb29d910aae44edf1878","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/119725;119721;119720;119695;119675;119670;119661;119648;119640;119639;119635;119631;119628;119607;119605;119601;119598;119586;119582;119579;119577;119565;119561;119560;119542;119539;119529;119527;119522;119518;119506;119501;119497;119489;119487;119479;119465;119455;119453;119450;119444;119439;119434;119430;119421;119416;119404;119399;119398;119377;119376;119369;119362;119361;119355;119353;119350;119342;119340;119328;119326;119321;119317;119313;119312;119311;119306;119304;119287;119275;119273;119270;119268;119267;119260;119256;119251;119248;119238;119237;119235;119231;119227;119221;119212;119211;119209;119207;119201;119195;119193;119190;119185;119180;118180;118175;118172;118168;118158;118155/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":119248,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"realhealth","profile_url":"https://biology.stackexchange.com/users/125048/realhealth","user_type":"registered"},"created_at":"2026-03-10T16:28:32+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"CE6CBC0E-D98C-4E8A-B0DA-E2614CE49691","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CE6CBC0E-D98C-4E8A-B0DA-E2614CE49691/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Markus Klyver","author_url":"https://biology.stackexchange.com/users/21293/markus-klyver","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Markus Klyver","profile_url":"https://biology.stackexchange.com/users/21293/markus-klyver","user_type":"registered"},"created_at":"2026-01-14T19:18:50+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"94B2E70B-19FD-4AC3-AAF5-C98A2F981755","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/94B2E70B-19FD-4AC3-AAF5-C98A2F981755/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2026-01-14T22:17:33+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"2D3BBC46-BA17-41F5-B128-8F9359B0F762","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2D3BBC46-BA17-41F5-B128-8F9359B0F762/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Markus Klyver","profile_url":"https://biology.stackexchange.com/users/21293/markus-klyver","user_type":"registered"},"created_at":"2026-01-16T23:17:08+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"8668B10A-FA75-4FD4-A075-6819BCAB57F6","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8668B10A-FA75-4FD4-A075-6819BCAB57F6/view-source"}],"url":"https://biology.stackexchange.com/questions/119248/how-is-evolutionary-fitness-usually-defined-in-models"},{"author":"realhealth","author_url":"https://biology.stackexchange.com/users/125048/realhealth","content_license":"CC BY-SA 4.0","context_id":"119367","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"realhealth","profile_url":"https://biology.stackexchange.com/users/125048/realhealth","user_type":"registered"},"created_at":"2026-03-10T16:28:32+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"CE6CBC0E-D98C-4E8A-B0DA-E2614CE49691","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CE6CBC0E-D98C-4E8A-B0DA-E2614CE49691/view-source"}],"url":"https://biology.stackexchange.com/a/119367"}],"contexts":[{"context_id":"question","html":"<p>Consider a (biological) species in which the concept of an individual is well-defined, and where the number of offspring is also well-defined. In the models I have encountered, evolutionary fitness of an individual <span class=\"math-container\">$i$</span> is usually then defined to be the <em>number of direct decedents of <span class=\"math-container\">$i$</span></em>.</p>\n<p>This seems fine as a crude measure of what evolutionary fitness is, but we could as well imagine two individuals <span class=\"math-container\">$i$</span> and <span class=\"math-container\">$j$</span>, where the lineage of <span class=\"math-container\">$i$</span> continues for multiple generations whilst the lineage of <span class=\"math-container\">$j$</span> dies off within one or two generations. It seems to me that we would want to say that <span class=\"math-container\">$i$</span> is more “fit” than <span class=\"math-container\">$j$</span>, even if <span class=\"math-container\">$j$</span> might have had more direct decedents than <span class=\"math-container\">$j$</span>.</p>\n<p>My immediate thought would be to incorporate all decedents of <span class=\"math-container\">$i$</span>, say that if <span class=\"math-container\">$x_n$</span> if the number of decedents of <span class=\"math-container\">$i$</span> in generation <span class=\"math-container\">$n$</span>, then the total fitness of <span class=\"math-container\">$i$</span> could be defined as the sum</p>\n<p><span class=\"math-container\">$$\\displaystyle\\sum_{n=1}^\\infty \\displaystyle\\frac{x_n}{2^n}$$</span></p>\n<p>giving each consecutive generation exponentially less importance. As long as <span class=\"math-container\">$x_n$</span> grows subexponentially, the above sum converges. In the case of bacteria or other microorganisms, this assumption might not hold true. This is not generally an issue. One might change <span class=\"math-container\">$2^n$</span> to some other term, say <span class=\"math-container\">$n!$</span>, to make the sum converge.</p>\n<p>But I am sure there are other (and better) measures of fitness than what I can come up with. <strong>In more sophisticated evolutionary models, how is fitness usually defined? What other common measures than the direct number of direct decedents are used in scientific modeling of evolutionary biological systems?</strong></p>\n<hr />\n<p><strong>EDIT</strong>: Some people in the comments asked which particular model I was thinking of. For example, the authors establish Fischer's fundamental theorem of natural selection using the aforementioned definition (of <code>fitness = # offspring</code>) <a href=\"https://link.springer.com/article/10.1007/s00285-024-02077-w\" rel=\"nofollow noreferrer\">here, in this paper</a>.</p>\n","text":"Consider a (biological) species in which the concept of an individual is well-defined, and where the number of offspring is also well-defined. In the models I have encountered, evolutionary fitness of an individual $i$ is usually then defined to be the number of direct decedents of $i$.\n\n\n\n\nThis seems fine as a crude measure of what evolutionary fitness is, but we could as well imagine two individuals $i$ and $j$, where the lineage of $i$ continues for multiple generations whilst the lineage of $j$ dies off within one or two generations. It seems to me that we would want to say that $i$ is more “fit” than $j$, even if $j$ might have had more direct decedents than $j$.\n\n\n\n\nMy immediate thought would be to incorporate all decedents of $i$, say that if $x_n$ if the number of decedents of $i$ in generation $n$, then the total fitness of $i$ could be defined as the sum\n\n\n\n\n$$\\displaystyle\\sum_{n=1}^\\infty \\displaystyle\\frac{x_n}{2^n}$$\n\n\n\n\ngiving each consecutive generation exponentially less importance. As long as $x_n$ grows subexponentially, the above sum converges. In the case of bacteria or other microorganisms, this assumption might not hold true. This is not generally an issue. One might change $2^n$ to some other term, say $n!$, to make the sum converge.\n\n\n\n\nBut I am sure there are other (and better) measures of fitness than what I can come up with. In more sophisticated evolutionary models, how is fitness usually defined? What other common measures than the direct number of direct decedents are used in scientific modeling of evolutionary biological systems?\n\n\n\n\n\n\n\nEDIT: Some people in the comments asked which particular model I was thinking of. For example, the authors establish Fischer's fundamental theorem of natural selection using the aforementioned definition (of fitness = # offspring) here, in this paper (https://link.springer.com/article/10.1007/s00285-024-02077-w)."},{"context_id":"119367","html":"<p>It obviously depends a lot on the model and its purpose, my experience is only with evolutionary algorithms in machine learning, but may be relevant.</p>\n<p>As with biological evolution, it is not only the individuals crude measurements such as direct descendants of the individual agent that define its fitness. Often, you will also measure its effect on the rest of the simulation, for example its niche members (other agents in its cluster). A good example of this is collateral descent, where one agents genetics may survive through relatives despite the main carrier having no descendants.</p>\n<p>As a parallel between this example and biological evolution, you can think of human groups, where one member may not directly have many descendants, but still makes major contributions to its own group regarding its total reproduction rates.</p>\n<p>In the end, it all depends on what the model is trying to achieve. Like you said, the success across time of certain clusters may also be taken into account, however, especially in computational evolutionary simulations, it usually does not matter if some cluster did better than another for longer, if another scored better fitness scores based on other parameters at the end of the simulation.</p>\n<p>Other examples of parameters that may be taken into account for fitness evaluation are generation time, reproductive variance, social network position, environmental resilience, extinction risk reduction, mutation rates and more.</p>\n","text":"It obviously depends a lot on the model and its purpose, my experience is only with evolutionary algorithms in machine learning, but may be relevant.\n\n\n\n\nAs with biological evolution, it is not only the individuals crude measurements such as direct descendants of the individual agent that define its fitness. Often, you will also measure its effect on the rest of the simulation, for example its niche members (other agents in its cluster). A good example of this is collateral descent, where one agents genetics may survive through relatives despite the main carrier having no descendants.\n\n\n\n\nAs a parallel between this example and biological evolution, you can think of human groups, where one member may not directly have many descendants, but still makes major contributions to its own group regarding its total reproduction rates.\n\n\n\n\nIn the end, it all depends on what the model is trying to achieve. Like you said, the success across time of certain clusters may also be taken into account, however, especially in computational evolutionary simulations, it usually does not matter if some cluster did better than another for longer, if another scored better fitness scores based on other parameters at the end of the simulation.\n\n\n\n\nOther examples of parameters that may be taken into account for fitness evaluation are generation time, reproductive variance, social network position, environmental resilience, extinction risk reduction, mutation rates and more."}],"domain":"biology","external_citations":["https://link.springer.com/article/10.1007/s00285-024-02077-w"],"ground_truth_type":"metadata_grounded","group_id":"34d746bddff82b6f38f86c19af360036abd969afae580fe8ab1b8c87700704b7","hard_case_family":["no_accepted_answer"],"id":"RHM-934c7c92b5652e60486102f6","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:02:59.816967+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/55bbc2350ddd64077cfc2cba10ad5323a3aabdbe06356ba63f9b4f2161e7b47f_0.json","raw_sha256":"816eaaa302266f8cc647e663e24b4d7ecdb9f8cc125751c689d3329286131873","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Markus Klyver","profile_url":"https://biology.stackexchange.com/users/21293/markus-klyver","user_type":"registered"},"created_at":"2026-01-14T19:18:50+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"94B2E70B-19FD-4AC3-AAF5-C98A2F981755","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/94B2E70B-19FD-4AC3-AAF5-C98A2F981755/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"David","profile_url":"https://biology.stackexchange.com/users/22057/david","user_type":"registered"},"created_at":"2026-01-14T22:17:33+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"2D3BBC46-BA17-41F5-B128-8F9359B0F762","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2D3BBC46-BA17-41F5-B128-8F9359B0F762/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Markus Klyver","profile_url":"https://biology.stackexchange.com/users/21293/markus-klyver","user_type":"registered"},"created_at":"2026-01-16T23:17:08+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"8668B10A-FA75-4FD4-A075-6819BCAB57F6","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8668B10A-FA75-4FD4-A075-6819BCAB57F6/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"119248","source_record_sha256":"2de91a2d7e38335b16c3a121a6abe70e745d8fe4cb15e653928b14f4a54ac490","source_url":"https://biology.stackexchange.com/questions/119248/how-is-evolutionary-fitness-usually-defined-in-models","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How is evolutionary fitness usually defined in models?\nConsider a (biological) species in which the concept of an individual is well-defined, and where the number of offspring is also well-defined. In the models I have encountered, evolutionary fitness of an individual $i$ is usually then defined to be the number of direct decedents of $i$.\n\n\n\n\nThis seems fine as a crude measure of what evolutionary fitness is, but we could as well imagine two individuals $i$ and $j$, where the lineage of $i$ continues for multiple generations whilst the lineage of $j$ dies off within one or two generations. It seems to me that we would want to say that $i$ is more “fit” than $j$, even if $j$ might have had more direct decedents than $j$.\n\n\n\n\nMy immediate thought would be to incorporate all decedents of $i$, say that if $x_n$ if the number of decedents of $i$ in generation $n$, then the total fitness of $i$ could be defined as the sum\n\n\n\n\n$$\\displaystyle\\sum_{n=1}^\\infty \\displaystyle\\frac{x_n}{2^n}$$\n\n\n\n\ngiving each consecutive generation exponentially less importance. As long as $x_n$ grows subexponentially, the above sum converges. In the case of bacteria or other microorganisms, this assumption might not hold true. This is not generally an issue. One might change $2^n$ to some other term, say $n!$, to make the sum converge.\n\n\n\n\nBut I am sure there are other (and better) measures of fitness than what I can come up with. In more sophisticated evolutionary models, how is fitness usually defined? What other common measures than the direct number of direct decedents are used in scientific modeling of evolutionary biological systems?\n\n\n\n\n\n\n\nEDIT: Some people in the comments asked which particular model I was thinking of. For example, the authors establish Fischer's fundamental theorem of natural selection using the aforementioned definition (of fitness = # offspring) here, in this paper (https://link.springer.com/article/10.1007/s00285-024-02077-w).","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":119367,"score":1}],"split":"test"}
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user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-03-08T22:55:39+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"6D0F2E62-14BF-4723-A551-B249CDAB21F3","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/6D0F2E62-14BF-4723-A551-B249CDAB21F3/view-source"}],"url":"https://biology.stackexchange.com/questions/119362/rock-or-fossil-vertebrae"},{"author":"John","author_url":"https://biology.stackexchange.com/users/28022/john","content_license":"CC BY-SA 4.0","context_id":"119363","revision_attribution":[{"content_license":"CC BY-SA 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4.0","contributor":{"display_name":"terdon","profile_url":"https://biology.stackexchange.com/users/1306/terdon","user_type":"moderator"},"created_at":"2026-03-09T13:28:30+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"F75F2451-D2C3-405C-8385-F83AEB9C2D06","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F75F2451-D2C3-405C-8385-F83AEB9C2D06/view-source"}],"url":"https://biology.stackexchange.com/a/119363"}],"contexts":[{"context_id":"question","html":"<p>I LOVE collecting interesting rock and fossils if I ever find any.  My knowledge base is BEGINNER.\nSo I found this in Wyoming (lots of cool rocks &amp; fossils here !)\nIs it a chert formation or is it a fossil vertabrae ?[fossil rock ??]</p>\n<p><img src=\"https://i.sstatic.net/JpyBksv2.png\" alt=\"side 1 view\" /></p>\n<p><img src=\"https://i.sstatic.net/AeRJWs8J.png\" alt=\"Side 2 view\" /></p>\n<p><img src=\"https://i.sstatic.net/KpoVWBGy.png\" alt=\"Side 3 view\" /></p>\n","text":"I LOVE collecting interesting rock and fossils if I ever find any.  My knowledge base is BEGINNER.\nSo I found this in Wyoming (lots of cool rocks & fossils here !)\nIs it a chert formation or is it a fossil vertabrae ?[fossil rock ??]\n\n\n\n\n[image: side 1 view; source: https://i.sstatic.net/JpyBksv2.png]\n\n\n\n\n[image: Side 2 view; source: https://i.sstatic.net/AeRJWs8J.png]\n\n\n\n\n[image: Side 3 view; source: https://i.sstatic.net/KpoVWBGy.png]"},{"context_id":"119363","html":"<p>Not a vertebra far too asymmetric, and the texture is all wrong, but it does look like petrified wood.</p>\n","text":"Not a vertebra far too asymmetric, and the texture is all wrong, but it does look like petrified wood."}],"domain":"biology","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"e63af30ceea620e8c8d7e7231fb76644f5a20cbd0651b7e83fd76b0c8ee2c062","hard_case_family":["no_accepted_answer"],"id":"RHM-2a51284588613f8ed896133e","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:02:59.816967+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/55bbc2350ddd64077cfc2cba10ad5323a3aabdbe06356ba63f9b4f2161e7b47f_0.json","raw_sha256":"816eaaa302266f8cc647e663e24b4d7ecdb9f8cc125751c689d3329286131873","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Nancie Waage","profile_url":"https://biology.stackexchange.com/users/125901/nancie-waage","user_type":"registered"},"created_at":"2026-03-08T02:02:13+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"DF4C1F97-A656-4221-871B-0DFA5BDD564A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DF4C1F97-A656-4221-871B-0DFA5BDD564A/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bob1","profile_url":"https://biology.stackexchange.com/users/65284/bob1","user_type":"registered"},"created_at":"2026-03-08T19:24:45+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"3100FD9C-E4F5-47F5-8E3F-4C765AB243DF","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3100FD9C-E4F5-47F5-8E3F-4C765AB243DF/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-03-08T22:55:39+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"6D0F2E62-14BF-4723-A551-B249CDAB21F3","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/6D0F2E62-14BF-4723-A551-B249CDAB21F3/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"119362","source_record_sha256":"29e0c5eeb4bc94201b4145850dcb214b4ded0150a2f0928a3393f113877b9d04","source_url":"https://biology.stackexchange.com/questions/119362/rock-or-fossil-vertebrae","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Rock or Fossil Vertebrae?\nI LOVE collecting interesting rock and fossils if I ever find any.  My knowledge base is BEGINNER.\nSo I found this in Wyoming (lots of cool rocks & fossils here !)\nIs it a chert formation or is it a fossil vertabrae ?[fossil rock ??]\n\n\n\n\n[image: side 1 view; source: https://i.sstatic.net/JpyBksv2.png]\n\n\n\n\n[image: Side 2 view; source: https://i.sstatic.net/AeRJWs8J.png]\n\n\n\n\n[image: Side 3 view; source: https://i.sstatic.net/KpoVWBGy.png]","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":119363,"score":9}],"split":"test"}
{"accepted_status":{"accepted_answer_id":119441,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Mimicry such as the kind you’ve found is not unusual in nature, especially in insects that are heavily preyed upon. Examples even more striking (imo) exist, including the Middle Eastern fruit fly Goniurellia tridens, which also has insect-like markings on its wings. This particular marking may confuse predators or may resemble an undesirable prey insect (e.g. an ant or spider) upon which the predator does not feed.</p>\n<p><a href=\"https://i.sstatic.net/XIhTMVGc.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/XIhTMVGc.png\" alt=\"enter image description here\" /></a></p>\n<p>Like your own example, this insect initially had a small mark that somehow provided a survival advantage, thereby  also giving it an advantage over others to mate and pass on the mark. Every time the mark changed a bit through mutation, the individual carrying the advantageous mark (as opposed to a disadvantageous or neutral mark) had a survival advantage it could pass on, until its progeny has become what you see today (and in which mutations are still occurring.)</p>\n<p>There is no example of the spontaneous development of such an intricate advantageous marking that I aware of. Tremendous survival advantages can occur with one mutation, but these tend to be in the changed expression of a gene (e.g. the continued expression of lactase beyond infancy in humans.)  Mimicry evolves over generations of selection.</p>\n<p><sub>See <a href=\"https://en.wikipedia.org/wiki/Mimicry\" rel=\"noreferrer\">mimicry</a> in Wikipedia.</sub></p>\n","answer_id":119441,"answer_text":"Mimicry such as the kind you’ve found is not unusual in nature, especially in insects that are heavily preyed upon. Examples even more striking (imo) exist, including the Middle Eastern fruit fly Goniurellia tridens, which also has insect-like markings on its wings. This particular marking may confuse predators or may resemble an undesirable prey insect (e.g. an ant or spider) upon which the predator does not feed.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/XIhTMVGc.png] (https://i.sstatic.net/XIhTMVGc.png)\n\n\n\n\nLike your own example, this insect initially had a small mark that somehow provided a survival advantage, thereby  also giving it an advantage over others to mate and pass on the mark. Every time the mark changed a bit through mutation, the individual carrying the advantageous mark (as opposed to a disadvantageous or neutral mark) had a survival advantage it could pass on, until its progeny has become what you see today (and in which mutations are still occurring.)\n\n\n\n\nThere is no example of the spontaneous development of such an intricate advantageous marking that I aware of. Tremendous survival advantages can occur with one mutation, but these tend to be in the changed expression of a gene (e.g. the continued expression of lactase beyond infancy in humans.)  Mimicry evolves over generations of selection.\n\n\n\n\nSee mimicry (https://en.wikipedia.org/wiki/Mimicry) in Wikipedia.","answer_url":"https://biology.stackexchange.com/a/119441","author":"anongoodnurse","author_url":"https://biology.stackexchange.com/users/5198/anongoodnurse","content_license":"CC BY-SA 4.0","created_at":"2026-04-20T16:34:25+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:14.203473+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/bc31fe4e1e84f43ae95f846a38e90acc9e22beb08e25c5d964f94cb8f2d4bfcb_0.json","raw_sha256":"d7cf716376a9764909548809f10c8760f535f0ca4093eb29d910aae44edf1878","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/119725;119721;119720;119695;119675;119670;119661;119648;119640;119639;119635;119631;119628;119607;119605;119601;119598;119586;119582;119579;119577;119565;119561;119560;119542;119539;119529;119527;119522;119518;119506;119501;119497;119489;119487;119479;119465;119455;119453;119450;119444;119439;119434;119430;119421;119416;119404;119399;119398;119377;119376;119369;119362;119361;119355;119353;119350;119342;119340;119328;119326;119321;119317;119313;119312;119311;119306;119304;119287;119275;119273;119270;119268;119267;119260;119256;119251;119248;119238;119237;119235;119231;119227;119221;119212;119211;119209;119207;119201;119195;119193;119190;119185;119180;118180;118175;118172;118168;118158;118155/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":119434,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"anongoodnurse","profile_url":"https://biology.stackexchange.com/users/5198/anongoodnurse","user_type":"registered"},"created_at":"2026-04-20T16:34:25+00:00","raw_file":"raw/codex_api_v1/579a4d2562ba9524cfbccb0521aa128aef0c357c985479e84dfae99b419043f3_1790824187996707100_0.json","raw_sha256":"498851e9e2788dd78c09b5bc32fc2c43c0983eaa43d2c56d9c618718c8202873","revision_guid":"62D723C0-5D13-437F-8A00-3773B41A7CF3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/62D723C0-5D13-437F-8A00-3773B41A7CF3/view-source"}],"score":5}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Dheghom","author_url":"https://biology.stackexchange.com/users/109743/dheghom","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Dheghom","profile_url":"https://biology.stackexchange.com/users/109743/dheghom","user_type":"registered"},"created_at":"2026-04-18T10:48:23+00:00","raw_file":"raw/codex_api_v1/579a4d2562ba9524cfbccb0521aa128aef0c357c985479e84dfae99b419043f3_1790824187996707100_0.json","raw_sha256":"498851e9e2788dd78c09b5bc32fc2c43c0983eaa43d2c56d9c618718c8202873","revision_guid":"F78ABCBA-B196-4B45-AF9C-5EEE90A320A7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F78ABCBA-B196-4B45-AF9C-5EEE90A320A7/view-source"}],"url":"https://biology.stackexchange.com/questions/119434/on-the-evolution-of-mimicry-in-macrocilix-maia"},{"author":"anongoodnurse","author_url":"https://biology.stackexchange.com/users/5198/anongoodnurse","content_license":"CC BY-SA 4.0","context_id":"119441","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"anongoodnurse","profile_url":"https://biology.stackexchange.com/users/5198/anongoodnurse","user_type":"registered"},"created_at":"2026-04-20T16:34:25+00:00","raw_file":"raw/codex_api_v1/579a4d2562ba9524cfbccb0521aa128aef0c357c985479e84dfae99b419043f3_1790824187996707100_0.json","raw_sha256":"498851e9e2788dd78c09b5bc32fc2c43c0983eaa43d2c56d9c618718c8202873","revision_guid":"62D723C0-5D13-437F-8A00-3773B41A7CF3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/62D723C0-5D13-437F-8A00-3773B41A7CF3/view-source"}],"url":"https://biology.stackexchange.com/a/119441"}],"contexts":[{"context_id":"question","html":"<p>Mimicry and mimesis are undoubtedly among the most fascinating aspects of evolution, at least for me. Recently, actually, more by coincidence through a social media post, I stumbled upon <a href=\"https://en.wikipedia.org/wiki/Macrocilix_maia\" rel=\"noreferrer\"><em>Macrocilix maia</em></a> (Family Drepanidae), a species of moth distributed in India, Japan, Korea, and Malaysia. I cannot resist posting a picture here of that creature:</p>\n<p><a href=\"https://i.sstatic.net/bafDOfUrm.jpg\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/bafDOfUrm.jpg\" alt=\"\" /></a></p>\n<p>(<em>Source</em>: Wikimedia &quot;<a href=\"https://commons.wikimedia.org/wiki/File:Macrocilix_maia.jpg\" rel=\"noreferrer\">Macrocilix maia (Drepanidae), Borneo</a>&quot;, Author: Alexey Yakovlev; not modified; under License <a href=\"https://creativecommons.org/licenses/by-sa/3.0/deed.en\" rel=\"noreferrer\">CC BY-SA 3.0</a>)</p>\n<p>So, as you can see, the drawing on its wings resembles two flies that feed essentially on something looking like bird droppings and thus likely deters predators by mimicking something unappetizing or easily overlooked.</p>\n<p>From an evolutionary perspective, how should one understand the mechanisms that give rise to such an amazing phenotype? Does a pattern like this originate from mutations in just a single individual? or does it emerge gradually over many generations through the accumulation of small changes? Does anyone have some insights on the genetic/evolutionary biological aspects of such a form of mimicry?</p>\n","text":"Mimicry and mimesis are undoubtedly among the most fascinating aspects of evolution, at least for me. Recently, actually, more by coincidence through a social media post, I stumbled upon Macrocilix maia (https://en.wikipedia.org/wiki/Macrocilix_maia) (Family Drepanidae), a species of moth distributed in India, Japan, Korea, and Malaysia. I cannot resist posting a picture here of that creature:\n\n\n\n\n[image: ; source: https://i.sstatic.net/bafDOfUrm.jpg] (https://i.sstatic.net/bafDOfUrm.jpg)\n\n\n\n\n(Source: Wikimedia \"Macrocilix maia (Drepanidae), Borneo (https://commons.wikimedia.org/wiki/File:Macrocilix_maia.jpg)\", Author: Alexey Yakovlev; not modified; under License CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0/deed.en))\n\n\n\n\nSo, as you can see, the drawing on its wings resembles two flies that feed essentially on something looking like bird droppings and thus likely deters predators by mimicking something unappetizing or easily overlooked.\n\n\n\n\nFrom an evolutionary perspective, how should one understand the mechanisms that give rise to such an amazing phenotype? Does a pattern like this originate from mutations in just a single individual? or does it emerge gradually over many generations through the accumulation of small changes? Does anyone have some insights on the genetic/evolutionary biological aspects of such a form of mimicry?"},{"context_id":"119441","html":"<p>Mimicry such as the kind you’ve found is not unusual in nature, especially in insects that are heavily preyed upon. Examples even more striking (imo) exist, including the Middle Eastern fruit fly Goniurellia tridens, which also has insect-like markings on its wings. This particular marking may confuse predators or may resemble an undesirable prey insect (e.g. an ant or spider) upon which the predator does not feed.</p>\n<p><a href=\"https://i.sstatic.net/XIhTMVGc.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/XIhTMVGc.png\" alt=\"enter image description here\" /></a></p>\n<p>Like your own example, this insect initially had a small mark that somehow provided a survival advantage, thereby  also giving it an advantage over others to mate and pass on the mark. Every time the mark changed a bit through mutation, the individual carrying the advantageous mark (as opposed to a disadvantageous or neutral mark) had a survival advantage it could pass on, until its progeny has become what you see today (and in which mutations are still occurring.)</p>\n<p>There is no example of the spontaneous development of such an intricate advantageous marking that I aware of. Tremendous survival advantages can occur with one mutation, but these tend to be in the changed expression of a gene (e.g. the continued expression of lactase beyond infancy in humans.)  Mimicry evolves over generations of selection.</p>\n<p><sub>See <a href=\"https://en.wikipedia.org/wiki/Mimicry\" rel=\"noreferrer\">mimicry</a> in Wikipedia.</sub></p>\n","text":"Mimicry such as the kind you’ve found is not unusual in nature, especially in insects that are heavily preyed upon. Examples even more striking (imo) exist, including the Middle Eastern fruit fly Goniurellia tridens, which also has insect-like markings on its wings. This particular marking may confuse predators or may resemble an undesirable prey insect (e.g. an ant or spider) upon which the predator does not feed.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/XIhTMVGc.png] (https://i.sstatic.net/XIhTMVGc.png)\n\n\n\n\nLike your own example, this insect initially had a small mark that somehow provided a survival advantage, thereby  also giving it an advantage over others to mate and pass on the mark. Every time the mark changed a bit through mutation, the individual carrying the advantageous mark (as opposed to a disadvantageous or neutral mark) had a survival advantage it could pass on, until its progeny has become what you see today (and in which mutations are still occurring.)\n\n\n\n\nThere is no example of the spontaneous development of such an intricate advantageous marking that I aware of. Tremendous survival advantages can occur with one mutation, but these tend to be in the changed expression of a gene (e.g. the continued expression of lactase beyond infancy in humans.)  Mimicry evolves over generations of selection.\n\n\n\n\nSee mimicry (https://en.wikipedia.org/wiki/Mimicry) in Wikipedia."}],"domain":"biology","external_citations":["https://commons.wikimedia.org/wiki/File:Macrocilix_maia.jpg","https://creativecommons.org/licenses/by-sa/3.0/deed.en","https://en.wikipedia.org/wiki/Macrocilix_maia","https://en.wikipedia.org/wiki/Mimicry","https://i.sstatic.net/XIhTMVGc.png","https://i.sstatic.net/bafDOfUrm.jpg"],"ground_truth_type":"metadata_grounded","group_id":"86605385f112908708357e199c0f4ba2538a656a25825f54320bc3d85c895c12","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-6a899d2fcdd0aa1a458d093b","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:02:59.816967+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/55bbc2350ddd64077cfc2cba10ad5323a3aabdbe06356ba63f9b4f2161e7b47f_0.json","raw_sha256":"816eaaa302266f8cc647e663e24b4d7ecdb9f8cc125751c689d3329286131873","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Dheghom","profile_url":"https://biology.stackexchange.com/users/109743/dheghom","user_type":"registered"},"created_at":"2026-04-18T10:48:23+00:00","raw_file":"raw/codex_api_v1/579a4d2562ba9524cfbccb0521aa128aef0c357c985479e84dfae99b419043f3_1790824187996707100_0.json","raw_sha256":"498851e9e2788dd78c09b5bc32fc2c43c0983eaa43d2c56d9c618718c8202873","revision_guid":"F78ABCBA-B196-4B45-AF9C-5EEE90A320A7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F78ABCBA-B196-4B45-AF9C-5EEE90A320A7/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"119434","source_record_sha256":"4856f2a9c5a2d645caf95561c8c6d36d475e26b55bfc9fc19e405cab55797178","source_url":"https://biology.stackexchange.com/questions/119434/on-the-evolution-of-mimicry-in-macrocilix-maia","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"On the evolution of mimicry in Macrocilix maia\nMimicry and mimesis are undoubtedly among the most fascinating aspects of evolution, at least for me. Recently, actually, more by coincidence through a social media post, I stumbled upon Macrocilix maia (https://en.wikipedia.org/wiki/Macrocilix_maia) (Family Drepanidae), a species of moth distributed in India, Japan, Korea, and Malaysia. I cannot resist posting a picture here of that creature:\n\n\n\n\n[image: ; source: https://i.sstatic.net/bafDOfUrm.jpg] (https://i.sstatic.net/bafDOfUrm.jpg)\n\n\n\n\n(Source: Wikimedia \"Macrocilix maia (Drepanidae), Borneo (https://commons.wikimedia.org/wiki/File:Macrocilix_maia.jpg)\", Author: Alexey Yakovlev; not modified; under License CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0/deed.en))\n\n\n\n\nSo, as you can see, the drawing on its wings resembles two flies that feed essentially on something looking like bird droppings and thus likely deters predators by mimicking something unappetizing or easily overlooked.\n\n\n\n\nFrom an evolutionary perspective, how should one understand the mechanisms that give rise to such an amazing phenotype? Does a pattern like this originate from mutations in just a single individual? or does it emerge gradually over many generations through the accumulation of small changes? Does anyone have some insights on the genetic/evolutionary biological aspects of such a form of mimicry?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":119441,"score":5}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Coincidence detection:</p>\n<p>easy: Neuron firing causes a signal in connected neuron. If the connected neuron has received input from neighboring neurons (let's say the activation pattern that occurs when learning a new task), it will change its sensitivity so that the same original signal is now stronger.</p>\n<p>more complex (but still superficial):</p>\n<p>On a neuronal level key players in learning are Glutamate and its receptors NMDA and AMPA. Typically some neuron releases glutamate, which then binds to the AMPA receptor at the postsynapse, transmitting its signal. NMDA receptors are also present, but are blocked by Magnesium ions except:\nIf the right inputs to the postsynaptic neuron occurred beforehand, the neuron becomes depolarized. This allows the Magnesium ions to diffuse away allowing for glutamate to activate NMDA receptors. Now there's an additional stream of Calcium ions.\nCalcium activates proteinkinases which phosphorylate AMPA receptors. This causes increased concentration of AMPA receptor in the postsynaptic membrane and therefore increased sensitivity to the signal from the presynaptic neuron. Because now with the same input signal and the same glutamate release, we get more receptor activation and a stronger signal in the postsynaptic neuron.\n<a href=\"https://i.sstatic.net/YFoeXWwx.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/YFoeXWwx.png\" alt=\"Coincidence detection, Long term potentiation\" /></a>\nSource:\n<a href=\"http://physiologie.cc/XVI.8.htm\" rel=\"nofollow noreferrer\">A nice German physiology site </a></p>\n","answer_id":119528,"answer_text":"Coincidence detection:\n\n\n\n\neasy: Neuron firing causes a signal in connected neuron. If the connected neuron has received input from neighboring neurons (let's say the activation pattern that occurs when learning a new task), it will change its sensitivity so that the same original signal is now stronger.\n\n\n\n\nmore complex (but still superficial):\n\n\n\n\nOn a neuronal level key players in learning are Glutamate and its receptors NMDA and AMPA. Typically some neuron releases glutamate, which then binds to the AMPA receptor at the postsynapse, transmitting its signal. NMDA receptors are also present, but are blocked by Magnesium ions except:\nIf the right inputs to the postsynaptic neuron occurred beforehand, the neuron becomes depolarized. This allows the Magnesium ions to diffuse away allowing for glutamate to activate NMDA receptors. Now there's an additional stream of Calcium ions.\nCalcium activates proteinkinases which phosphorylate AMPA receptors. This causes increased concentration of AMPA receptor in the postsynaptic membrane and therefore increased sensitivity to the signal from the presynaptic neuron. Because now with the same input signal and the same glutamate release, we get more receptor activation and a stronger signal in the postsynaptic neuron.\n[image: Coincidence detection, Long term potentiation; source: https://i.sstatic.net/YFoeXWwx.png] (https://i.sstatic.net/YFoeXWwx.png)\nSource:\nA nice German physiology site  (http://physiologie.cc/XVI.8.htm)","answer_url":"https://biology.stackexchange.com/a/119528","author":"Lukas4235","author_url":"https://biology.stackexchange.com/users/83315/lukas4235","content_license":"CC BY-SA 4.0","created_at":"2026-06-05T08:47:43+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:14.203473+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/bc31fe4e1e84f43ae95f846a38e90acc9e22beb08e25c5d964f94cb8f2d4bfcb_0.json","raw_sha256":"d7cf716376a9764909548809f10c8760f535f0ca4093eb29d910aae44edf1878","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/119725;119721;119720;119695;119675;119670;119661;119648;119640;119639;119635;119631;119628;119607;119605;119601;119598;119586;119582;119579;119577;119565;119561;119560;119542;119539;119529;119527;119522;119518;119506;119501;119497;119489;119487;119479;119465;119455;119453;119450;119444;119439;119434;119430;119421;119416;119404;119399;119398;119377;119376;119369;119362;119361;119355;119353;119350;119342;119340;119328;119326;119321;119317;119313;119312;119311;119306;119304;119287;119275;119273;119270;119268;119267;119260;119256;119251;119248;119238;119237;119235;119231;119227;119221;119212;119211;119209;119207;119201;119195;119193;119190;119185;119180;118180;118175;118172;118168;118158;118155/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":119527,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lukas4235","profile_url":"https://biology.stackexchange.com/users/83315/lukas4235","user_type":"registered"},"created_at":"2026-06-05T08:47:43+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"325EBBED-C873-4F7B-984D-8B2E167998AE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/325EBBED-C873-4F7B-984D-8B2E167998AE/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lukas4235","profile_url":"https://biology.stackexchange.com/users/83315/lukas4235","user_type":"registered"},"created_at":"2026-06-05T14:27:50+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"CB21EAB9-09BB-49D8-81F0-F135DDDA0DD2","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CB21EAB9-09BB-49D8-81F0-F135DDDA0DD2/view-source"}],"score":5}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Elizabeth","author_url":"https://biology.stackexchange.com/users/128585/elizabeth","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Elizabeth","profile_url":"https://biology.stackexchange.com/users/128585/elizabeth","user_type":"registered"},"created_at":"2026-06-05T07:21:26+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"05595D0E-90A6-485A-9BD7-15E941312BA9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/05595D0E-90A6-485A-9BD7-15E941312BA9/view-source"}],"url":"https://biology.stackexchange.com/questions/119527/what-is-the-actual-mechanism-of-neuroplasticity-during-cognitive-exercises"},{"author":"Lukas4235","author_url":"https://biology.stackexchange.com/users/83315/lukas4235","content_license":"CC BY-SA 4.0","context_id":"119528","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lukas4235","profile_url":"https://biology.stackexchange.com/users/83315/lukas4235","user_type":"registered"},"created_at":"2026-06-05T08:47:43+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"325EBBED-C873-4F7B-984D-8B2E167998AE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/325EBBED-C873-4F7B-984D-8B2E167998AE/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lukas4235","profile_url":"https://biology.stackexchange.com/users/83315/lukas4235","user_type":"registered"},"created_at":"2026-06-05T14:27:50+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"CB21EAB9-09BB-49D8-81F0-F135DDDA0DD2","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CB21EAB9-09BB-49D8-81F0-F135DDDA0DD2/view-source"}],"url":"https://biology.stackexchange.com/a/119528"}],"contexts":[{"context_id":"question","html":"<p>I want to understand the exact science behind how the brain changes when we perform mental training. I know that neuroplasticity is the core process, but what is the primary mechanism of neuroplasticity during cognitive exercises? Specifically, how do synapses physically change, and what role do factors like Long-Term Potentiation (LTP) or myelination play when we regularly practice these mental tasks? I would love a breakdown that balances the biological details with an easy-to-understand explanation.</p>\n","text":"I want to understand the exact science behind how the brain changes when we perform mental training. I know that neuroplasticity is the core process, but what is the primary mechanism of neuroplasticity during cognitive exercises? Specifically, how do synapses physically change, and what role do factors like Long-Term Potentiation (LTP) or myelination play when we regularly practice these mental tasks? I would love a breakdown that balances the biological details with an easy-to-understand explanation."},{"context_id":"119528","html":"<p>Coincidence detection:</p>\n<p>easy: Neuron firing causes a signal in connected neuron. If the connected neuron has received input from neighboring neurons (let's say the activation pattern that occurs when learning a new task), it will change its sensitivity so that the same original signal is now stronger.</p>\n<p>more complex (but still superficial):</p>\n<p>On a neuronal level key players in learning are Glutamate and its receptors NMDA and AMPA. Typically some neuron releases glutamate, which then binds to the AMPA receptor at the postsynapse, transmitting its signal. NMDA receptors are also present, but are blocked by Magnesium ions except:\nIf the right inputs to the postsynaptic neuron occurred beforehand, the neuron becomes depolarized. This allows the Magnesium ions to diffuse away allowing for glutamate to activate NMDA receptors. Now there's an additional stream of Calcium ions.\nCalcium activates proteinkinases which phosphorylate AMPA receptors. This causes increased concentration of AMPA receptor in the postsynaptic membrane and therefore increased sensitivity to the signal from the presynaptic neuron. Because now with the same input signal and the same glutamate release, we get more receptor activation and a stronger signal in the postsynaptic neuron.\n<a href=\"https://i.sstatic.net/YFoeXWwx.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/YFoeXWwx.png\" alt=\"Coincidence detection, Long term potentiation\" /></a>\nSource:\n<a href=\"http://physiologie.cc/XVI.8.htm\" rel=\"nofollow noreferrer\">A nice German physiology site </a></p>\n","text":"Coincidence detection:\n\n\n\n\neasy: Neuron firing causes a signal in connected neuron. If the connected neuron has received input from neighboring neurons (let's say the activation pattern that occurs when learning a new task), it will change its sensitivity so that the same original signal is now stronger.\n\n\n\n\nmore complex (but still superficial):\n\n\n\n\nOn a neuronal level key players in learning are Glutamate and its receptors NMDA and AMPA. Typically some neuron releases glutamate, which then binds to the AMPA receptor at the postsynapse, transmitting its signal. NMDA receptors are also present, but are blocked by Magnesium ions except:\nIf the right inputs to the postsynaptic neuron occurred beforehand, the neuron becomes depolarized. This allows the Magnesium ions to diffuse away allowing for glutamate to activate NMDA receptors. Now there's an additional stream of Calcium ions.\nCalcium activates proteinkinases which phosphorylate AMPA receptors. This causes increased concentration of AMPA receptor in the postsynaptic membrane and therefore increased sensitivity to the signal from the presynaptic neuron. Because now with the same input signal and the same glutamate release, we get more receptor activation and a stronger signal in the postsynaptic neuron.\n[image: Coincidence detection, Long term potentiation; source: https://i.sstatic.net/YFoeXWwx.png] (https://i.sstatic.net/YFoeXWwx.png)\nSource:\nA nice German physiology site  (http://physiologie.cc/XVI.8.htm)"}],"domain":"biology","external_citations":["http://physiologie.cc/XVI.8.htm","https://i.sstatic.net/YFoeXWwx.png"],"ground_truth_type":"metadata_grounded","group_id":"7f02670c12ed3ab1b8b96ef5eed70f90a6213ba9125ed37b53e41a0a9dc83a53","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-b92f1b31c05a35fe4b3a5f8e","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:02:59.816967+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/55bbc2350ddd64077cfc2cba10ad5323a3aabdbe06356ba63f9b4f2161e7b47f_0.json","raw_sha256":"816eaaa302266f8cc647e663e24b4d7ecdb9f8cc125751c689d3329286131873","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Elizabeth","profile_url":"https://biology.stackexchange.com/users/128585/elizabeth","user_type":"registered"},"created_at":"2026-06-05T07:21:26+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"05595D0E-90A6-485A-9BD7-15E941312BA9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/05595D0E-90A6-485A-9BD7-15E941312BA9/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"119527","source_record_sha256":"5ba6b778b8e11bee4e764e86f2e89747c7532a414e3ba618824689980bfe4016","source_url":"https://biology.stackexchange.com/questions/119527/what-is-the-actual-mechanism-of-neuroplasticity-during-cognitive-exercises","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What is the actual mechanism of neuroplasticity during cognitive exercises?\nI want to understand the exact science behind how the brain changes when we perform mental training. I know that neuroplasticity is the core process, but what is the primary mechanism of neuroplasticity during cognitive exercises? Specifically, how do synapses physically change, and what role do factors like Long-Term Potentiation (LTP) or myelination play when we regularly practice these mental tasks? I would love a breakdown that balances the biological details with an easy-to-understand explanation.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":119528,"score":5}],"split":"test"}
{"accepted_status":{"accepted_answer_id":119587,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<h3><strong>Dragonfly Nymph (Naiad).</strong></h3>\n<p><a href=\"https://i.sstatic.net/A2NxHIN8.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/A2NxHIN8.png\" alt=\"Water insect larval stage of dragonfly.\" /></a></p>\n<p><sup>Image Credit RODTUK/FLICKR. Found <a href=\"https://www.thoughtco.com/dragonfly-life-cycle-1968257\" rel=\"noreferrer\">thoughtco.com</a> January 2020, copyright uncertain, fair usage claimed here.</sup></p>\n<p>This is part of the life-cycle of the dragonfly which resides in still, fresh-water, i.e. ponds and lakes. They feed on tadpoles, arthropods and small fish using a specially modified lower jaw that can dart forward quickly to snag prey. The gills are surprisingly, inside their rectums.</p>\n<p>From hatching from an egg, the nymph will moult between 9 and 17 times, the wings growing larger towards the final moults. This process can take many months down to a single month in warm climate with plentiful food.</p>\n<p>Source: <a href=\"https://www.thoughtco.com/dragonfly-life-cycle-1968257\" rel=\"noreferrer\">The Dragonfly Life Cycle</a>.</p>\n<p>Note. As to the spider, that also seems to be a moulted exoskeleton, but a clearer picture would be required for identification.</p>\n","answer_id":119587,"answer_text":"Dragonfly Nymph (Naiad).\n\n\n\n\n[image: Water insect larval stage of dragonfly.; source: https://i.sstatic.net/A2NxHIN8.png] (https://i.sstatic.net/A2NxHIN8.png)\n\n\n\n\nImage Credit RODTUK/FLICKR. Found thoughtco.com (https://www.thoughtco.com/dragonfly-life-cycle-1968257) January 2020, copyright uncertain, fair usage claimed here.\n\n\n\n\nThis is part of the life-cycle of the dragonfly which resides in still, fresh-water, i.e. ponds and lakes. They feed on tadpoles, arthropods and small fish using a specially modified lower jaw that can dart forward quickly to snag prey. The gills are surprisingly, inside their rectums.\n\n\n\n\nFrom hatching from an egg, the nymph will moult between 9 and 17 times, the wings growing larger towards the final moults. This process can take many months down to a single month in warm climate with plentiful food.\n\n\n\n\nSource: The Dragonfly Life Cycle (https://www.thoughtco.com/dragonfly-life-cycle-1968257).\n\n\n\n\nNote. As to the spider, that also seems to be a moulted exoskeleton, but a clearer picture would be required for identification.","answer_url":"https://biology.stackexchange.com/a/119587","author":"Jiminy Cricket.","author_url":"https://biology.stackexchange.com/users/5509/jiminy-cricket","content_license":"CC BY-SA 4.0","created_at":"2026-07-10T15:09:43+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:14.203473+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/bc31fe4e1e84f43ae95f846a38e90acc9e22beb08e25c5d964f94cb8f2d4bfcb_0.json","raw_sha256":"d7cf716376a9764909548809f10c8760f535f0ca4093eb29d910aae44edf1878","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/119725;119721;119720;119695;119675;119670;119661;119648;119640;119639;119635;119631;119628;119607;119605;119601;119598;119586;119582;119579;119577;119565;119561;119560;119542;119539;119529;119527;119522;119518;119506;119501;119497;119489;119487;119479;119465;119455;119453;119450;119444;119439;119434;119430;119421;119416;119404;119399;119398;119377;119376;119369;119362;119361;119355;119353;119350;119342;119340;119328;119326;119321;119317;119313;119312;119311;119306;119304;119287;119275;119273;119270;119268;119267;119260;119256;119251;119248;119238;119237;119235;119231;119227;119221;119212;119211;119209;119207;119201;119195;119193;119190;119185;119180;118180;118175;118172;118168;118158;118155/answers?filter=withbody&order=asc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":119586,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Jiminy Cricket.","profile_url":"https://biology.stackexchange.com/users/5509/jiminy-cricket","user_type":"registered"},"created_at":"2026-07-10T15:09:43+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"0C70EF22-5FB8-4D0A-A047-E15BD1F75D40","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0C70EF22-5FB8-4D0A-A047-E15BD1F75D40/view-source"}],"score":6}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"trejder","author_url":"https://biology.stackexchange.com/users/8986/trejder","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"trejder","profile_url":"https://biology.stackexchange.com/users/8986/trejder","user_type":"registered"},"created_at":"2026-07-10T14:10:18+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"899E178E-8675-4232-8413-8EACD4D46629","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/899E178E-8675-4232-8413-8EACD4D46629/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-07-10T22:22:42+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"6A97D9D7-6A97-4AF5-BEDD-C5013E36E795","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/6A97D9D7-6A97-4AF5-BEDD-C5013E36E795/view-source"}],"url":"https://biology.stackexchange.com/questions/119586/identify-northern-poland-masuria-region-molt-or-a-dead-insect"},{"author":"Jiminy Cricket.","author_url":"https://biology.stackexchange.com/users/5509/jiminy-cricket","content_license":"CC BY-SA 4.0","context_id":"119587","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Jiminy Cricket.","profile_url":"https://biology.stackexchange.com/users/5509/jiminy-cricket","user_type":"registered"},"created_at":"2026-07-10T15:09:43+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"0C70EF22-5FB8-4D0A-A047-E15BD1F75D40","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0C70EF22-5FB8-4D0A-A047-E15BD1F75D40/view-source"}],"url":"https://biology.stackexchange.com/a/119587"}],"contexts":[{"context_id":"question","html":"<p>I found this empty insect shell indoors, and I'm trying to identify what creature left it behind. Can you help me with that?</p>\n<p><a href=\"https://i.sstatic.net/bZcS7OrU.jpg\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/bZcS7OrU.jpg\" alt=\"Main image\" /></a></p>\n<p><a href=\"https://i.sstatic.net/zOu0RTl5.jpg\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/zOu0RTl5.jpg\" alt=\"Close-up\" /></a></p>\n<p><a href=\"https://i.sstatic.net/KbRrOJGy.jpg\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/KbRrOJGy.jpg\" alt=\"Size reference\" /></a></p>\n<ol>\n<li><strong>Exact location</strong>: <a href=\"https://maps.app.goo.gl/xYgEHftC6qeqtjTs9\" rel=\"noreferrer\">53°40'15.3&quot;N 21°28'58.7&quot;E</a></li>\n<li><strong>Location description</strong>: Europe, Northern Poland, Masuria region (wooded area near river Krutynia).</li>\n<li><strong>Size</strong>: For scale, I've included a matchstick in one of the photos (a standard matchstick is about 4.5 cm / 1.8 inches long).</li>\n</ol>\n<p>At first glance, the body shape made me think it might be the remains or a molt of some kind of wasp or a bee, but I am completely unsure. There is also a tiny spider attached to one of its back legs, though that might just be a coincidence.</p>\n<p>Is this an insect molt (exuvia), or a dead insect eaten from the inside? Can anyone help me identify the species or family?</p>\n<p>Can you also try to identify this tiny spider (if photo quality isn't to low)?</p>\n","text":"I found this empty insect shell indoors, and I'm trying to identify what creature left it behind. Can you help me with that?\n\n\n\n\n[image: Main image; source: https://i.sstatic.net/bZcS7OrU.jpg] (https://i.sstatic.net/bZcS7OrU.jpg)\n\n\n\n\n[image: Close-up; source: https://i.sstatic.net/zOu0RTl5.jpg] (https://i.sstatic.net/zOu0RTl5.jpg)\n\n\n\n\n[image: Size reference; source: https://i.sstatic.net/KbRrOJGy.jpg] (https://i.sstatic.net/KbRrOJGy.jpg)\n\n\n\n\n\nExact location: 53°40'15.3\"N 21°28'58.7\"E (https://maps.app.goo.gl/xYgEHftC6qeqtjTs9)\n\n\n\n\nLocation description: Europe, Northern Poland, Masuria region (wooded area near river Krutynia).\n\n\n\n\nSize: For scale, I've included a matchstick in one of the photos (a standard matchstick is about 4.5 cm / 1.8 inches long).\n\n\n\n\n\nAt first glance, the body shape made me think it might be the remains or a molt of some kind of wasp or a bee, but I am completely unsure. There is also a tiny spider attached to one of its back legs, though that might just be a coincidence.\n\n\n\n\nIs this an insect molt (exuvia), or a dead insect eaten from the inside? Can anyone help me identify the species or family?\n\n\n\n\nCan you also try to identify this tiny spider (if photo quality isn't to low)?"},{"context_id":"119587","html":"<h3><strong>Dragonfly Nymph (Naiad).</strong></h3>\n<p><a href=\"https://i.sstatic.net/A2NxHIN8.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/A2NxHIN8.png\" alt=\"Water insect larval stage of dragonfly.\" /></a></p>\n<p><sup>Image Credit RODTUK/FLICKR. Found <a href=\"https://www.thoughtco.com/dragonfly-life-cycle-1968257\" rel=\"noreferrer\">thoughtco.com</a> January 2020, copyright uncertain, fair usage claimed here.</sup></p>\n<p>This is part of the life-cycle of the dragonfly which resides in still, fresh-water, i.e. ponds and lakes. They feed on tadpoles, arthropods and small fish using a specially modified lower jaw that can dart forward quickly to snag prey. The gills are surprisingly, inside their rectums.</p>\n<p>From hatching from an egg, the nymph will moult between 9 and 17 times, the wings growing larger towards the final moults. This process can take many months down to a single month in warm climate with plentiful food.</p>\n<p>Source: <a href=\"https://www.thoughtco.com/dragonfly-life-cycle-1968257\" rel=\"noreferrer\">The Dragonfly Life Cycle</a>.</p>\n<p>Note. As to the spider, that also seems to be a moulted exoskeleton, but a clearer picture would be required for identification.</p>\n","text":"Dragonfly Nymph (Naiad).\n\n\n\n\n[image: Water insect larval stage of dragonfly.; source: https://i.sstatic.net/A2NxHIN8.png] (https://i.sstatic.net/A2NxHIN8.png)\n\n\n\n\nImage Credit RODTUK/FLICKR. Found thoughtco.com (https://www.thoughtco.com/dragonfly-life-cycle-1968257) January 2020, copyright uncertain, fair usage claimed here.\n\n\n\n\nThis is part of the life-cycle of the dragonfly which resides in still, fresh-water, i.e. ponds and lakes. They feed on tadpoles, arthropods and small fish using a specially modified lower jaw that can dart forward quickly to snag prey. The gills are surprisingly, inside their rectums.\n\n\n\n\nFrom hatching from an egg, the nymph will moult between 9 and 17 times, the wings growing larger towards the final moults. This process can take many months down to a single month in warm climate with plentiful food.\n\n\n\n\nSource: The Dragonfly Life Cycle (https://www.thoughtco.com/dragonfly-life-cycle-1968257).\n\n\n\n\nNote. As to the spider, that also seems to be a moulted exoskeleton, but a clearer picture would be required for identification."}],"domain":"biology","external_citations":["https://i.sstatic.net/A2NxHIN8.png","https://i.sstatic.net/KbRrOJGy.jpg","https://i.sstatic.net/bZcS7OrU.jpg","https://i.sstatic.net/zOu0RTl5.jpg","https://maps.app.goo.gl/xYgEHftC6qeqtjTs9","https://www.thoughtco.com/dragonfly-life-cycle-1968257"],"ground_truth_type":"metadata_grounded","group_id":"fbf24df08bf72b032f04ed9c7b372bb27652433d933558d1d76cb56f23f92214","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-7d9b7844a8d14bff68df1591","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:02:59.816967+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/55bbc2350ddd64077cfc2cba10ad5323a3aabdbe06356ba63f9b4f2161e7b47f_0.json","raw_sha256":"816eaaa302266f8cc647e663e24b4d7ecdb9f8cc125751c689d3329286131873","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"trejder","profile_url":"https://biology.stackexchange.com/users/8986/trejder","user_type":"registered"},"created_at":"2026-07-10T14:10:18+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"899E178E-8675-4232-8413-8EACD4D46629","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/899E178E-8675-4232-8413-8EACD4D46629/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-07-10T22:22:42+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"6A97D9D7-6A97-4AF5-BEDD-C5013E36E795","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/6A97D9D7-6A97-4AF5-BEDD-C5013E36E795/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"119586","source_record_sha256":"b090c1bda08df2509bdba4ca166e48b70b31036f2f426e43423b52290ffed09c","source_url":"https://biology.stackexchange.com/questions/119586/identify-northern-poland-masuria-region-molt-or-a-dead-insect","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Identify Northern Poland / Masuria region molt or a dead insect\nI found this empty insect shell indoors, and I'm trying to identify what creature left it behind. Can you help me with that?\n\n\n\n\n[image: Main image; source: https://i.sstatic.net/bZcS7OrU.jpg] (https://i.sstatic.net/bZcS7OrU.jpg)\n\n\n\n\n[image: Close-up; source: https://i.sstatic.net/zOu0RTl5.jpg] (https://i.sstatic.net/zOu0RTl5.jpg)\n\n\n\n\n[image: Size reference; source: https://i.sstatic.net/KbRrOJGy.jpg] (https://i.sstatic.net/KbRrOJGy.jpg)\n\n\n\n\n\nExact location: 53°40'15.3\"N 21°28'58.7\"E (https://maps.app.goo.gl/xYgEHftC6qeqtjTs9)\n\n\n\n\nLocation description: Europe, Northern Poland, Masuria region (wooded area near river Krutynia).\n\n\n\n\nSize: For scale, I've included a matchstick in one of the photos (a standard matchstick is about 4.5 cm / 1.8 inches long).\n\n\n\n\n\nAt first glance, the body shape made me think it might be the remains or a molt of some kind of wasp or a bee, but I am completely unsure. There is also a tiny spider attached to one of its back legs, though that might just be a coincidence.\n\n\n\n\nIs this an insect molt (exuvia), or a dead insect eaten from the inside? Can anyone help me identify the species or family?\n\n\n\n\nCan you also try to identify this tiny spider (if photo quality isn't to low)?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":119587,"score":6}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p><a href=\"https://en.wikipedia.org/wiki/All_models_are_wrong\" rel=\"noreferrer\">&quot;All models are wrong, but some are useful&quot;</a>.</p>\n<p>If you spend enough time studying biology, you'll find exceptions for basically everything. But, if you deal with all the exceptions as you reach them, you'd never get to any real understanding, you'd be permanently lost in the weeds.</p>\n<p>Similarly, &quot;F = m*a&quot; is simply <em>wrong</em>. Einstein showed as much. Yet, it's still used in physics because it's close enough to true within distant rounding error for most problems on the scale that humans encounter.</p>\n<p>The examples you give: the improbable case where biologically produced photons land on the photosynthetic machinery of another organism, is too much an edge case to matter. It's lost in the rounding error and is not at all worth considering at the ecosystem level. Predictions you would make with the simpler unidirectional model are sufficient.</p>\n<p>It often makes good sense to use a model of the world that you know is wrong when you also know it's good enough for some purpose.</p>\n","answer_id":119696,"answer_text":"\"All models are wrong, but some are useful\" (https://en.wikipedia.org/wiki/All_models_are_wrong).\n\n\n\n\nIf you spend enough time studying biology, you'll find exceptions for basically everything. But, if you deal with all the exceptions as you reach them, you'd never get to any real understanding, you'd be permanently lost in the weeds.\n\n\n\n\nSimilarly, \"F = m*a\" is simply wrong. Einstein showed as much. Yet, it's still used in physics because it's close enough to true within distant rounding error for most problems on the scale that humans encounter.\n\n\n\n\nThe examples you give: the improbable case where biologically produced photons land on the photosynthetic machinery of another organism, is too much an edge case to matter. It's lost in the rounding error and is not at all worth considering at the ecosystem level. Predictions you would make with the simpler unidirectional model are sufficient.\n\n\n\n\nIt often makes good sense to use a model of the world that you know is wrong when you also know it's good enough for some purpose.","answer_url":"https://biology.stackexchange.com/a/119696","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2026-09-06T16:43:49+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:15.662681+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/a3538a112d2673cfffa93fc560422c19505faae6be4a1f12e2257fdcf1f73be7_0.json","raw_sha256":"7acb3bc453a966dfabe30ea4b4512b47f05762b670683f81362bb1dd4500b9a8","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/119725;119721;119720;119695;119675;119670;119661;119648;119640;119639;119635;119631;119628;119607;119605;119601;119598;119586;119582;119579;119577;119565;119561;119560;119542;119539;119529;119527;119522;119518;119506;119501;119497;119489;119487;119479;119465;119455;119453;119450;119444;119439;119434;119430;119421;119416;119404;119399;119398;119377;119376;119369;119362;119361;119355;119353;119350;119342;119340;119328;119326;119321;119317;119313;119312;119311;119306;119304;119287;119275;119273;119270;119268;119267;119260;119256;119251;119248;119238;119237;119235;119231;119227;119221;119212;119211;119209;119207;119201;119195;119193;119190;119185;119180;118180;118175;118172;118168;118158;118155/answers?filter=withbody&order=asc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":119695,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Bryan Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2026-09-06T16:43:49+00:00","raw_file":"raw/codex_api_v1/05a07ac5b899aedc4a355e74e14372bb9f5c68880d960b52e1cb7db2e69e21a7_1790824192733506600_0.json","raw_sha256":"a95113893b680d2f015d30e681bff685c192aae637f6399ca4974513858f935d","revision_guid":"F0BCF718-970C-41BD-871E-91F1CC8024FA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F0BCF718-970C-41BD-871E-91F1CC8024FA/view-source"}],"score":19},{"answer_html":"<p>The linear flow model is a generalization, and to be very precise you can think of it as a one way stream with lots of tiny exceptions and loops which represent way less than 1,000th of the total energy flow. Exceptions are cases like bacteria, mycorrhyzea, mushrooms, bioluminescence, animal exothermy.</p>\n","answer_id":119699,"answer_text":"The linear flow model is a generalization, and to be very precise you can think of it as a one way stream with lots of tiny exceptions and loops which represent way less than 1,000th of the total energy flow. Exceptions are cases like bacteria, mycorrhyzea, mushrooms, bioluminescence, animal exothermy.","answer_url":"https://biology.stackexchange.com/a/119699","author":"bandybabboon","author_url":"https://biology.stackexchange.com/users/8952/bandybabboon","content_license":"CC BY-SA 4.0","created_at":"2026-09-07T11:39:20+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:15.662681+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/a3538a112d2673cfffa93fc560422c19505faae6be4a1f12e2257fdcf1f73be7_0.json","raw_sha256":"7acb3bc453a966dfabe30ea4b4512b47f05762b670683f81362bb1dd4500b9a8","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/119725;119721;119720;119695;119675;119670;119661;119648;119640;119639;119635;119631;119628;119607;119605;119601;119598;119586;119582;119579;119577;119565;119561;119560;119542;119539;119529;119527;119522;119518;119506;119501;119497;119489;119487;119479;119465;119455;119453;119450;119444;119439;119434;119430;119421;119416;119404;119399;119398;119377;119376;119369;119362;119361;119355;119353;119350;119342;119340;119328;119326;119321;119317;119313;119312;119311;119306;119304;119287;119275;119273;119270;119268;119267;119260;119256;119251;119248;119238;119237;119235;119231;119227;119221;119212;119211;119209;119207;119201;119195;119193;119190;119185;119180;118180;118175;118172;118168;118158;118155/answers?filter=withbody&order=asc&page=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":119695,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"bandybabboon","profile_url":"https://biology.stackexchange.com/users/8952/bandybabboon","user_type":"registered"},"created_at":"2026-09-07T11:39:20+00:00","raw_file":"raw/codex_api_v1/05a07ac5b899aedc4a355e74e14372bb9f5c68880d960b52e1cb7db2e69e21a7_1790824192733506600_0.json","raw_sha256":"a95113893b680d2f015d30e681bff685c192aae637f6399ca4974513858f935d","revision_guid":"937D4379-2C89-4522-9C68-ACF6295006C5","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/937D4379-2C89-4522-9C68-ACF6295006C5/view-source"}],"score":0}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Md . 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Couldn't certain organisms create minor, albeit negligible, feedback loops? Specifically, I am thinking about bioluminescent organisms (e.g., Fireflies, Foxfire Fungi): These organisms convert chemical energy back into light energy. Even if the amount is tiny, if this light hits a plant leaf and falls within the visible spectrum accepted by chlorophyll, wouldn't it technically be re-entered into photosynthesis?</p>\n<p>Wouldn't this mean a consumer is returning energy to a producer?Decomposers and Symbionts: We know that gut fauna break down materials and produce short-chain fatty acids that directly power the cells of their host's gut lining. Even if these energy returns are highly inefficient or minor, wouldn't they technically make the ecosystem more of an open cycle rather than a strictly one-way, linear line?</p>\n<p>Here is the screenshot from Pearson's biology global edition:</p>\n<p><a href=\"https://i.sstatic.net/nS61sABP.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/nS61sABP.png\" alt=\"in the description of the image caption it says one way \" /></a></p>\n","text":"I fully understand the 10% Rule of ecosystems—I get that energy is used for metabolism and lost as heat at each trophic level, causing the total available energy to decrease dramatically as you move up the food chain.\n\n\n\n\nHowever, I am confused about why energy flow is defined as strictly linear and unidirectional, with zero energy returning to producers. Couldn't certain organisms create minor, albeit negligible, feedback loops? Specifically, I am thinking about bioluminescent organisms (e.g., Fireflies, Foxfire Fungi): These organisms convert chemical energy back into light energy. Even if the amount is tiny, if this light hits a plant leaf and falls within the visible spectrum accepted by chlorophyll, wouldn't it technically be re-entered into photosynthesis?\n\n\n\n\nWouldn't this mean a consumer is returning energy to a producer?Decomposers and Symbionts: We know that gut fauna break down materials and produce short-chain fatty acids that directly power the cells of their host's gut lining. Even if these energy returns are highly inefficient or minor, wouldn't they technically make the ecosystem more of an open cycle rather than a strictly one-way, linear line?\n\n\n\n\nHere is the screenshot from Pearson's biology global edition:\n\n\n\n\n[image: in the description of the image caption it says one way ; source: https://i.sstatic.net/nS61sABP.png] (https://i.sstatic.net/nS61sABP.png)"},{"context_id":"119696","html":"<p><a href=\"https://en.wikipedia.org/wiki/All_models_are_wrong\" rel=\"noreferrer\">&quot;All models are wrong, but some are useful&quot;</a>.</p>\n<p>If you spend enough time studying biology, you'll find exceptions for basically everything. But, if you deal with all the exceptions as you reach them, you'd never get to any real understanding, you'd be permanently lost in the weeds.</p>\n<p>Similarly, &quot;F = m*a&quot; is simply <em>wrong</em>. Einstein showed as much. Yet, it's still used in physics because it's close enough to true within distant rounding error for most problems on the scale that humans encounter.</p>\n<p>The examples you give: the improbable case where biologically produced photons land on the photosynthetic machinery of another organism, is too much an edge case to matter. It's lost in the rounding error and is not at all worth considering at the ecosystem level. Predictions you would make with the simpler unidirectional model are sufficient.</p>\n<p>It often makes good sense to use a model of the world that you know is wrong when you also know it's good enough for some purpose.</p>\n","text":"\"All models are wrong, but some are useful\" (https://en.wikipedia.org/wiki/All_models_are_wrong).\n\n\n\n\nIf you spend enough time studying biology, you'll find exceptions for basically everything. But, if you deal with all the exceptions as you reach them, you'd never get to any real understanding, you'd be permanently lost in the weeds.\n\n\n\n\nSimilarly, \"F = m*a\" is simply wrong. Einstein showed as much. Yet, it's still used in physics because it's close enough to true within distant rounding error for most problems on the scale that humans encounter.\n\n\n\n\nThe examples you give: the improbable case where biologically produced photons land on the photosynthetic machinery of another organism, is too much an edge case to matter. It's lost in the rounding error and is not at all worth considering at the ecosystem level. Predictions you would make with the simpler unidirectional model are sufficient.\n\n\n\n\nIt often makes good sense to use a model of the world that you know is wrong when you also know it's good enough for some purpose."},{"context_id":"119699","html":"<p>The linear flow model is a generalization, and to be very precise you can think of it as a one way stream with lots of tiny exceptions and loops which represent way less than 1,000th of the total energy flow. Exceptions are cases like bacteria, mycorrhyzea, mushrooms, bioluminescence, animal exothermy.</p>\n","text":"The linear flow model is a generalization, and to be very precise you can think of it as a one way stream with lots of tiny exceptions and loops which represent way less than 1,000th of the total energy flow. Exceptions are cases like bacteria, mycorrhyzea, mushrooms, bioluminescence, animal exothermy."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/All_models_are_wrong","https://i.sstatic.net/nS61sABP.png"],"ground_truth_type":"metadata_grounded","group_id":"fef3fe95812506e6c2b2528ca4250ea8b4230d7dbcc1118a6703489886c2d560","hard_case_family":["no_accepted_answer","multiple_sources","multiple_answer_candidates"],"id":"RHM-8efe0f8613304aed91822dc4","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:02:59.816967+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/55bbc2350ddd64077cfc2cba10ad5323a3aabdbe06356ba63f9b4f2161e7b47f_0.json","raw_sha256":"816eaaa302266f8cc647e663e24b4d7ecdb9f8cc125751c689d3329286131873","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Md . 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Rafatul islam","profile_url":"https://biology.stackexchange.com/users/130609/md-rafatul-islam","user_type":"registered"},"created_at":"2026-09-06T12:23:02+00:00","raw_file":"raw/codex_api_v1/05a07ac5b899aedc4a355e74e14372bb9f5c68880d960b52e1cb7db2e69e21a7_1790824192733506600_0.json","raw_sha256":"a95113893b680d2f015d30e681bff685c192aae637f6399ca4974513858f935d","revision_guid":"5025D7F3-5D0B-4562-9BA8-B8E27B4458CE","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5025D7F3-5D0B-4562-9BA8-B8E27B4458CE/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"terdon","profile_url":"https://biology.stackexchange.com/users/1306/terdon","user_type":"moderator"},"created_at":"2026-09-07T09:26:33+00:00","raw_file":"raw/codex_api_v1/05a07ac5b899aedc4a355e74e14372bb9f5c68880d960b52e1cb7db2e69e21a7_1790824192733506600_0.json","raw_sha256":"a95113893b680d2f015d30e681bff685c192aae637f6399ca4974513858f935d","revision_guid":"E03ADEC8-74BD-40E4-80DF-0ECCE8F6E9F7","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E03ADEC8-74BD-40E4-80DF-0ECCE8F6E9F7/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-09-07T09:30:27+00:00","raw_file":"raw/codex_api_v1/05a07ac5b899aedc4a355e74e14372bb9f5c68880d960b52e1cb7db2e69e21a7_1790824192733506600_0.json","raw_sha256":"a95113893b680d2f015d30e681bff685c192aae637f6399ca4974513858f935d","revision_guid":"C7E7F68A-24A6-4DBB-B760-FABC4E85E2DF","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/C7E7F68A-24A6-4DBB-B760-FABC4E85E2DF/view-source"}],"source_commit":"049a9227f533c13bbc10d1a38c271e055da0ed6e","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Biology-QA","source_license":"CC BY-SA 4.0","source_record_id":"119695","source_record_sha256":"48b36f968d267053b37ca36600aa8d0eb57efb5e357fee73b8e277b9c6af50ba","source_url":"https://biology.stackexchange.com/questions/119695/why-is-ecosystem-energy-flow-strictly-unidirectional-are-there-no-tiny-energy-f","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Why is ecosystem energy flow strictly unidirectional? Are there no tiny energy feedback loops?\nI fully understand the 10% Rule of ecosystems—I get that energy is used for metabolism and lost as heat at each trophic level, causing the total available energy to decrease dramatically as you move up the food chain.\n\n\n\n\nHowever, I am confused about why energy flow is defined as strictly linear and unidirectional, with zero energy returning to producers. Couldn't certain organisms create minor, albeit negligible, feedback loops? Specifically, I am thinking about bioluminescent organisms (e.g., Fireflies, Foxfire Fungi): These organisms convert chemical energy back into light energy. Even if the amount is tiny, if this light hits a plant leaf and falls within the visible spectrum accepted by chlorophyll, wouldn't it technically be re-entered into photosynthesis?\n\n\n\n\nWouldn't this mean a consumer is returning energy to a producer?Decomposers and Symbionts: We know that gut fauna break down materials and produce short-chain fatty acids that directly power the cells of their host's gut lining. Even if these energy returns are highly inefficient or minor, wouldn't they technically make the ecosystem more of an open cycle rather than a strictly one-way, linear line?\n\n\n\n\nHere is the screenshot from Pearson's biology global edition:\n\n\n\n\n[image: in the description of the image caption it says one way ; source: https://i.sstatic.net/nS61sABP.png] (https://i.sstatic.net/nS61sABP.png)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":119696,"score":19},{"answer_id":119699,"score":0}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I am aware of some discussion of how to bootstrap residuals in (non-linear, but that's more coincidental) mixed effects models in <a href=\"https://doi.org/10.1016/S0378-3758(98)00145-1\" rel=\"nofollow noreferrer\">Das and Krishen 1999</a>. This is, again, from the pharmacometrics field like the 2013 paper you found (perhaps where they go their ideas from?).</p>\n<p>A search additionally let me find <a href=\"https://www.bristol.ac.uk/media-library/sites/cmm/migrated/documents/new7-2.pdf\" rel=\"nofollow noreferrer\">Meijer, van der Leeden and Busing 1995</a>, which refers to a user manual for a software called MLA (I've never heard of) from 1994.</p>\n<p>That's still 15 years after the <a href=\"https://doi.org/10.1214%2Faos%2F1176344552\" rel=\"nofollow noreferrer\">start of the bootstrap literature</a> in 1979 and something like 38 to 45 from the beginnings of the jackknife (and mixed models have been around for about that long, too, I think). So there's definitely scope that someone did/published stuff before then. However, older stuff I found like</p>\n<ul>\n<li>J. G. Bagaka. Two Level Nested Hierarchical Linear Model with Random\nIntercepts via the Bootstrap. PhD thesis, Michigan State University, East Lansing, MI, 1992. (Available from University Microfilms International, publication number AAT 9302972, <a href=\"http://www.umi.com\" rel=\"nofollow noreferrer\">http://www.umi.com</a>)</li>\n</ul>\n<p>is about resampling cases (i.e. hierachical units) rather than residuals, or</p>\n<ul>\n<li>Bellmann, L., Breitung, J. and Wagner, J., 1989. Bias correction and bootstrapping of error component models for panel data: Theory and applications. Empirical Economics, 14(4), pp.329-342.</li>\n</ul>\n<p>where it's parametric bootstrapping of residuals.</p>\n","answer_id":676840,"answer_text":"I am aware of some discussion of how to bootstrap residuals in (non-linear, but that's more coincidental) mixed effects models in Das and Krishen 1999 (https://doi.org/10.1016/S0378-3758(98)00145-1). This is, again, from the pharmacometrics field like the 2013 paper you found (perhaps where they go their ideas from?).\n\n\n\n\nA search additionally let me find Meijer, van der Leeden and Busing 1995 (https://www.bristol.ac.uk/media-library/sites/cmm/migrated/documents/new7-2.pdf), which refers to a user manual for a software called MLA (I've never heard of) from 1994.\n\n\n\n\nThat's still 15 years after the start of the bootstrap literature (https://doi.org/10.1214%2Faos%2F1176344552) in 1979 and something like 38 to 45 from the beginnings of the jackknife (and mixed models have been around for about that long, too, I think). So there's definitely scope that someone did/published stuff before then. However, older stuff I found like\n\n\n\n\n\nJ. G. Bagaka. Two Level Nested Hierarchical Linear Model with Random\nIntercepts via the Bootstrap. PhD thesis, Michigan State University, East Lansing, MI, 1992. (Available from University Microfilms International, publication number AAT 9302972, http://www.umi.com (http://www.umi.com))\n\n\n\n\n\nis about resampling cases (i.e. hierachical units) rather than residuals, or\n\n\n\n\n\nBellmann, L., Breitung, J. and Wagner, J., 1989. Bias correction and bootstrapping of error component models for panel data: Theory and applications. Empirical Economics, 14(4), pp.329-342.\n\n\n\n\n\nwhere it's parametric bootstrapping of residuals.","answer_url":"https://stats.stackexchange.com/a/676840","author":"Björn","author_url":"https://stats.stackexchange.com/users/86652/bj%c3%b6rn","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-08-11T07:33:29+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:27:06.169765+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/9155f81b0f1dac4b0f83fad58469033af46ad34ee8d731e569d063b41b3df6b6_1790825226563497500_0.json","raw_sha256":"cbac4b1b24e2159f1c17ea9902eaf89a0a5260344e6dba6f75790ba955f0d04b","source_api":"Stack Exchange API 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Bolker","profile_url":"https://stats.stackexchange.com/users/2126/ben-bolker","user_type":"registered"},"created_at":"2026-08-10T18:14:05+00:00","raw_file":"raw/codex_api_v1/4f74c7234d8d68222a97a637c85bc14d5aa045a3d3f336d95a6178b29bc656cd_1790825248437413600_0.json","raw_sha256":"8385102f4bd0517d9240ab820144fa12ccb111d0c4dd000e66bdc0e0ba0294fe","revision_guid":"D42FF201-3D9E-41EE-AD38-D701B246BD21","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/D42FF201-3D9E-41EE-AD38-D701B246BD21/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Ben Bolker","profile_url":"https://stats.stackexchange.com/users/2126/ben-bolker","user_type":"registered"},"created_at":"2026-08-10T18:34:39+00:00","raw_file":"raw/codex_api_v1/4f74c7234d8d68222a97a637c85bc14d5aa045a3d3f336d95a6178b29bc656cd_1790825248437413600_0.json","raw_sha256":"8385102f4bd0517d9240ab820144fa12ccb111d0c4dd000e66bdc0e0ba0294fe","revision_guid":"30821CFD-69CB-49E7-8636-CD19053C6EFF","revision_number":2,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/30821CFD-69CB-49E7-8636-CD19053C6EFF/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-08-11T09:36:33+00:00","raw_file":"raw/codex_api_v1/4f74c7234d8d68222a97a637c85bc14d5aa045a3d3f336d95a6178b29bc656cd_1790825248437413600_0.json","raw_sha256":"8385102f4bd0517d9240ab820144fa12ccb111d0c4dd000e66bdc0e0ba0294fe","revision_guid":"4D25C7FB-5C99-4487-BCBA-B001C9D9782A","revision_number":null,"revision_type":"vote_based","revision_url":"https://stats.stackexchange.com/revisions/4D25C7FB-5C99-4487-BCBA-B001C9D9782A/view-source"}],"url":"https://stats.stackexchange.com/questions/676832/references-on-semiparametric-bootstrapping-in-mixed-multilevel-models"},{"author":"Björn","author_url":"https://stats.stackexchange.com/users/86652/bj%c3%b6rn","content_license":"CC BY-SA 4.0","context_id":"676840","revision_attribution":[{"content_license":"CC BY-SA 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4.0","contributor":{"display_name":"Björn","profile_url":"https://stats.stackexchange.com/users/86652/bj%c3%b6rn","user_type":"registered"},"created_at":"2026-08-11T07:43:14+00:00","raw_file":"raw/codex_api_v1/4f74c7234d8d68222a97a637c85bc14d5aa045a3d3f336d95a6178b29bc656cd_1790825248437413600_0.json","raw_sha256":"8385102f4bd0517d9240ab820144fa12ccb111d0c4dd000e66bdc0e0ba0294fe","revision_guid":"3E76600E-590B-459B-BAD0-E785E7ABDDA0","revision_number":2,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/3E76600E-590B-459B-BAD0-E785E7ABDDA0/view-source"}],"url":"https://stats.stackexchange.com/a/676840"}],"contexts":[{"context_id":"question","html":"<p>I'm having a hard time finding primary references on semiparametric bootstrapping (i.e. residual bootstrapping) for multilevel/mixed models. <a href=\"https://stats.stackexchange.com/questions/29500/parametric-semiparametric-and-nonparametric-bootstrapping-for-mixed-models\">This CV question</a> refers to Shang and Cavanaugh (2008), but that paper doesn't provide anything going further back. I can't find anything in Chernick (2011) or Efron and Tibshirani (1994) (I haven't looked at Davis and Hinckley, but I would be surprised if there was anything there ...) The other references listed below are interesting, but not useful as far as I can tell.</p>\n<p>The basic question is how one should do residual-based bootstrapping for linear mixed models; do you resample both BLUPs/latent variables and residuals based on cluster-level residuals <span class=\"math-container\">$\\mathbf y - \\mathbf X \\hat{\\boldsymbol \\beta} - \\mathbf Z \\hat{\\mathbf b}$</span> (Morris 2002 says this doesn't work)?  Simulate <span class=\"math-container\">$\\mathbf b$</span> from the unconditional MVN distribution of latent variables (i.e., using the estimated random effects covariance matrices) and add those values to resampled cluster-level residuals and population-level predictions? Use resampled population-level residuals <span class=\"math-container\">$\\mathbf y - \\mathbf X \\hat{\\boldsymbol \\beta}$</span> added back to the population-level predictions?</p>\n<p>The last option seems to be what's recommended, but I would really like to see the original discussion/theoretical justification for this ...</p>\n<hr />\n<p>Chernick, Michael R. Bootstrap Methods: A Guide for Practitioners and Researchers. John Wiley &amp; Sons, 2011.</p>\n<p>Efron, Bradley, and R. J. Tibshirani. An Introduction to the Bootstrap. CRC Press, 1994.</p>\n<p>Morris, Jeffrey S. “The BLUPs Are Not ‘Best’ When It Comes to Bootstrapping.” Statistics &amp; Probability Letters 56, no. 4 (2002): 425–30. <a href=\"https://doi.org/10.1016/S0167-7152(02)00041-X\" rel=\"noreferrer\">https://doi.org/10.1016/S0167-7152(02)00041-X</a>.</p>\n<p>Shang, Junfeng, and Joseph E. Cavanaugh. “An Assumption for the Development of Bootstrap Variants of the Akaike Information Criterion in Mixed Models.” Statistics &amp; Probability Letters 78, no. 12 (2008): 1422–29. <a href=\"https://doi.org/10.1016/j.spl.2007.12.015\" rel=\"noreferrer\">https://doi.org/10.1016/j.spl.2007.12.015</a>.</p>\n<p>Thai, Hoai-Thu, France Mentré, Nicholas H. G. Holford, Christine Veyrat-Follet, and Emmanuelle Comets. “A Comparison of Bootstrap Approaches for Estimating Uncertainty of Parameters in Linear Mixed-Effects Models.” Pharmaceutical Statistics 12, no. 3 (2013): 129–40. <a href=\"https://doi.org/10.1002/pst.1561\" rel=\"noreferrer\">https://doi.org/10.1002/pst.1561</a>.</p>\n","text":"I'm having a hard time finding primary references on semiparametric bootstrapping (i.e. residual bootstrapping) for multilevel/mixed models. This CV question (https://stats.stackexchange.com/questions/29500/parametric-semiparametric-and-nonparametric-bootstrapping-for-mixed-models) refers to Shang and Cavanaugh (2008), but that paper doesn't provide anything going further back. I can't find anything in Chernick (2011) or Efron and Tibshirani (1994) (I haven't looked at Davis and Hinckley, but I would be surprised if there was anything there ...) The other references listed below are interesting, but not useful as far as I can tell.\n\n\n\n\nThe basic question is how one should do residual-based bootstrapping for linear mixed models; do you resample both BLUPs/latent variables and residuals based on cluster-level residuals $\\mathbf y - \\mathbf X \\hat{\\boldsymbol \\beta} - \\mathbf Z \\hat{\\mathbf b}$ (Morris 2002 says this doesn't work)?  Simulate $\\mathbf b$ from the unconditional MVN distribution of latent variables (i.e., using the estimated random effects covariance matrices) and add those values to resampled cluster-level residuals and population-level predictions? Use resampled population-level residuals $\\mathbf y - \\mathbf X \\hat{\\boldsymbol \\beta}$ added back to the population-level predictions?\n\n\n\n\nThe last option seems to be what's recommended, but I would really like to see the original discussion/theoretical justification for this ...\n\n\n\n\n\n\n\nChernick, Michael R. Bootstrap Methods: A Guide for Practitioners and Researchers. John Wiley & Sons, 2011.\n\n\n\n\nEfron, Bradley, and R. J. Tibshirani. An Introduction to the Bootstrap. CRC Press, 1994.\n\n\n\n\nMorris, Jeffrey S. “The BLUPs Are Not ‘Best’ When It Comes to Bootstrapping.” Statistics & Probability Letters 56, no. 4 (2002): 425–30. https://doi.org/10.1016/S0167-7152(02)00041-X (https://doi.org/10.1016/S0167-7152(02)00041-X).\n\n\n\n\nShang, Junfeng, and Joseph E. Cavanaugh. “An Assumption for the Development of Bootstrap Variants of the Akaike Information Criterion in Mixed Models.” Statistics & Probability Letters 78, no. 12 (2008): 1422–29. https://doi.org/10.1016/j.spl.2007.12.015 (https://doi.org/10.1016/j.spl.2007.12.015).\n\n\n\n\nThai, Hoai-Thu, France Mentré, Nicholas H. G. Holford, Christine Veyrat-Follet, and Emmanuelle Comets. “A Comparison of Bootstrap Approaches for Estimating Uncertainty of Parameters in Linear Mixed-Effects Models.” Pharmaceutical Statistics 12, no. 3 (2013): 129–40. https://doi.org/10.1002/pst.1561 (https://doi.org/10.1002/pst.1561)."},{"context_id":"676840","html":"<p>I am aware of some discussion of how to bootstrap residuals in (non-linear, but that's more coincidental) mixed effects models in <a href=\"https://doi.org/10.1016/S0378-3758(98)00145-1\" rel=\"nofollow noreferrer\">Das and Krishen 1999</a>. This is, again, from the pharmacometrics field like the 2013 paper you found (perhaps where they go their ideas from?).</p>\n<p>A search additionally let me find <a href=\"https://www.bristol.ac.uk/media-library/sites/cmm/migrated/documents/new7-2.pdf\" rel=\"nofollow noreferrer\">Meijer, van der Leeden and Busing 1995</a>, which refers to a user manual for a software called MLA (I've never heard of) from 1994.</p>\n<p>That's still 15 years after the <a href=\"https://doi.org/10.1214%2Faos%2F1176344552\" rel=\"nofollow noreferrer\">start of the bootstrap literature</a> in 1979 and something like 38 to 45 from the beginnings of the jackknife (and mixed models have been around for about that long, too, I think). So there's definitely scope that someone did/published stuff before then. However, older stuff I found like</p>\n<ul>\n<li>J. G. Bagaka. Two Level Nested Hierarchical Linear Model with Random\nIntercepts via the Bootstrap. PhD thesis, Michigan State University, East Lansing, MI, 1992. (Available from University Microfilms International, publication number AAT 9302972, <a href=\"http://www.umi.com\" rel=\"nofollow noreferrer\">http://www.umi.com</a>)</li>\n</ul>\n<p>is about resampling cases (i.e. hierachical units) rather than residuals, or</p>\n<ul>\n<li>Bellmann, L., Breitung, J. and Wagner, J., 1989. Bias correction and bootstrapping of error component models for panel data: Theory and applications. Empirical Economics, 14(4), pp.329-342.</li>\n</ul>\n<p>where it's parametric bootstrapping of residuals.</p>\n","text":"I am aware of some discussion of how to bootstrap residuals in (non-linear, but that's more coincidental) mixed effects models in Das and Krishen 1999 (https://doi.org/10.1016/S0378-3758(98)00145-1). This is, again, from the pharmacometrics field like the 2013 paper you found (perhaps where they go their ideas from?).\n\n\n\n\nA search additionally let me find Meijer, van der Leeden and Busing 1995 (https://www.bristol.ac.uk/media-library/sites/cmm/migrated/documents/new7-2.pdf), which refers to a user manual for a software called MLA (I've never heard of) from 1994.\n\n\n\n\nThat's still 15 years after the start of the bootstrap literature (https://doi.org/10.1214%2Faos%2F1176344552) in 1979 and something like 38 to 45 from the beginnings of the jackknife (and mixed models have been around for about that long, too, I think). So there's definitely scope that someone did/published stuff before then. However, older stuff I found like\n\n\n\n\n\nJ. G. Bagaka. Two Level Nested Hierarchical Linear Model with Random\nIntercepts via the Bootstrap. PhD thesis, Michigan State University, East Lansing, MI, 1992. (Available from University Microfilms International, publication number AAT 9302972, http://www.umi.com (http://www.umi.com))\n\n\n\n\n\nis about resampling cases (i.e. hierachical units) rather than residuals, or\n\n\n\n\n\nBellmann, L., Breitung, J. and Wagner, J., 1989. Bias correction and bootstrapping of error component models for panel data: Theory and applications. Empirical Economics, 14(4), pp.329-342.\n\n\n\n\n\nwhere it's parametric bootstrapping of residuals."}],"domain":"statistics","external_citations":["http://www.umi.com","https://doi.org/10.1002/pst.1561","https://doi.org/10.1016/S0167-7152(02)00041-X","https://doi.org/10.1016/S0378-3758(98)00145-1","https://doi.org/10.1016/j.spl.2007.12.015","https://doi.org/10.1214%2Faos%2F1176344552","https://stats.stackexchange.com/questions/29500/parametric-semiparametric-and-nonparametric-bootstrapping-for-mixed-models","https://www.bristol.ac.uk/media-library/sites/cmm/migrated/documents/new7-2.pdf"],"ground_truth_type":"metadata_grounded","group_id":"5de4f609d2920f0c25856cc41e558cd2785801c87529a937cbaf38756bdaf1c6","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-fa6b9ff6a22cb483dcfad114","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:27:03.428408+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/774052c18cd9e8fa951e893347bfa3c1a85e743fc46ec4667572002cadb10cbf_1790825224163423600_0.json","raw_sha256":"fe4dd06d3de6c0b1bb33ba88aee0ed4284118e01f76a58dcdce220a4946329b2","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=stats&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Ben Bolker","profile_url":"https://stats.stackexchange.com/users/2126/ben-bolker","user_type":"registered"},"created_at":"2026-08-10T18:14:05+00:00","raw_file":"raw/codex_api_v1/4f74c7234d8d68222a97a637c85bc14d5aa045a3d3f336d95a6178b29bc656cd_1790825248437413600_0.json","raw_sha256":"8385102f4bd0517d9240ab820144fa12ccb111d0c4dd000e66bdc0e0ba0294fe","revision_guid":"D42FF201-3D9E-41EE-AD38-D701B246BD21","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/D42FF201-3D9E-41EE-AD38-D701B246BD21/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Ben Bolker","profile_url":"https://stats.stackexchange.com/users/2126/ben-bolker","user_type":"registered"},"created_at":"2026-08-10T18:34:39+00:00","raw_file":"raw/codex_api_v1/4f74c7234d8d68222a97a637c85bc14d5aa045a3d3f336d95a6178b29bc656cd_1790825248437413600_0.json","raw_sha256":"8385102f4bd0517d9240ab820144fa12ccb111d0c4dd000e66bdc0e0ba0294fe","revision_guid":"30821CFD-69CB-49E7-8636-CD19053C6EFF","revision_number":2,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/30821CFD-69CB-49E7-8636-CD19053C6EFF/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-08-11T09:36:33+00:00","raw_file":"raw/codex_api_v1/4f74c7234d8d68222a97a637c85bc14d5aa045a3d3f336d95a6178b29bc656cd_1790825248437413600_0.json","raw_sha256":"8385102f4bd0517d9240ab820144fa12ccb111d0c4dd000e66bdc0e0ba0294fe","revision_guid":"4D25C7FB-5C99-4487-BCBA-B001C9D9782A","revision_number":null,"revision_type":"vote_based","revision_url":"https://stats.stackexchange.com/revisions/4D25C7FB-5C99-4487-BCBA-B001C9D9782A/view-source"}],"source_commit":"3f6db230c4afe97d558b23fe2bfdb56dc0010d95","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Statistics-QA","source_license":"CC BY-SA 4.0","source_record_id":"Scientific-Statistics-QA:stats:676832","source_record_sha256":"2d97b361c97aed6b28e83f7263e99fa5a8edf430beaa25fb681747acae142092","source_url":"https://stats.stackexchange.com/questions/676832/references-on-semiparametric-bootstrapping-in-mixed-multilevel-models","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"references on semiparametric bootstrapping in mixed/multilevel models\nI'm having a hard time finding primary references on semiparametric bootstrapping (i.e. residual bootstrapping) for multilevel/mixed models. This CV question (https://stats.stackexchange.com/questions/29500/parametric-semiparametric-and-nonparametric-bootstrapping-for-mixed-models) refers to Shang and Cavanaugh (2008), but that paper doesn't provide anything going further back. I can't find anything in Chernick (2011) or Efron and Tibshirani (1994) (I haven't looked at Davis and Hinckley, but I would be surprised if there was anything there ...) The other references listed below are interesting, but not useful as far as I can tell.\n\n\n\n\nThe basic question is how one should do residual-based bootstrapping for linear mixed models; do you resample both BLUPs/latent variables and residuals based on cluster-level residuals $\\mathbf y - \\mathbf X \\hat{\\boldsymbol \\beta} - \\mathbf Z \\hat{\\mathbf b}$ (Morris 2002 says this doesn't work)?  Simulate $\\mathbf b$ from the unconditional MVN distribution of latent variables (i.e., using the estimated random effects covariance matrices) and add those values to resampled cluster-level residuals and population-level predictions? Use resampled population-level residuals $\\mathbf y - \\mathbf X \\hat{\\boldsymbol \\beta}$ added back to the population-level predictions?\n\n\n\n\nThe last option seems to be what's recommended, but I would really like to see the original discussion/theoretical justification for this ...\n\n\n\n\n\n\n\nChernick, Michael R. Bootstrap Methods: A Guide for Practitioners and Researchers. John Wiley & Sons, 2011.\n\n\n\n\nEfron, Bradley, and R. J. Tibshirani. An Introduction to the Bootstrap. CRC Press, 1994.\n\n\n\n\nMorris, Jeffrey S. “The BLUPs Are Not ‘Best’ When It Comes to Bootstrapping.” Statistics & Probability Letters 56, no. 4 (2002): 425–30. https://doi.org/10.1016/S0167-7152(02)00041-X (https://doi.org/10.1016/S0167-7152(02)00041-X).\n\n\n\n\nShang, Junfeng, and Joseph E. Cavanaugh. “An Assumption for the Development of Bootstrap Variants of the Akaike Information Criterion in Mixed Models.” Statistics & Probability Letters 78, no. 12 (2008): 1422–29. https://doi.org/10.1016/j.spl.2007.12.015 (https://doi.org/10.1016/j.spl.2007.12.015).\n\n\n\n\nThai, Hoai-Thu, France Mentré, Nicholas H. G. Holford, Christine Veyrat-Follet, and Emmanuelle Comets. “A Comparison of Bootstrap Approaches for Estimating Uncertainty of Parameters in Linear Mixed-Effects Models.” Pharmaceutical Statistics 12, no. 3 (2013): 129–40. https://doi.org/10.1002/pst.1561 (https://doi.org/10.1002/pst.1561).","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":676840,"score":4}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Welcome to CV!</p>\n<p>So you want to compare 2 proportions; e.g. “<em>Is the proportion of students who receive an A grade in MA101 the same as the proportion of students who receive an A grade in all other MA courses?</em>”.</p>\n<p>Well, the “canonical” way to compare 2 proportions is via a <a href=\"https://en.wikipedia.org/wiki/Contingency_table\" rel=\"nofollow noreferrer\">2x2 contingency table</a> (aka crosstab). And the “canonical” tests are either a <a href=\"https://en.wikipedia.org/wiki/Chi-squared_test\" rel=\"nofollow noreferrer\">chi-square</a> test, or a <a href=\"https://en.wikipedia.org/wiki/Fisher%27s_exact_test\" rel=\"nofollow noreferrer\">Fisher-exact</a> test (aka Fisher-0Irwin test).<br />\nNow, using binomial CI’s will not really answer your 2 questions, unless the answer is obvious” if the 2 CI’s do not overlap, you have a significant difference. And if they overlap to a large extent, you do not have a significant difference. But in between, you can not simply eyeball the CI’s.<br />\nNow, given that you are dealing with (very?) low proportions or counts (how many F’s in a given class? Maybe 2-3?), the chi-square test is not recommended (it is based on a normal approximation, which is not warranted for such low proportions/counts). Nor for that matter are CI’s based on normal approximations, a group the Wilson CI belongs to. And forget about continuity corrections, they do not work properly with very small proportions.<br />\nSo you are left with the Fisher-exact test, or some newer versions of it (which are less “conservative, while remaining “exact”, that is based on exactly the binomial distribution), such as the <a href=\"https://cran.r-universe.dev/exact2x2/doc/exact2x2.pdf\" rel=\"nofollow noreferrer\">Blaker test</a>.</p>\n<p>But there is a subtlety in what you are trying to compare. On one hand, you have the proportion of A’s in one class: easy. On the other hand you have the proportion of A’s in all other MA courses (the scenario is the same for the other question, so I will only address the first). How do you express that 2nd proportion?<br />\nOne option is to simply take the count of all A grades in all other MA courses, and the count of all students enrolled in all other MA classes. And then you can/should indeed use a Fisher-exact (or a Blaker-exact) test. But this will weight each student equally, but not each class (the classes with a large enrollment are more heavily weighted than the classes with a low enrollment). That may be what you want (as it reflects the experience of all students enrolled in all other MA classes), but it may not.\nAn alternative would be to look at all the proportions in all other MA classes, and take the average of these proportions. This weights all classes equally (but not all students). In that case, your test can be done with a single CI. You compute an binomial CI (again using an exact method given your possibly low proportions/counts), and simply see if the average proportion in included in that CI. If it is not, you have established a significant difference (at what ever significance level you chose for the CI).</p>\n<p>Last, you ask about multiple comparisons. The fact that you compute multiple CI’s is not relevant; multiple comparisons only occur when you are making a comparison to a significance level (or checking if a CI contains 0, or 1).. And since you seem to only have 2 questions, then you are only making 2 comparisons.<br />\nThe cautious thing to do would be to use a multiple comparison correction (MCC). Given only 2 comparisons, just use Bonferroni, and halve your significance level.<br />\nBut bolder statisticians could argue that your 2 hypotheses are different, and independent. And therefore, a MCC is not warranted... (should a researcher correct for all the various hypotheses he/she will test in their career?). So depending on your ultimate goal (why only these 2 questions? what are you really trying to show), you may be able to dispense with a MCC.</p>\n","answer_id":677108,"answer_text":"Welcome to CV!\n\n\n\n\nSo you want to compare 2 proportions; e.g. “Is the proportion of students who receive an A grade in MA101 the same as the proportion of students who receive an A grade in all other MA courses?”.\n\n\n\n\nWell, the “canonical” way to compare 2 proportions is via a 2x2 contingency table (https://en.wikipedia.org/wiki/Contingency_table) (aka crosstab). And the “canonical” tests are either a chi-square (https://en.wikipedia.org/wiki/Chi-squared_test) test, or a Fisher-exact (https://en.wikipedia.org/wiki/Fisher%27s_exact_test) test (aka Fisher-0Irwin test).\n\nNow, using binomial CI’s will not really answer your 2 questions, unless the answer is obvious” if the 2 CI’s do not overlap, you have a significant difference. And if they overlap to a large extent, you do not have a significant difference. But in between, you can not simply eyeball the CI’s.\n\nNow, given that you are dealing with (very?) low proportions or counts (how many F’s in a given class? Maybe 2-3?), the chi-square test is not recommended (it is based on a normal approximation, which is not warranted for such low proportions/counts). Nor for that matter are CI’s based on normal approximations, a group the Wilson CI belongs to. And forget about continuity corrections, they do not work properly with very small proportions.\n\nSo you are left with the Fisher-exact test, or some newer versions of it (which are less “conservative, while remaining “exact”, that is based on exactly the binomial distribution), such as the Blaker test (https://cran.r-universe.dev/exact2x2/doc/exact2x2.pdf).\n\n\n\n\nBut there is a subtlety in what you are trying to compare. On one hand, you have the proportion of A’s in one class: easy. On the other hand you have the proportion of A’s in all other MA courses (the scenario is the same for the other question, so I will only address the first). How do you express that 2nd proportion?\n\nOne option is to simply take the count of all A grades in all other MA courses, and the count of all students enrolled in all other MA classes. And then you can/should indeed use a Fisher-exact (or a Blaker-exact) test. But this will weight each student equally, but not each class (the classes with a large enrollment are more heavily weighted than the classes with a low enrollment). That may be what you want (as it reflects the experience of all students enrolled in all other MA classes), but it may not.\nAn alternative would be to look at all the proportions in all other MA classes, and take the average of these proportions. This weights all classes equally (but not all students). In that case, your test can be done with a single CI. You compute an binomial CI (again using an exact method given your possibly low proportions/counts), and simply see if the average proportion in included in that CI. If it is not, you have established a significant difference (at what ever significance level you chose for the CI).\n\n\n\n\nLast, you ask about multiple comparisons. The fact that you compute multiple CI’s is not relevant; multiple comparisons only occur when you are making a comparison to a significance level (or checking if a CI contains 0, or 1).. And since you seem to only have 2 questions, then you are only making 2 comparisons.\n\nThe cautious thing to do would be to use a multiple comparison correction (MCC). Given only 2 comparisons, just use Bonferroni, and halve your significance level.\n\nBut bolder statisticians could argue that your 2 hypotheses are different, and independent. And therefore, a MCC is not warranted... (should a researcher correct for all the various hypotheses he/she will test in their career?). So depending on your ultimate goal (why only these 2 questions? what are you really trying to show), you may be able to dispense with a MCC.","answer_url":"https://stats.stackexchange.com/a/677108","author":"jginestet","author_url":"https://stats.stackexchange.com/users/380096/jginestet","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-09-09T02:03:39+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:27:06.169765+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/9155f81b0f1dac4b0f83fad58469033af46ad34ee8d731e569d063b41b3df6b6_1790825226563497500_0.json","raw_sha256":"cbac4b1b24e2159f1c17ea9902eaf89a0a5260344e6dba6f75790ba955f0d04b","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/677298;677295;677280;677279;677278;677275;677269;677266;677262;677256;677245;677243;677242;677226;677225;677217;677211;677201;677194;677193;677186;677183;677179;677177;677171;677169;677168;677151;677149;677147;677137;677135;677131;677129;677115;677110;677109;677101;677099;677098;677096;677095;677094;677085;677083;677079;677078;677075;677071;677066;677065;677062;677058;677045;677041;677035;677033;677023;677021;676999;676997;676991;676982;676981;676979;676977;676975;676971;676966;676961;676958;676956;676952;676947;676945;676937;676935;676933;676924;676922;676899;676898;676893;676889;676888;676879;676874;676873;676870;676867;676865;676858;676855;676850;676842;676832;676830;676824;676823;676821/answers?filter=withbody&order=asc&page=1&pagesize=100&site=stats&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":677095,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"jginestet","profile_url":"https://stats.stackexchange.com/users/380096/jginestet","user_type":"registered"},"created_at":"2026-09-09T02:03:39+00:00","raw_file":"raw/codex_api_v1/3f959895a29b33d83894e5370d82e1c0cf87f20ac57fa423ebc923738357c657_1790825253957066500_0.json","raw_sha256":"ddd8808039e410ca99f97e2a7f12c307f046c4e5c3e184683bc12f816e6f49fc","revision_guid":"CCDFB1CA-F81D-4A03-BE27-16DD0ED2D9AE","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/CCDFB1CA-F81D-4A03-BE27-16DD0ED2D9AE/view-source"}],"score":1,"updated_at":"2026-09-09T02:03:39+00:00"}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"LST","author_url":"https://stats.stackexchange.com/users/516373/lst","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"LST","profile_url":"https://stats.stackexchange.com/users/516373/lst","user_type":"registered"},"created_at":"2026-09-07T16:47:08+00:00","raw_file":"raw/codex_api_v1/3f959895a29b33d83894e5370d82e1c0cf87f20ac57fa423ebc923738357c657_1790825253957066500_0.json","raw_sha256":"ddd8808039e410ca99f97e2a7f12c307f046c4e5c3e184683bc12f816e6f49fc","revision_guid":"77370A41-A452-40D5-9FE9-E2D1C2A53F6B","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/77370A41-A452-40D5-9FE9-E2D1C2A53F6B/view-source"}],"url":"https://stats.stackexchange.com/questions/677095/testing-differences-in-proportions-wilson-cis-continuity-corrections-and-mult"},{"author":"jginestet","author_url":"https://stats.stackexchange.com/users/380096/jginestet","content_license":"CC BY-SA 4.0","context_id":"677108","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"jginestet","profile_url":"https://stats.stackexchange.com/users/380096/jginestet","user_type":"registered"},"created_at":"2026-09-09T02:03:39+00:00","raw_file":"raw/codex_api_v1/3f959895a29b33d83894e5370d82e1c0cf87f20ac57fa423ebc923738357c657_1790825253957066500_0.json","raw_sha256":"ddd8808039e410ca99f97e2a7f12c307f046c4e5c3e184683bc12f816e6f49fc","revision_guid":"CCDFB1CA-F81D-4A03-BE27-16DD0ED2D9AE","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/CCDFB1CA-F81D-4A03-BE27-16DD0ED2D9AE/view-source"}],"url":"https://stats.stackexchange.com/a/677108"}],"contexts":[{"context_id":"question","html":"<p>I have records of student grades for some university courses. I want to investigate whether any of these courses award significantly different proportions of the best (A) or worst (F) grades, compared to the other courses.</p>\n<p>I have individual student data, but some aggregated dummy data would be:</p>\n<pre><code>modules &lt;- c(\n  &quot;MA101&quot;,&quot;MA102&quot;,&quot;MA103&quot;,&quot;MA201&quot;,&quot;MA202&quot;,&quot;MA301&quot;,&quot;MA302&quot;,\n  &quot;FR101&quot;,&quot;FR102&quot;,&quot;FR104&quot;,&quot;FR201&quot;,&quot;FR202&quot;,&quot;FR203&quot;,&quot;FR301&quot;,\n  &quot;EN101&quot;,&quot;EN102&quot;,&quot;EN201&quot;,&quot;EN202&quot;,&quot;EN203&quot;,&quot;EN301&quot;,&quot;EN302&quot;\n)\ntotals &lt;- sample(30:400, length(modules), replace = TRUE)\ngrade_counts &lt;- t(\n  sapply(totals, function(n) {\n    as.vector(rmultinom(1, n, rep(1, 5)))\n  })\n)\ncolnames(grade_counts) &lt;- LETTERS[1:5]\n\ndummy_data &lt;- data.frame(\n  Module = modules,\n  grade_counts,\n  Total = totals\n)\n</code></pre>\n<p>And the questions I would like to ask are</p>\n<ul>\n<li>Is the proportion of students who receive an A grade in MA101 the same as the proportion of students who receive an A grade in all other MA courses?</li>\n<li>Is the proportion of students who get an F grade in FR202 the same as the proportion of students who get an F grade in other xx200 level courses?</li>\n</ul>\n<p>I did some reading and from <a href=\"https://moderndive.com/8-confidence-intervals.html\" rel=\"nofollow noreferrer\">Chapter 8 Bootstrapping and Confidence Intervals | Statistical Inference via Data Science</a> started out by calculating bootstrap confidence intervals around the proportion of A/F grades awarded in each course, and seeing if these overlapped with the proportion of A/F grades awarded for other courses (e.g. all other MA courses, all other xx200 courses).</p>\n<p>However, having dug a bit further (e.g. <a href=\"https://www.allendowney.com/blog/2024/10/15/bootstrapping-a-proportion/\" rel=\"nofollow noreferrer\">Bootstrapping a Proportion - Probably Overthinking It,</a> <a href=\"https://corplingstats.wordpress.com/2024/12/12/bootstrap-intervals/\" rel=\"nofollow noreferrer\">Bootstrap intervals for the single proportion – corp.ling.stats</a>) it seems that bootstrapping probably wasn’t the way, and I should have instead calculated Wilson CIs.</p>\n<p>Before I go down the wrong path again, I’d love a sense check from some more experienced hands.</p>\n<ul>\n<li>Are Wilson intervals the right approach for these sorts of questions?</li>\n<li>Given that I sometimes have small numbers (&lt;30 students on a course) and rare outcomes (F grades are not common!) I think I should use a continuity correction (<a href=\"https://corplingstats.wordpress.com/2019/04/27/correcting-for-continuity/\" rel=\"nofollow noreferrer\">Correcting for continuity – corp.ling.stats</a>), is that right?</li>\n<li>Any pointers on how to adjust for multiple comparisons, given that I’ll be calculating two CIs each (prop A and prop F) for multiple courses (e.g. each of 7 MA courses against the other 6 MA courses)?</li>\n</ul>\n<p>I have some formal stats training, but not done much that isn't regression for a while. I understand I could run a regression of prop A/prop F with module dummy variables, but I'd like to try branching out to some other skills, where appropriate.</p>\n<p>Thank you.</p>\n","text":"I have records of student grades for some university courses. I want to investigate whether any of these courses award significantly different proportions of the best (A) or worst (F) grades, compared to the other courses.\n\n\n\n\nI have individual student data, but some aggregated dummy data would be:\n\n\n\n\nmodules <- c(\n  \"MA101\",\"MA102\",\"MA103\",\"MA201\",\"MA202\",\"MA301\",\"MA302\",\n  \"FR101\",\"FR102\",\"FR104\",\"FR201\",\"FR202\",\"FR203\",\"FR301\",\n  \"EN101\",\"EN102\",\"EN201\",\"EN202\",\"EN203\",\"EN301\",\"EN302\"\n)\ntotals <- sample(30:400, length(modules), replace = TRUE)\ngrade_counts <- t(\n  sapply(totals, function(n) {\n    as.vector(rmultinom(1, n, rep(1, 5)))\n  })\n)\ncolnames(grade_counts) <- LETTERS[1:5]\n\ndummy_data <- data.frame(\n  Module = modules,\n  grade_counts,\n  Total = totals\n)\n\n\n\n\n\nAnd the questions I would like to ask are\n\n\n\n\n\nIs the proportion of students who receive an A grade in MA101 the same as the proportion of students who receive an A grade in all other MA courses?\n\n\n\n\nIs the proportion of students who get an F grade in FR202 the same as the proportion of students who get an F grade in other xx200 level courses?\n\n\n\n\n\nI did some reading and from Chapter 8 Bootstrapping and Confidence Intervals | Statistical Inference via Data Science (https://moderndive.com/8-confidence-intervals.html) started out by calculating bootstrap confidence intervals around the proportion of A/F grades awarded in each course, and seeing if these overlapped with the proportion of A/F grades awarded for other courses (e.g. all other MA courses, all other xx200 courses).\n\n\n\n\nHowever, having dug a bit further (e.g. Bootstrapping a Proportion - Probably Overthinking It, (https://www.allendowney.com/blog/2024/10/15/bootstrapping-a-proportion/) Bootstrap intervals for the single proportion – corp.ling.stats (https://corplingstats.wordpress.com/2024/12/12/bootstrap-intervals/)) it seems that bootstrapping probably wasn’t the way, and I should have instead calculated Wilson CIs.\n\n\n\n\nBefore I go down the wrong path again, I’d love a sense check from some more experienced hands.\n\n\n\n\n\nAre Wilson intervals the right approach for these sorts of questions?\n\n\n\n\nGiven that I sometimes have small numbers (<30 students on a course) and rare outcomes (F grades are not common!) I think I should use a continuity correction (Correcting for continuity – corp.ling.stats (https://corplingstats.wordpress.com/2019/04/27/correcting-for-continuity/)), is that right?\n\n\n\n\nAny pointers on how to adjust for multiple comparisons, given that I’ll be calculating two CIs each (prop A and prop F) for multiple courses (e.g. each of 7 MA courses against the other 6 MA courses)?\n\n\n\n\n\nI have some formal stats training, but not done much that isn't regression for a while. I understand I could run a regression of prop A/prop F with module dummy variables, but I'd like to try branching out to some other skills, where appropriate.\n\n\n\n\nThank you."},{"context_id":"677108","html":"<p>Welcome to CV!</p>\n<p>So you want to compare 2 proportions; e.g. “<em>Is the proportion of students who receive an A grade in MA101 the same as the proportion of students who receive an A grade in all other MA courses?</em>”.</p>\n<p>Well, the “canonical” way to compare 2 proportions is via a <a href=\"https://en.wikipedia.org/wiki/Contingency_table\" rel=\"nofollow noreferrer\">2x2 contingency table</a> (aka crosstab). And the “canonical” tests are either a <a href=\"https://en.wikipedia.org/wiki/Chi-squared_test\" rel=\"nofollow noreferrer\">chi-square</a> test, or a <a href=\"https://en.wikipedia.org/wiki/Fisher%27s_exact_test\" rel=\"nofollow noreferrer\">Fisher-exact</a> test (aka Fisher-0Irwin test).<br />\nNow, using binomial CI’s will not really answer your 2 questions, unless the answer is obvious” if the 2 CI’s do not overlap, you have a significant difference. And if they overlap to a large extent, you do not have a significant difference. But in between, you can not simply eyeball the CI’s.<br />\nNow, given that you are dealing with (very?) low proportions or counts (how many F’s in a given class? Maybe 2-3?), the chi-square test is not recommended (it is based on a normal approximation, which is not warranted for such low proportions/counts). Nor for that matter are CI’s based on normal approximations, a group the Wilson CI belongs to. And forget about continuity corrections, they do not work properly with very small proportions.<br />\nSo you are left with the Fisher-exact test, or some newer versions of it (which are less “conservative, while remaining “exact”, that is based on exactly the binomial distribution), such as the <a href=\"https://cran.r-universe.dev/exact2x2/doc/exact2x2.pdf\" rel=\"nofollow noreferrer\">Blaker test</a>.</p>\n<p>But there is a subtlety in what you are trying to compare. On one hand, you have the proportion of A’s in one class: easy. On the other hand you have the proportion of A’s in all other MA courses (the scenario is the same for the other question, so I will only address the first). How do you express that 2nd proportion?<br />\nOne option is to simply take the count of all A grades in all other MA courses, and the count of all students enrolled in all other MA classes. And then you can/should indeed use a Fisher-exact (or a Blaker-exact) test. But this will weight each student equally, but not each class (the classes with a large enrollment are more heavily weighted than the classes with a low enrollment). That may be what you want (as it reflects the experience of all students enrolled in all other MA classes), but it may not.\nAn alternative would be to look at all the proportions in all other MA classes, and take the average of these proportions. This weights all classes equally (but not all students). In that case, your test can be done with a single CI. You compute an binomial CI (again using an exact method given your possibly low proportions/counts), and simply see if the average proportion in included in that CI. If it is not, you have established a significant difference (at what ever significance level you chose for the CI).</p>\n<p>Last, you ask about multiple comparisons. The fact that you compute multiple CI’s is not relevant; multiple comparisons only occur when you are making a comparison to a significance level (or checking if a CI contains 0, or 1).. And since you seem to only have 2 questions, then you are only making 2 comparisons.<br />\nThe cautious thing to do would be to use a multiple comparison correction (MCC). Given only 2 comparisons, just use Bonferroni, and halve your significance level.<br />\nBut bolder statisticians could argue that your 2 hypotheses are different, and independent. And therefore, a MCC is not warranted... (should a researcher correct for all the various hypotheses he/she will test in their career?). So depending on your ultimate goal (why only these 2 questions? what are you really trying to show), you may be able to dispense with a MCC.</p>\n","text":"Welcome to CV!\n\n\n\n\nSo you want to compare 2 proportions; e.g. “Is the proportion of students who receive an A grade in MA101 the same as the proportion of students who receive an A grade in all other MA courses?”.\n\n\n\n\nWell, the “canonical” way to compare 2 proportions is via a 2x2 contingency table (https://en.wikipedia.org/wiki/Contingency_table) (aka crosstab). And the “canonical” tests are either a chi-square (https://en.wikipedia.org/wiki/Chi-squared_test) test, or a Fisher-exact (https://en.wikipedia.org/wiki/Fisher%27s_exact_test) test (aka Fisher-0Irwin test).\n\nNow, using binomial CI’s will not really answer your 2 questions, unless the answer is obvious” if the 2 CI’s do not overlap, you have a significant difference. And if they overlap to a large extent, you do not have a significant difference. But in between, you can not simply eyeball the CI’s.\n\nNow, given that you are dealing with (very?) low proportions or counts (how many F’s in a given class? Maybe 2-3?), the chi-square test is not recommended (it is based on a normal approximation, which is not warranted for such low proportions/counts). Nor for that matter are CI’s based on normal approximations, a group the Wilson CI belongs to. And forget about continuity corrections, they do not work properly with very small proportions.\n\nSo you are left with the Fisher-exact test, or some newer versions of it (which are less “conservative, while remaining “exact”, that is based on exactly the binomial distribution), such as the Blaker test (https://cran.r-universe.dev/exact2x2/doc/exact2x2.pdf).\n\n\n\n\nBut there is a subtlety in what you are trying to compare. On one hand, you have the proportion of A’s in one class: easy. On the other hand you have the proportion of A’s in all other MA courses (the scenario is the same for the other question, so I will only address the first). How do you express that 2nd proportion?\n\nOne option is to simply take the count of all A grades in all other MA courses, and the count of all students enrolled in all other MA classes. And then you can/should indeed use a Fisher-exact (or a Blaker-exact) test. But this will weight each student equally, but not each class (the classes with a large enrollment are more heavily weighted than the classes with a low enrollment). That may be what you want (as it reflects the experience of all students enrolled in all other MA classes), but it may not.\nAn alternative would be to look at all the proportions in all other MA classes, and take the average of these proportions. This weights all classes equally (but not all students). In that case, your test can be done with a single CI. You compute an binomial CI (again using an exact method given your possibly low proportions/counts), and simply see if the average proportion in included in that CI. If it is not, you have established a significant difference (at what ever significance level you chose for the CI).\n\n\n\n\nLast, you ask about multiple comparisons. The fact that you compute multiple CI’s is not relevant; multiple comparisons only occur when you are making a comparison to a significance level (or checking if a CI contains 0, or 1).. And since you seem to only have 2 questions, then you are only making 2 comparisons.\n\nThe cautious thing to do would be to use a multiple comparison correction (MCC). Given only 2 comparisons, just use Bonferroni, and halve your significance level.\n\nBut bolder statisticians could argue that your 2 hypotheses are different, and independent. And therefore, a MCC is not warranted... (should a researcher correct for all the various hypotheses he/she will test in their career?). So depending on your ultimate goal (why only these 2 questions? what are you really trying to show), you may be able to dispense with a MCC."}],"domain":"statistics","external_citations":["https://corplingstats.wordpress.com/2019/04/27/correcting-for-continuity/","https://corplingstats.wordpress.com/2024/12/12/bootstrap-intervals/","https://cran.r-universe.dev/exact2x2/doc/exact2x2.pdf","https://en.wikipedia.org/wiki/Chi-squared_test","https://en.wikipedia.org/wiki/Contingency_table","https://en.wikipedia.org/wiki/Fisher%27s_exact_test","https://moderndive.com/8-confidence-intervals.html","https://www.allendowney.com/blog/2024/10/15/bootstrapping-a-proportion/"],"ground_truth_type":"metadata_grounded","group_id":"6067403de8d4d10c98e25e84e769ee976b9bd9419586ec57b09e70ad30f14367","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-784a774b6763d0de5331e029","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:27:03.428408+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/774052c18cd9e8fa951e893347bfa3c1a85e743fc46ec4667572002cadb10cbf_1790825224163423600_0.json","raw_sha256":"fe4dd06d3de6c0b1bb33ba88aee0ed4284118e01f76a58dcdce220a4946329b2","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=stats&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"LST","profile_url":"https://stats.stackexchange.com/users/516373/lst","user_type":"registered"},"created_at":"2026-09-07T16:47:08+00:00","raw_file":"raw/codex_api_v1/3f959895a29b33d83894e5370d82e1c0cf87f20ac57fa423ebc923738357c657_1790825253957066500_0.json","raw_sha256":"ddd8808039e410ca99f97e2a7f12c307f046c4e5c3e184683bc12f816e6f49fc","revision_guid":"77370A41-A452-40D5-9FE9-E2D1C2A53F6B","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/77370A41-A452-40D5-9FE9-E2D1C2A53F6B/view-source"}],"source_commit":"3f6db230c4afe97d558b23fe2bfdb56dc0010d95","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Statistics-QA","source_license":"CC BY-SA 4.0","source_record_id":"Scientific-Statistics-QA:stats:677095","source_record_sha256":"024eb7eff7d18dacf072cca8f59943c40702d3b85cc2956093304361402edce1","source_url":"https://stats.stackexchange.com/questions/677095/testing-differences-in-proportions-wilson-cis-continuity-corrections-and-mult","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Testing differences in proportions - Wilson CIs, continuity corrections and multiple comparisons\nI have records of student grades for some university courses. I want to investigate whether any of these courses award significantly different proportions of the best (A) or worst (F) grades, compared to the other courses.\n\n\n\n\nI have individual student data, but some aggregated dummy data would be:\n\n\n\n\nmodules <- c(\n  \"MA101\",\"MA102\",\"MA103\",\"MA201\",\"MA202\",\"MA301\",\"MA302\",\n  \"FR101\",\"FR102\",\"FR104\",\"FR201\",\"FR202\",\"FR203\",\"FR301\",\n  \"EN101\",\"EN102\",\"EN201\",\"EN202\",\"EN203\",\"EN301\",\"EN302\"\n)\ntotals <- sample(30:400, length(modules), replace = TRUE)\ngrade_counts <- t(\n  sapply(totals, function(n) {\n    as.vector(rmultinom(1, n, rep(1, 5)))\n  })\n)\ncolnames(grade_counts) <- LETTERS[1:5]\n\ndummy_data <- data.frame(\n  Module = modules,\n  grade_counts,\n  Total = totals\n)\n\n\n\n\n\nAnd the questions I would like to ask are\n\n\n\n\n\nIs the proportion of students who receive an A grade in MA101 the same as the proportion of students who receive an A grade in all other MA courses?\n\n\n\n\nIs the proportion of students who get an F grade in FR202 the same as the proportion of students who get an F grade in other xx200 level courses?\n\n\n\n\n\nI did some reading and from Chapter 8 Bootstrapping and Confidence Intervals | Statistical Inference via Data Science (https://moderndive.com/8-confidence-intervals.html) started out by calculating bootstrap confidence intervals around the proportion of A/F grades awarded in each course, and seeing if these overlapped with the proportion of A/F grades awarded for other courses (e.g. all other MA courses, all other xx200 courses).\n\n\n\n\nHowever, having dug a bit further (e.g. Bootstrapping a Proportion - Probably Overthinking It, (https://www.allendowney.com/blog/2024/10/15/bootstrapping-a-proportion/) Bootstrap intervals for the single proportion – corp.ling.stats (https://corplingstats.wordpress.com/2024/12/12/bootstrap-intervals/)) it seems that bootstrapping probably wasn’t the way, and I should have instead calculated Wilson CIs.\n\n\n\n\nBefore I go down the wrong path again, I’d love a sense check from some more experienced hands.\n\n\n\n\n\nAre Wilson intervals the right approach for these sorts of questions?\n\n\n\n\nGiven that I sometimes have small numbers (<30 students on a course) and rare outcomes (F grades are not common!) I think I should use a continuity correction (Correcting for continuity – corp.ling.stats (https://corplingstats.wordpress.com/2019/04/27/correcting-for-continuity/)), is that right?\n\n\n\n\nAny pointers on how to adjust for multiple comparisons, given that I’ll be calculating two CIs each (prop A and prop F) for multiple courses (e.g. each of 7 MA courses against the other 6 MA courses)?\n\n\n\n\n\nI have some formal stats training, but not done much that isn't regression for a while. I understand I could run a regression of prop A/prop F with module dummy variables, but I'd like to try branching out to some other skills, where appropriate.\n\n\n\n\nThank you.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":677108,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I will start by saying that the way the question bins the data (as opposed to just giving a list of observations) made my hair stand on end. We have a saying that goes “<em>statistician friends do not let friends bin their data</em>” (ok, I just made it up, but it should exist). This is such a bad habit, and to see students exposed to it, at such an early stage, gave me the creeps.</p>\n<p>Then there is the fact that the question wants to use a chi-square test to test normality, which is, to put it mildly, odd (there are much better tests for normality. I would not want students to be left with an impression that a binned chi-square test is an option.<br />\nYou need to add that the chi-square statistic will be computed on data which includes 6 cells with counts below 5, and 3 with counts of 0, conditions under which the statistic is very unlikely to be chi-square distributed (the chi-square fit is asymptotic, justified only for “large” counts: rules of thumb say things like “all cells with counts 5 or larger”, which can be softened, but with more than 30% of the counts at or below 3, this is pushing it...)</p>\n<p>That being as it may, you have to deal with the data, and the question, given to you by this syllabus...</p>\n<p>First let me state that the <em>upper bound</em> for the d.f. should be 9, not 7; you actually have 9 observations (the 2 extreme bins): the fact that they contain no counts is itself information (in fact, the expected count for the upper extreme bin would be 1 not 0...).<br />\nThen there is the question of what that d.f should be. If we used a “typical” goodness of fit test (GOFt), the d.f. would simply be 8 (you compare an observed set of counts to a “theoretical” set of counts: so you “lose” only 1 d.f. – if you compared 2 observed sets of counts, you would lose 2 d.f.’s).<br />\nThe post @whuber’s linked in his comment explains very well why degrees of freedom are a complex, tricky concept, and have very little to do with number of estimated parameters, etc...<br />\nAnd I would tend to state that estimating the mean and sd of the theoretical normal does in no way impact this d.f.; but I will leave it to other contributors much more versed in the subtleties of d.f.’s to disagree with me, and explain their reasons.<br />\nAnd hence I will stick with 8 d.f’s.</p>\n<p>Now, wrt your alternative hypotheses, let me start by saying that an alternative hypothesis (<span class=\"math-container\">$H_1$</span>) can only be the exact logical opposite of the null (<span class=\"math-container\">$H_1 = \\neg H_0$</span>). If you reject the null, all you can “accept” is its logical negation.<br />\nSo your first option is semantically correct (we have (<span class=\"math-container\">$H_1 = \\neg H_0$</span>). But you did not really test if the distribution was normal, you tested if it was normal with a specific set of parameters. To test whether it is normal, you would have had to test the observed counts against all possible normal distributions, and find at least one such which it was compatible with.<br />\nSince the result of the chi-square test is a non-significant result (and not by a little...), the point is moot, and indeed you failed to reject that the distribution is normal (because it is compatible with at least that one normal distribution... And in fact, you certainly could find a surface in 2D space around the observed <span class=\"math-container\">$\\bar x$</span> and <span class=\"math-container\">$\\bar s$</span> for which the GOFt would be non-significant).</p>\n<p>The 2nd option is ambiguous semantically. The issue is that the logical negation of your null would be: “the distribution is either normal but with different parameters, or has the same parameters but is not normal, or is neither normal nor shares the same parameters”. As you can see, quite a messy alternative.<br />\nMaybe a better phrasing could have been: <span class=\"math-container\">$$H_0 \\text{: the data comes from }N(8.10971,.26756)$$</span>, and <span class=\"math-container\">$$H_1 \\text{: the data does not come from }N(8.10971,.26756)$$</span>\nIt could be slightly altered to be &quot;the data is compatible with coming... / The data is not compatible ...&quot;. To me this is the clearer formulation of the null, and the alternative: it really states what was tested (against a single normal) and the alternative is the logical negation (it is not this single normal).<br />\nSimilar comments can be made for the other options.</p>\n","answer_id":677122,"answer_text":"I will start by saying that the way the question bins the data (as opposed to just giving a list of observations) made my hair stand on end. We have a saying that goes “statistician friends do not let friends bin their data” (ok, I just made it up, but it should exist). This is such a bad habit, and to see students exposed to it, at such an early stage, gave me the creeps.\n\n\n\n\nThen there is the fact that the question wants to use a chi-square test to test normality, which is, to put it mildly, odd (there are much better tests for normality. I would not want students to be left with an impression that a binned chi-square test is an option.\n\nYou need to add that the chi-square statistic will be computed on data which includes 6 cells with counts below 5, and 3 with counts of 0, conditions under which the statistic is very unlikely to be chi-square distributed (the chi-square fit is asymptotic, justified only for “large” counts: rules of thumb say things like “all cells with counts 5 or larger”, which can be softened, but with more than 30% of the counts at or below 3, this is pushing it...)\n\n\n\n\nThat being as it may, you have to deal with the data, and the question, given to you by this syllabus...\n\n\n\n\nFirst let me state that the upper bound for the d.f. should be 9, not 7; you actually have 9 observations (the 2 extreme bins): the fact that they contain no counts is itself information (in fact, the expected count for the upper extreme bin would be 1 not 0...).\n\nThen there is the question of what that d.f should be. If we used a “typical” goodness of fit test (GOFt), the d.f. would simply be 8 (you compare an observed set of counts to a “theoretical” set of counts: so you “lose” only 1 d.f. – if you compared 2 observed sets of counts, you would lose 2 d.f.’s).\n\nThe post @whuber’s linked in his comment explains very well why degrees of freedom are a complex, tricky concept, and have very little to do with number of estimated parameters, etc...\n\nAnd I would tend to state that estimating the mean and sd of the theoretical normal does in no way impact this d.f.; but I will leave it to other contributors much more versed in the subtleties of d.f.’s to disagree with me, and explain their reasons.\n\nAnd hence I will stick with 8 d.f’s.\n\n\n\n\nNow, wrt your alternative hypotheses, let me start by saying that an alternative hypothesis ($H_1$) can only be the exact logical opposite of the null ($H_1 = \\neg H_0$). If you reject the null, all you can “accept” is its logical negation.\n\nSo your first option is semantically correct (we have ($H_1 = \\neg H_0$). But you did not really test if the distribution was normal, you tested if it was normal with a specific set of parameters. To test whether it is normal, you would have had to test the observed counts against all possible normal distributions, and find at least one such which it was compatible with.\n\nSince the result of the chi-square test is a non-significant result (and not by a little...), the point is moot, and indeed you failed to reject that the distribution is normal (because it is compatible with at least that one normal distribution... And in fact, you certainly could find a surface in 2D space around the observed $\\bar x$ and $\\bar s$ for which the GOFt would be non-significant).\n\n\n\n\nThe 2nd option is ambiguous semantically. The issue is that the logical negation of your null would be: “the distribution is either normal but with different parameters, or has the same parameters but is not normal, or is neither normal nor shares the same parameters”. As you can see, quite a messy alternative.\n\nMaybe a better phrasing could have been: $$H_0 \\text{: the data comes from }N(8.10971,.26756)$$, and $$H_1 \\text{: the data does not come from }N(8.10971,.26756)$$\nIt could be slightly altered to be \"the data is compatible with coming... / The data is not compatible ...\". To me this is the clearer formulation of the null, and the alternative: it really states what was tested (against a single normal) and the alternative is the logical negation (it is not this single normal).\n\nSimilar comments can be made for the other options.","answer_url":"https://stats.stackexchange.com/a/677122","author":"jginestet","author_url":"https://stats.stackexchange.com/users/380096/jginestet","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-09-09T21:58:15+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:27:06.169765+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/9155f81b0f1dac4b0f83fad58469033af46ad34ee8d731e569d063b41b3df6b6_1790825226563497500_0.json","raw_sha256":"cbac4b1b24e2159f1c17ea9902eaf89a0a5260344e6dba6f75790ba955f0d04b","source_api":"Stack Exchange API 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following observed frequencies:</p>\n<ul>\n<li>less than 6.6: 0</li>\n<li>between 6.6 and 7: 3</li>\n<li>between 7 and 7.4: 13</li>\n<li>between 7.4 and 7.8: 52</li>\n<li>between 7.8 and 8.2: 69</li>\n<li>between 8.2 and 8.6: 59</li>\n<li>between 8.6 and 9: 30</li>\n<li>between 9 and 9.4: 11</li>\n<li>above 9.4: 0</li>\n</ul>\n<p>The goal is to check whether this is consistent with the assumption that the data is coming from a normal distribution.</p>\n<p>The syllabus calls for approximating the mean and standard deviation using the mid-values of the intervals (I get 8.10970... for the mean and 0.513890... for the estimate of the standard deviation of the population), and use these to calculate expected frequencies.</p>\n<p>My question is the following.\nWhat is the proper way of stating the null and alternative hypothesis and what degrees of freedom shall I use for the chi squared goodness of fit test?</p>\n<p>I can think of the following options, but give me any other if none of these are appropriate:</p>\n<p>option 1:</p>\n<ul>\n<li>null hypothesis: the distribution is normal</li>\n<li>alternative hypothesis: the distribution is not normal</li>\n<li>degrees of freedom: 7-1-1-1=4</li>\n</ul>\n<p>option 2:</p>\n<ul>\n<li>null hypothesis: the distribution is normal with parameters estimated from the data</li>\n<li>alternative hypothesis: the distribution is not normal with parameters estimated from the data</li>\n<li>degrees of freedom: 7-1-1-1=4</li>\n</ul>\n<p>option 3:</p>\n<ul>\n<li>null hypothesis: the distribution is normal with mean 8.10970... and standard deviation 0.513890...</li>\n<li>alternative hypothesis: the distribution is not normal with mean 8.10970... and standard deviation 0.513890...</li>\n<li>degrees of freedom: 7-1-1-1=4</li>\n</ul>\n<p>option 4:</p>\n<ul>\n<li>null hypothesis: the distribution is normal with mean 8.10970... and standard deviation 0.513890...</li>\n<li>alternative hypothesis: the distribution is not normal with mean 8.10970... and standard deviation 0.513890...</li>\n<li>degrees of freedom: 7-1=6</li>\n</ul>\n<p>Please note that I read that removing 1 from the degrees of freedom for each estimated parameter is debatable, but that is what the syllabus I am teaching is asking students to do.</p>\n","text":"I am a high school mathematics teacher (teaching the International Baccalaureate) and the syllabus requires students to understand the chi squared goodness of fit test when parameters of the expected distribution are approximated from the data.\n\n\n\n\nHere is an example:\n\n\n\n\nI have the following observed frequencies:\n\n\n\n\n\nless than 6.6: 0\n\n\n\n\nbetween 6.6 and 7: 3\n\n\n\n\nbetween 7 and 7.4: 13\n\n\n\n\nbetween 7.4 and 7.8: 52\n\n\n\n\nbetween 7.8 and 8.2: 69\n\n\n\n\nbetween 8.2 and 8.6: 59\n\n\n\n\nbetween 8.6 and 9: 30\n\n\n\n\nbetween 9 and 9.4: 11\n\n\n\n\nabove 9.4: 0\n\n\n\n\n\nThe goal is to check whether this is consistent with the assumption that the data is coming from a normal distribution.\n\n\n\n\nThe syllabus calls for approximating the mean and standard deviation using the mid-values of the intervals (I get 8.10970... for the mean and 0.513890... for the estimate of the standard deviation of the population), and use these to calculate expected frequencies.\n\n\n\n\nMy question is the following.\nWhat is the proper way of stating the null and alternative hypothesis and what degrees of freedom shall I use for the chi squared goodness of fit test?\n\n\n\n\nI can think of the following options, but give me any other if none of these are appropriate:\n\n\n\n\noption 1:\n\n\n\n\n\nnull hypothesis: the distribution is normal\n\n\n\n\nalternative hypothesis: the distribution is not normal\n\n\n\n\ndegrees of freedom: 7-1-1-1=4\n\n\n\n\n\noption 2:\n\n\n\n\n\nnull hypothesis: the distribution is normal with parameters estimated from the data\n\n\n\n\nalternative hypothesis: the distribution is not normal with parameters estimated from the data\n\n\n\n\ndegrees of freedom: 7-1-1-1=4\n\n\n\n\n\noption 3:\n\n\n\n\n\nnull hypothesis: the distribution is normal with mean 8.10970... and standard deviation 0.513890...\n\n\n\n\nalternative hypothesis: the distribution is not normal with mean 8.10970... and standard deviation 0.513890...\n\n\n\n\ndegrees of freedom: 7-1-1-1=4\n\n\n\n\n\noption 4:\n\n\n\n\n\nnull hypothesis: the distribution is normal with mean 8.10970... and standard deviation 0.513890...\n\n\n\n\nalternative hypothesis: the distribution is not normal with mean 8.10970... and standard deviation 0.513890...\n\n\n\n\ndegrees of freedom: 7-1=6\n\n\n\n\n\nPlease note that I read that removing 1 from the degrees of freedom for each estimated parameter is debatable, but that is what the syllabus I am teaching is asking students to do."},{"context_id":"677122","html":"<p>I will start by saying that the way the question bins the data (as opposed to just giving a list of observations) made my hair stand on end. We have a saying that goes “<em>statistician friends do not let friends bin their data</em>” (ok, I just made it up, but it should exist). This is such a bad habit, and to see students exposed to it, at such an early stage, gave me the creeps.</p>\n<p>Then there is the fact that the question wants to use a chi-square test to test normality, which is, to put it mildly, odd (there are much better tests for normality. I would not want students to be left with an impression that a binned chi-square test is an option.<br />\nYou need to add that the chi-square statistic will be computed on data which includes 6 cells with counts below 5, and 3 with counts of 0, conditions under which the statistic is very unlikely to be chi-square distributed (the chi-square fit is asymptotic, justified only for “large” counts: rules of thumb say things like “all cells with counts 5 or larger”, which can be softened, but with more than 30% of the counts at or below 3, this is pushing it...)</p>\n<p>That being as it may, you have to deal with the data, and the question, given to you by this syllabus...</p>\n<p>First let me state that the <em>upper bound</em> for the d.f. should be 9, not 7; you actually have 9 observations (the 2 extreme bins): the fact that they contain no counts is itself information (in fact, the expected count for the upper extreme bin would be 1 not 0...).<br />\nThen there is the question of what that d.f should be. If we used a “typical” goodness of fit test (GOFt), the d.f. would simply be 8 (you compare an observed set of counts to a “theoretical” set of counts: so you “lose” only 1 d.f. – if you compared 2 observed sets of counts, you would lose 2 d.f.’s).<br />\nThe post @whuber’s linked in his comment explains very well why degrees of freedom are a complex, tricky concept, and have very little to do with number of estimated parameters, etc...<br />\nAnd I would tend to state that estimating the mean and sd of the theoretical normal does in no way impact this d.f.; but I will leave it to other contributors much more versed in the subtleties of d.f.’s to disagree with me, and explain their reasons.<br />\nAnd hence I will stick with 8 d.f’s.</p>\n<p>Now, wrt your alternative hypotheses, let me start by saying that an alternative hypothesis (<span class=\"math-container\">$H_1$</span>) can only be the exact logical opposite of the null (<span class=\"math-container\">$H_1 = \\neg H_0$</span>). If you reject the null, all you can “accept” is its logical negation.<br />\nSo your first option is semantically correct (we have (<span class=\"math-container\">$H_1 = \\neg H_0$</span>). But you did not really test if the distribution was normal, you tested if it was normal with a specific set of parameters. To test whether it is normal, you would have had to test the observed counts against all possible normal distributions, and find at least one such which it was compatible with.<br />\nSince the result of the chi-square test is a non-significant result (and not by a little...), the point is moot, and indeed you failed to reject that the distribution is normal (because it is compatible with at least that one normal distribution... And in fact, you certainly could find a surface in 2D space around the observed <span class=\"math-container\">$\\bar x$</span> and <span class=\"math-container\">$\\bar s$</span> for which the GOFt would be non-significant).</p>\n<p>The 2nd option is ambiguous semantically. The issue is that the logical negation of your null would be: “the distribution is either normal but with different parameters, or has the same parameters but is not normal, or is neither normal nor shares the same parameters”. As you can see, quite a messy alternative.<br />\nMaybe a better phrasing could have been: <span class=\"math-container\">$$H_0 \\text{: the data comes from }N(8.10971,.26756)$$</span>, and <span class=\"math-container\">$$H_1 \\text{: the data does not come from }N(8.10971,.26756)$$</span>\nIt could be slightly altered to be &quot;the data is compatible with coming... / The data is not compatible ...&quot;. To me this is the clearer formulation of the null, and the alternative: it really states what was tested (against a single normal) and the alternative is the logical negation (it is not this single normal).<br />\nSimilar comments can be made for the other options.</p>\n","text":"I will start by saying that the way the question bins the data (as opposed to just giving a list of observations) made my hair stand on end. We have a saying that goes “statistician friends do not let friends bin their data” (ok, I just made it up, but it should exist). This is such a bad habit, and to see students exposed to it, at such an early stage, gave me the creeps.\n\n\n\n\nThen there is the fact that the question wants to use a chi-square test to test normality, which is, to put it mildly, odd (there are much better tests for normality. I would not want students to be left with an impression that a binned chi-square test is an option.\n\nYou need to add that the chi-square statistic will be computed on data which includes 6 cells with counts below 5, and 3 with counts of 0, conditions under which the statistic is very unlikely to be chi-square distributed (the chi-square fit is asymptotic, justified only for “large” counts: rules of thumb say things like “all cells with counts 5 or larger”, which can be softened, but with more than 30% of the counts at or below 3, this is pushing it...)\n\n\n\n\nThat being as it may, you have to deal with the data, and the question, given to you by this syllabus...\n\n\n\n\nFirst let me state that the upper bound for the d.f. should be 9, not 7; you actually have 9 observations (the 2 extreme bins): the fact that they contain no counts is itself information (in fact, the expected count for the upper extreme bin would be 1 not 0...).\n\nThen there is the question of what that d.f should be. If we used a “typical” goodness of fit test (GOFt), the d.f. would simply be 8 (you compare an observed set of counts to a “theoretical” set of counts: so you “lose” only 1 d.f. – if you compared 2 observed sets of counts, you would lose 2 d.f.’s).\n\nThe post @whuber’s linked in his comment explains very well why degrees of freedom are a complex, tricky concept, and have very little to do with number of estimated parameters, etc...\n\nAnd I would tend to state that estimating the mean and sd of the theoretical normal does in no way impact this d.f.; but I will leave it to other contributors much more versed in the subtleties of d.f.’s to disagree with me, and explain their reasons.\n\nAnd hence I will stick with 8 d.f’s.\n\n\n\n\nNow, wrt your alternative hypotheses, let me start by saying that an alternative hypothesis ($H_1$) can only be the exact logical opposite of the null ($H_1 = \\neg H_0$). If you reject the null, all you can “accept” is its logical negation.\n\nSo your first option is semantically correct (we have ($H_1 = \\neg H_0$). But you did not really test if the distribution was normal, you tested if it was normal with a specific set of parameters. To test whether it is normal, you would have had to test the observed counts against all possible normal distributions, and find at least one such which it was compatible with.\n\nSince the result of the chi-square test is a non-significant result (and not by a little...), the point is moot, and indeed you failed to reject that the distribution is normal (because it is compatible with at least that one normal distribution... And in fact, you certainly could find a surface in 2D space around the observed $\\bar x$ and $\\bar s$ for which the GOFt would be non-significant).\n\n\n\n\nThe 2nd option is ambiguous semantically. The issue is that the logical negation of your null would be: “the distribution is either normal but with different parameters, or has the same parameters but is not normal, or is neither normal nor shares the same parameters”. As you can see, quite a messy alternative.\n\nMaybe a better phrasing could have been: $$H_0 \\text{: the data comes from }N(8.10971,.26756)$$, and $$H_1 \\text{: the data does not come from }N(8.10971,.26756)$$\nIt could be slightly altered to be \"the data is compatible with coming... / The data is not compatible ...\". To me this is the clearer formulation of the null, and the alternative: it really states what was tested (against a single normal) and the alternative is the logical negation (it is not this single normal).\n\nSimilar comments can be made for the other options."}],"domain":"statistics","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"62170f2e1f7b5f7acd34cd2d39acab745b7bdac68ec21632145261b6649458b1","hard_case_family":["no_accepted_answer"],"id":"RHM-a632629fdb50fc8df7db5280","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:27:03.428408+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/774052c18cd9e8fa951e893347bfa3c1a85e743fc46ec4667572002cadb10cbf_1790825224163423600_0.json","raw_sha256":"fe4dd06d3de6c0b1bb33ba88aee0ed4284118e01f76a58dcdce220a4946329b2","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=stats&sort=creation","transformation":"API HTML retained; 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no LLM truth labels"},"query":"What are the hypotheses in a chi squared goodness of fit test when parameters of the expected distribution are approximated from the data?\nI am a high school mathematics teacher (teaching the International Baccalaureate) and the syllabus requires students to understand the chi squared goodness of fit test when parameters of the expected distribution are approximated from the data.\n\n\n\n\nHere is an example:\n\n\n\n\nI have the following observed frequencies:\n\n\n\n\n\nless than 6.6: 0\n\n\n\n\nbetween 6.6 and 7: 3\n\n\n\n\nbetween 7 and 7.4: 13\n\n\n\n\nbetween 7.4 and 7.8: 52\n\n\n\n\nbetween 7.8 and 8.2: 69\n\n\n\n\nbetween 8.2 and 8.6: 59\n\n\n\n\nbetween 8.6 and 9: 30\n\n\n\n\nbetween 9 and 9.4: 11\n\n\n\n\nabove 9.4: 0\n\n\n\n\n\nThe goal is to check whether this is consistent with the assumption that the data is coming from a normal distribution.\n\n\n\n\nThe syllabus calls for approximating the mean and standard deviation using the mid-values of the intervals (I get 8.10970... for the mean and 0.513890... for the estimate of the standard deviation of the population), and use these to calculate expected frequencies.\n\n\n\n\nMy question is the following.\nWhat is the proper way of stating the null and alternative hypothesis and what degrees of freedom shall I use for the chi squared goodness of fit test?\n\n\n\n\nI can think of the following options, but give me any other if none of these are appropriate:\n\n\n\n\noption 1:\n\n\n\n\n\nnull hypothesis: the distribution is normal\n\n\n\n\nalternative hypothesis: the distribution is not normal\n\n\n\n\ndegrees of freedom: 7-1-1-1=4\n\n\n\n\n\noption 2:\n\n\n\n\n\nnull hypothesis: the distribution is normal with parameters estimated from the data\n\n\n\n\nalternative hypothesis: the distribution is not normal with parameters estimated from the data\n\n\n\n\ndegrees of freedom: 7-1-1-1=4\n\n\n\n\n\noption 3:\n\n\n\n\n\nnull hypothesis: the distribution is normal with mean 8.10970... and standard deviation 0.513890...\n\n\n\n\nalternative hypothesis: the distribution is not normal with mean 8.10970... and standard deviation 0.513890...\n\n\n\n\ndegrees of freedom: 7-1-1-1=4\n\n\n\n\n\noption 4:\n\n\n\n\n\nnull hypothesis: the distribution is normal with mean 8.10970... and standard deviation 0.513890...\n\n\n\n\nalternative hypothesis: the distribution is not normal with mean 8.10970... and standard deviation 0.513890...\n\n\n\n\ndegrees of freedom: 7-1=6\n\n\n\n\n\nPlease note that I read that removing 1 from the degrees of freedom for each estimated parameter is debatable, but that is what the syllabus I am teaching is asking students to do.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":677122,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>First: That is much too simple a rule. A better rule of thumb is one regressor for every ten observations, so if you have a really big data set, you could use more variables without overfitting.</p>\n<p>Second, it does matter whether your outcome is categorical. For categorical outcomes, a common rule of thumb is 10 observations in the least common category for each regressor. This can be much more restrictive, if some categories are rare.</p>\n<p>Third, overfitting is not the only problem. When you have many variables, it can be hard to interpret the model. Mathematically, it's straightforward: You're controlling for all the other variables. But what that means, substantively, can be tricky.</p>\n<p>Fourth, with a lot of regressors, collinearity is often a problem, at least if you want to interpret the model (it doesn't affect prediction).</p>\n<p>Finally, choosing a good model is a huge subject, with many threads here. Browse the <code>model-selection</code> tag for lots of material.</p>\n","answer_id":677170,"answer_text":"First: That is much too simple a rule. A better rule of thumb is one regressor for every ten observations, so if you have a really big data set, you could use more variables without overfitting.\n\n\n\n\nSecond, it does matter whether your outcome is categorical. For categorical outcomes, a common rule of thumb is 10 observations in the least common category for each regressor. This can be much more restrictive, if some categories are rare.\n\n\n\n\nThird, overfitting is not the only problem. When you have many variables, it can be hard to interpret the model. Mathematically, it's straightforward: You're controlling for all the other variables. But what that means, substantively, can be tricky.\n\n\n\n\nFourth, with a lot of regressors, collinearity is often a problem, at least if you want to interpret the model (it doesn't affect prediction).\n\n\n\n\nFinally, choosing a good model is a huge subject, with many threads here. Browse the model-selection tag for lots of material.","answer_url":"https://stats.stackexchange.com/a/677170","author":"Peter Flom","author_url":"https://stats.stackexchange.com/users/686/peter-flom","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-09-14T19:41:01+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:27:08.569053+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/ba8a114171cbec551f0a7f4b9f04e95c559131a62357d51e159434d4acc7183d_1790825228829630100_0.json","raw_sha256":"a03822ca860dd0b0fb0cc402754ae4cdbaad51d18873dfd19aed56ffe1cf7ec8","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/677298;677295;677280;677279;677278;677275;677269;677266;677262;677256;677245;677243;677242;677226;677225;677217;677211;677201;677194;677193;677186;677183;677179;677177;677171;677169;677168;677151;677149;677147;677137;677135;677131;677129;677115;677110;677109;677101;677099;677098;677096;677095;677094;677085;677083;677079;677078;677075;677071;677066;677065;677062;677058;677045;677041;677035;677033;677023;677021;676999;676997;676991;676982;676981;676979;676977;676975;676971;676966;676961;676958;676956;676952;676947;676945;676937;676935;676933;676924;676922;676899;676898;676893;676889;676888;676879;676874;676873;676870;676867;676865;676858;676855;676850;676842;676832;676830;676824;676823;676821/answers?filter=withbody&order=asc&page=2&pagesize=100&site=stats&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":677169,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Peter Flom","profile_url":"https://stats.stackexchange.com/users/686/peter-flom","user_type":"registered"},"created_at":"2026-09-14T19:41:01+00:00","raw_file":"raw/codex_api_v1/59f98009db0ac38325a869c60e3993040b07f5fbd07014051415831400b70d25_1790825251781774200_0.json","raw_sha256":"2876465103b1eeb5d593dd46b1ec52a862c1da72f8e4767e5f8ee70ff0564119","revision_guid":"24267A3D-EFFC-4C8A-BBD5-56E85D075DAA","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/24267A3D-EFFC-4C8A-BBD5-56E85D075DAA/view-source"}],"score":9,"updated_at":"2026-09-14T19:41:01+00:00"},{"answer_html":"<p>You should try one or more kinds of regularizers: e.g. Ridge Regression (L2 penalty on the coefficients) or Lasso Regression (L1 penalties on the coefficients); or some of both together.  Playing with the regularization penalties essentially converts your question to a model selection problem.  Fit as many things as you like, and the Lasso will zero out the coefficients for the less relevant ones.  The more data you have, the more coefficients it makes sense to keep, or the smaller penalties you can use and still get meaningful results.  If reducing your penalties a little changes your coefficients much, you should go the other way.</p>\n","answer_id":677198,"answer_text":"You should try one or more kinds of regularizers: e.g. Ridge Regression (L2 penalty on the coefficients) or Lasso Regression (L1 penalties on the coefficients); or some of both together.  Playing with the regularization penalties essentially converts your question to a model selection problem.  Fit as many things as you like, and the Lasso will zero out the coefficients for the less relevant ones.  The more data you have, the more coefficients it makes sense to keep, or the smaller penalties you can use and still get meaningful results.  If reducing your penalties a little changes your coefficients much, you should go the other way.","answer_url":"https://stats.stackexchange.com/a/677198","author":"Richard Lyon","author_url":"https://stats.stackexchange.com/users/516789/richard-lyon","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-09-17T23:10:31+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:27:08.569053+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/ba8a114171cbec551f0a7f4b9f04e95c559131a62357d51e159434d4acc7183d_1790825228829630100_0.json","raw_sha256":"a03822ca860dd0b0fb0cc402754ae4cdbaad51d18873dfd19aed56ffe1cf7ec8","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/677298;677295;677280;677279;677278;677275;677269;677266;677262;677256;677245;677243;677242;677226;677225;677217;677211;677201;677194;677193;677186;677183;677179;677177;677171;677169;677168;677151;677149;677147;677137;677135;677131;677129;677115;677110;677109;677101;677099;677098;677096;677095;677094;677085;677083;677079;677078;677075;677071;677066;677065;677062;677058;677045;677041;677035;677033;677023;677021;676999;676997;676991;676982;676981;676979;676977;676975;676971;676966;676961;676958;676956;676952;676947;676945;676937;676935;676933;676924;676922;676899;676898;676893;676889;676888;676879;676874;676873;676870;676867;676865;676858;676855;676850;676842;676832;676830;676824;676823;676821/answers?filter=withbody&order=asc&page=2&pagesize=100&site=stats&sort=creation","transformation":"API HTML retained; 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However, what if you were working with a dataset that has for instance 50 variables and around 40 of them are variables that you would adjust for, how would you prevent overfitting?</p>\n<p>Would it be okay to adjust for more than 10 variables in the same model?</p>\n<p>I would greatly appreciate an easy to understand answer.</p>\n<p>My outcome is either categorical or continuous but I don’t think it matters for the explanation I need.</p>\n","text":"In my intro to biostats classes I was taught that one shouldn’t adjust for more than 10 variables in a regression model because it would overfit the data. However, what if you were working with a dataset that has for instance 50 variables and around 40 of them are variables that you would adjust for, how would you prevent overfitting?\n\n\n\n\nWould it be okay to adjust for more than 10 variables in the same model?\n\n\n\n\nI would greatly appreciate an easy to understand answer.\n\n\n\n\nMy outcome is either categorical or continuous but I don’t think it matters for the explanation I need."},{"context_id":"677170","html":"<p>First: That is much too simple a rule. A better rule of thumb is one regressor for every ten observations, so if you have a really big data set, you could use more variables without overfitting.</p>\n<p>Second, it does matter whether your outcome is categorical. For categorical outcomes, a common rule of thumb is 10 observations in the least common category for each regressor. This can be much more restrictive, if some categories are rare.</p>\n<p>Third, overfitting is not the only problem. When you have many variables, it can be hard to interpret the model. Mathematically, it's straightforward: You're controlling for all the other variables. But what that means, substantively, can be tricky.</p>\n<p>Fourth, with a lot of regressors, collinearity is often a problem, at least if you want to interpret the model (it doesn't affect prediction).</p>\n<p>Finally, choosing a good model is a huge subject, with many threads here. Browse the <code>model-selection</code> tag for lots of material.</p>\n","text":"First: That is much too simple a rule. A better rule of thumb is one regressor for every ten observations, so if you have a really big data set, you could use more variables without overfitting.\n\n\n\n\nSecond, it does matter whether your outcome is categorical. For categorical outcomes, a common rule of thumb is 10 observations in the least common category for each regressor. This can be much more restrictive, if some categories are rare.\n\n\n\n\nThird, overfitting is not the only problem. When you have many variables, it can be hard to interpret the model. Mathematically, it's straightforward: You're controlling for all the other variables. But what that means, substantively, can be tricky.\n\n\n\n\nFourth, with a lot of regressors, collinearity is often a problem, at least if you want to interpret the model (it doesn't affect prediction).\n\n\n\n\nFinally, choosing a good model is a huge subject, with many threads here. Browse the model-selection tag for lots of material."},{"context_id":"677198","html":"<p>You should try one or more kinds of regularizers: e.g. Ridge Regression (L2 penalty on the coefficients) or Lasso Regression (L1 penalties on the coefficients); or some of both together.  Playing with the regularization penalties essentially converts your question to a model selection problem.  Fit as many things as you like, and the Lasso will zero out the coefficients for the less relevant ones.  The more data you have, the more coefficients it makes sense to keep, or the smaller penalties you can use and still get meaningful results.  If reducing your penalties a little changes your coefficients much, you should go the other way.</p>\n","text":"You should try one or more kinds of regularizers: e.g. Ridge Regression (L2 penalty on the coefficients) or Lasso Regression (L1 penalties on the coefficients); or some of both together.  Playing with the regularization penalties essentially converts your question to a model selection problem.  Fit as many things as you like, and the Lasso will zero out the coefficients for the less relevant ones.  The more data you have, the more coefficients it makes sense to keep, or the smaller penalties you can use and still get meaningful results.  If reducing your penalties a little changes your coefficients much, you should go the other way."}],"domain":"statistics","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"9c1262fe902280f03dc66e5c2d5def73a6484a60c07bd073414652ed36e8042c","hard_case_family":["no_accepted_answer","multiple_answer_candidates"],"id":"RHM-a0a7a2c5ef4b1bf5f92f2051","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:27:03.428408+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/774052c18cd9e8fa951e893347bfa3c1a85e743fc46ec4667572002cadb10cbf_1790825224163423600_0.json","raw_sha256":"fe4dd06d3de6c0b1bb33ba88aee0ed4284118e01f76a58dcdce220a4946329b2","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=stats&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"ineedhelp","profile_url":"https://stats.stackexchange.com/users/328519/ineedhelp","user_type":"registered"},"created_at":"2026-09-14T19:13:21+00:00","raw_file":"raw/codex_api_v1/59f98009db0ac38325a869c60e3993040b07f5fbd07014051415831400b70d25_1790825251781774200_0.json","raw_sha256":"2876465103b1eeb5d593dd46b1ec52a862c1da72f8e4767e5f8ee70ff0564119","revision_guid":"2972E220-ADB4-4C69-843D-CFAFF417E7A3","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/2972E220-ADB4-4C69-843D-CFAFF417E7A3/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-09-15T03:21:56+00:00","raw_file":"raw/codex_api_v1/59f98009db0ac38325a869c60e3993040b07f5fbd07014051415831400b70d25_1790825251781774200_0.json","raw_sha256":"2876465103b1eeb5d593dd46b1ec52a862c1da72f8e4767e5f8ee70ff0564119","revision_guid":"7F9A7C91-F9E9-41BB-B0D1-513212A717A8","revision_number":null,"revision_type":"vote_based","revision_url":"https://stats.stackexchange.com/revisions/7F9A7C91-F9E9-41BB-B0D1-513212A717A8/view-source"},{"content_license":null,"contributor":{"display_name":"Richard Hardy","profile_url":"https://stats.stackexchange.com/users/53690/richard-hardy","user_type":"registered"},"created_at":"2026-09-16T19:18:53+00:00","raw_file":"raw/codex_api_v1/59f98009db0ac38325a869c60e3993040b07f5fbd07014051415831400b70d25_1790825251781774200_0.json","raw_sha256":"2876465103b1eeb5d593dd46b1ec52a862c1da72f8e4767e5f8ee70ff0564119","revision_guid":"A5EF3AEF-D5BC-422F-926A-4E678B350FE2","revision_number":2,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/A5EF3AEF-D5BC-422F-926A-4E678B350FE2/view-source"}],"source_commit":"3f6db230c4afe97d558b23fe2bfdb56dc0010d95","source_data_file":"dataset.jsonl","source_dataset":"RegalFire/Scientific-Statistics-QA","source_license":"CC BY-SA 4.0","source_record_id":"Scientific-Statistics-QA:stats:677169","source_record_sha256":"ae5badb4c8a0578e510721d948e75ca7983c2cf95f9157b8c7a6d5e48b2f63e0","source_url":"https://stats.stackexchange.com/questions/677169/how-do-you-prevent-overfitting-regression-models-when-you-adjust-for-more-than-1","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How do you prevent overfitting regression models when you adjust for more than 10 variables?\nIn my intro to biostats classes I was taught that one shouldn’t adjust for more than 10 variables in a regression model because it would overfit the data. However, what if you were working with a dataset that has for instance 50 variables and around 40 of them are variables that you would adjust for, how would you prevent overfitting?\n\n\n\n\nWould it be okay to adjust for more than 10 variables in the same model?\n\n\n\n\nI would greatly appreciate an easy to understand answer.\n\n\n\n\nMy outcome is either categorical or continuous but I don’t think it matters for the explanation I need.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":677170,"score":9},{"answer_id":677198,"score":2}],"split":"test"}
{"accepted_status":{"accepted_answer_id":45135,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>As others mentioned in the comments, calculating the quadrature rule ahead of time is usually the fastest approach. However, you do not want to do that, you have a few options:</p>\n<ul>\n<li><p><a href=\"https://www.ams.org/journals/mcom/1969-23-106/S0025-5718-69-99647-1/S0025-5718-69-99647-1.pdf\" rel=\"nofollow noreferrer\">Golub-Welsch algorithm</a>: Basically, you create a triadigonal matrix and calculate its eigendecomposition. The eigenvalues are the nodes and the weights are obtained from the first row of eigenvectors. For a matlab implementation, see this <a href=\"https://github.com/tcew/nodal-dg/blob/master/Codes1.1/Codes1D/JacobiGQ.m\" rel=\"nofollow noreferrer\">code</a> where the coefficients <code>alpha</code> and <code>beta</code> correspond to the Jacobi polynomial associated with the quadrature (For Legendre quadrature use <code>alpha=beta=0</code>)</p>\n</li>\n<li><p>Calculate the roots of the n-th Legendre polynomial (or other orthogonal polynomial) using Newton's method. You need a good initial guess, and you should use the derivative formulas to obtain the derivatives of the polynomial from its values as well as the recurrence relation. Here's a <a href=\"https://www.mathworks.com/matlabcentral/fileexchange/4540-legendre-gauss-quadrature-weights-and-nodes\" rel=\"nofollow noreferrer\">Matlab implementation</a> as an example.</p>\n</li>\n<li><p>For very high order quadrature rules, you can consider using an asymptotic formula for the roots and weights like the ones discussed in this <a href=\"https://doi.org/10.1137/140954969\" rel=\"nofollow noreferrer\">recent paper</a>.</p>\n</li>\n</ul>\n<p>Some libraries/packages might use a mixture of these approaches. For instance, the Julia package <a href=\"https://github.com/JuliaApproximation/FastGaussQuadrature.jl\" rel=\"nofollow noreferrer\">FastGaussQuadrature</a> uses tabulated values for <span class=\"math-container\">$n\\le 5$</span>, Newton's iteration for <span class=\"math-container\">$5&lt;n\\le 60$</span> and the asymptotic formulas for <span class=\"math-container\">$n&gt; 60$</span>.</p>\n","answer_id":45135,"answer_text":"As others mentioned in the comments, calculating the quadrature rule ahead of time is usually the fastest approach. However, you do not want to do that, you have a few options:\n\n\n\n\n\n\n\nGolub-Welsch algorithm (https://www.ams.org/journals/mcom/1969-23-106/S0025-5718-69-99647-1/S0025-5718-69-99647-1.pdf): Basically, you create a triadigonal matrix and calculate its eigendecomposition. The eigenvalues are the nodes and the weights are obtained from the first row of eigenvectors. For a matlab implementation, see this code (https://github.com/tcew/nodal-dg/blob/master/Codes1.1/Codes1D/JacobiGQ.m) where the coefficients alpha and beta correspond to the Jacobi polynomial associated with the quadrature (For Legendre quadrature use alpha=beta=0)\n\n\n\n\n\n\n\n\n\nCalculate the roots of the n-th Legendre polynomial (or other orthogonal polynomial) using Newton's method. You need a good initial guess, and you should use the derivative formulas to obtain the derivatives of the polynomial from its values as well as the recurrence relation. Here's a Matlab implementation (https://www.mathworks.com/matlabcentral/fileexchange/4540-legendre-gauss-quadrature-weights-and-nodes) as an example.\n\n\n\n\n\n\n\n\n\nFor very high order quadrature rules, you can consider using an asymptotic formula for the roots and weights like the ones discussed in this recent paper (https://doi.org/10.1137/140954969).\n\n\n\n\n\n\n\n\nSome libraries/packages might use a mixture of these approaches. For instance, the Julia package FastGaussQuadrature (https://github.com/JuliaApproximation/FastGaussQuadrature.jl) uses tabulated values for $n\\le 5$, Newton's iteration for $5<n\\le 60$ and the asymptotic formulas for $n> 60$.","answer_url":"https://scicomp.stackexchange.com/a/45135","author":"HMe","author_url":"https://scicomp.stackexchange.com/users/52227/hme","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2025-06-23T02:23:34+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:47.033952+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/cb6e5f564c84a92c4e121c0637c99292018f8935652e423630f2001099a2410f_1790825327386675300_0.json","raw_sha256":"1a957289f56621bebd21cb45dd99baaedb2c3bc11cb28d700558e4bbcaa19695","source_api":"Stack Exchange API 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Menshov","profile_url":"https://scicomp.stackexchange.com/users/20688/anton-menshov","user_type":"moderator"},"created_at":"2025-06-24T22:14:07+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"5EA1A740-F16C-4BC6-BEC6-176E698E39EB","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/5EA1A740-F16C-4BC6-BEC6-176E698E39EB/view-source"}],"url":"https://scicomp.stackexchange.com/questions/45134/generating-the-quadrature-points-for-gauss-legendre"},{"author":"HMe","author_url":"https://scicomp.stackexchange.com/users/52227/hme","content_license":"CC BY-SA 4.0","context_id":"45135","revision_attribution":[{"content_license":"CC BY-SA 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papers I have found that talk about iteration-less methods as well.</p>\n<p>If I care about computation speed much more than I do robustness, what would a good method to approximate the 0's be?</p>\n","text":"The Wikipedia entry on Gauss-Legendre (https://en.wikipedia.org/wiki/Gauss%E2%80%93Legendre_quadrature) says that there is a tri-diagonal matrix whose eigenvalues yield good approximations for the nodes of the Legendre polynomials.\n\n\n\n\nThere are a couple of papers I have found that talk about iteration-less methods as well.\n\n\n\n\nIf I care about computation speed much more than I do robustness, what would a good method to approximate the 0's be?"},{"context_id":"45135","html":"<p>As others mentioned in the comments, calculating the quadrature rule ahead of time is usually the fastest approach. However, you do not want to do that, you have a few options:</p>\n<ul>\n<li><p><a href=\"https://www.ams.org/journals/mcom/1969-23-106/S0025-5718-69-99647-1/S0025-5718-69-99647-1.pdf\" rel=\"nofollow noreferrer\">Golub-Welsch algorithm</a>: Basically, you create a triadigonal matrix and calculate its eigendecomposition. The eigenvalues are the nodes and the weights are obtained from the first row of eigenvectors. For a matlab implementation, see this <a href=\"https://github.com/tcew/nodal-dg/blob/master/Codes1.1/Codes1D/JacobiGQ.m\" rel=\"nofollow noreferrer\">code</a> where the coefficients <code>alpha</code> and <code>beta</code> correspond to the Jacobi polynomial associated with the quadrature (For Legendre quadrature use <code>alpha=beta=0</code>)</p>\n</li>\n<li><p>Calculate the roots of the n-th Legendre polynomial (or other orthogonal polynomial) using Newton's method. You need a good initial guess, and you should use the derivative formulas to obtain the derivatives of the polynomial from its values as well as the recurrence relation. Here's a <a href=\"https://www.mathworks.com/matlabcentral/fileexchange/4540-legendre-gauss-quadrature-weights-and-nodes\" rel=\"nofollow noreferrer\">Matlab implementation</a> as an example.</p>\n</li>\n<li><p>For very high order quadrature rules, you can consider using an asymptotic formula for the roots and weights like the ones discussed in this <a href=\"https://doi.org/10.1137/140954969\" rel=\"nofollow noreferrer\">recent paper</a>.</p>\n</li>\n</ul>\n<p>Some libraries/packages might use a mixture of these approaches. For instance, the Julia package <a href=\"https://github.com/JuliaApproximation/FastGaussQuadrature.jl\" rel=\"nofollow noreferrer\">FastGaussQuadrature</a> uses tabulated values for <span class=\"math-container\">$n\\le 5$</span>, Newton's iteration for <span class=\"math-container\">$5&lt;n\\le 60$</span> and the asymptotic formulas for <span class=\"math-container\">$n&gt; 60$</span>.</p>\n","text":"As others mentioned in the comments, calculating the quadrature rule ahead of time is usually the fastest approach. However, you do not want to do that, you have a few options:\n\n\n\n\n\n\n\nGolub-Welsch algorithm (https://www.ams.org/journals/mcom/1969-23-106/S0025-5718-69-99647-1/S0025-5718-69-99647-1.pdf): Basically, you create a triadigonal matrix and calculate its eigendecomposition. The eigenvalues are the nodes and the weights are obtained from the first row of eigenvectors. For a matlab implementation, see this code (https://github.com/tcew/nodal-dg/blob/master/Codes1.1/Codes1D/JacobiGQ.m) where the coefficients alpha and beta correspond to the Jacobi polynomial associated with the quadrature (For Legendre quadrature use alpha=beta=0)\n\n\n\n\n\n\n\n\n\nCalculate the roots of the n-th Legendre polynomial (or other orthogonal polynomial) using Newton's method. You need a good initial guess, and you should use the derivative formulas to obtain the derivatives of the polynomial from its values as well as the recurrence relation. Here's a Matlab implementation (https://www.mathworks.com/matlabcentral/fileexchange/4540-legendre-gauss-quadrature-weights-and-nodes) as an example.\n\n\n\n\n\n\n\n\n\nFor very high order quadrature rules, you can consider using an asymptotic formula for the roots and weights like the ones discussed in this recent paper (https://doi.org/10.1137/140954969).\n\n\n\n\n\n\n\n\nSome libraries/packages might use a mixture of these approaches. For instance, the Julia package FastGaussQuadrature (https://github.com/JuliaApproximation/FastGaussQuadrature.jl) uses tabulated values for $n\\le 5$, Newton's iteration for $5<n\\le 60$ and the asymptotic formulas for $n> 60$."}],"domain":"computational_science","external_citations":["https://doi.org/10.1137/140954969","https://en.wikipedia.org/wiki/Gauss%E2%80%93Legendre_quadrature","https://github.com/JuliaApproximation/FastGaussQuadrature.jl","https://github.com/tcew/nodal-dg/blob/master/Codes1.1/Codes1D/JacobiGQ.m","https://www.ams.org/journals/mcom/1969-23-106/S0025-5718-69-99647-1/S0025-5718-69-99647-1.pdf","https://www.mathworks.com/matlabcentral/fileexchange/4540-legendre-gauss-quadrature-weights-and-nodes"],"ground_truth_type":"metadata_grounded","group_id":"1222a19e405c3ea024daba46aed1f792993e172d2b707644bf55c00c2c4314dc","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-d4f9d86a4215d7de9d127fc7","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:44.584971+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/272744bcc95b58699f7df6e6979b288bb8b00a80ab9c7982dbe170a6d0b63584_1790825325025901700_0.json","raw_sha256":"27a81850a40920682c29ada76a2b55e80340a5c82764a3e9dde8a9c2ba23db4e","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Makogan","profile_url":"https://scicomp.stackexchange.com/users/38908/makogan","user_type":"registered"},"created_at":"2025-06-22T15:37:39+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"07553FF8-9272-42C5-A2B7-1B148A7B7192","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/07553FF8-9272-42C5-A2B7-1B148A7B7192/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-06-23T15:58:46+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"D9C93E64-BD3E-4570-AC26-631D0D18E64C","revision_number":null,"revision_type":"vote_based","revision_url":"https://scicomp.stackexchange.com/revisions/D9C93E64-BD3E-4570-AC26-631D0D18E64C/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Anton Menshov","profile_url":"https://scicomp.stackexchange.com/users/20688/anton-menshov","user_type":"moderator"},"created_at":"2025-06-24T22:14:07+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"5EA1A740-F16C-4BC6-BEC6-176E698E39EB","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/5EA1A740-F16C-4BC6-BEC6-176E698E39EB/view-source"}],"source_commit":null,"source_data_file":"native_scicomp_source.jsonl","source_dataset":"RegalFire/Scientific-Native-Scicomp","source_license":"CC BY-SA 4.0","source_record_id":"45134","source_record_sha256":"a0a2124d30179990df319c6eb766cbb36d0a58f5380cbda33fa5bfea76bba7ae","source_url":"https://scicomp.stackexchange.com/questions/45134/generating-the-quadrature-points-for-gauss-legendre","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Generating the quadrature points for Gauss Legendre?\nThe Wikipedia entry on Gauss-Legendre (https://en.wikipedia.org/wiki/Gauss%E2%80%93Legendre_quadrature) says that there is a tri-diagonal matrix whose eigenvalues yield good approximations for the nodes of the Legendre polynomials.\n\n\n\n\nThere are a couple of papers I have found that talk about iteration-less methods as well.\n\n\n\n\nIf I care about computation speed much more than I do robustness, what would a good method to approximate the 0's be?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45135,"score":7}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I might have found the solution, of which I'm listing the main points/observations here below:</p>\n<ul>\n<li>the FFT/IFFT implementation in the code is consistent with the Fourier transform computed as <span class=\"math-container\">$\\tilde{F}(\\omega)=\\int^{+\\infty}_{-\\infty}f(t)e^{-i\\omega t}dt$</span> and correspondingly <span class=\"math-container\">$f(t)=\\frac{1}{2\\pi}\\int^{+\\infty}_{-\\infty}\\tilde{F}(\\omega)e^{i\\omega t}dt$</span>: to be sure about this I tried with the simple case of a Gaussian, but the multiplicative constants all turned out to be ok</li>\n<li>the dispersion operator should be written in the form <span class=\"math-container\">$D_{op}(\\omega)=-\\frac i2 \\beta_2 \\omega^2-\\frac i6 \\beta_3 \\omega^3$</span> to have the correct chirp sign at the output</li>\n<li>SPM should be taken into account with the factor <span class=\"math-container\">$e^{-i\\gamma \\Delta z I}$</span> (once again I made sure about this by just considering the SPM term and by computing the instantaneous frequency, which we know how it should look like)</li>\n<li>a spectral phase term <span class=\"math-container\">$\\varphi(\\omega)=-\\kappa \\omega^2, \\kappa&gt;0$</span> corresponds to a positive chirp, meaning that lower frequencies (shorter wavelengths) arrive later (just a note about the convention used, so that all signs are consistent now)</li>\n</ul>\n<p>Of course, if you have any further comments or observations let me know!</p>\n","answer_id":45186,"answer_text":"I might have found the solution, of which I'm listing the main points/observations here below:\n\n\n\n\n\nthe FFT/IFFT implementation in the code is consistent with the Fourier transform computed as $\\tilde{F}(\\omega)=\\int^{+\\infty}_{-\\infty}f(t)e^{-i\\omega t}dt$ and correspondingly $f(t)=\\frac{1}{2\\pi}\\int^{+\\infty}_{-\\infty}\\tilde{F}(\\omega)e^{i\\omega t}dt$: to be sure about this I tried with the simple case of a Gaussian, but the multiplicative constants all turned out to be ok\n\n\n\n\nthe dispersion operator should be written in the form $D_{op}(\\omega)=-\\frac i2 \\beta_2 \\omega^2-\\frac i6 \\beta_3 \\omega^3$ to have the correct chirp sign at the output\n\n\n\n\nSPM should be taken into account with the factor $e^{-i\\gamma \\Delta z I}$ (once again I made sure about this by just considering the SPM term and by computing the instantaneous frequency, which we know how it should look like)\n\n\n\n\na spectral phase term $\\varphi(\\omega)=-\\kappa \\omega^2, \\kappa>0$ corresponds to a positive chirp, meaning that lower frequencies (shorter wavelengths) arrive later (just a note about the convention used, so that all signs are consistent now)\n\n\n\n\n\nOf course, if you have any further comments or observations let me know!","answer_url":"https://scicomp.stackexchange.com/a/45186","author":"Lorenzo Iori","author_url":"https://scicomp.stackexchange.com/users/54430/lorenzo-iori","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2025-07-29T14:07:20+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:47.033952+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/cb6e5f564c84a92c4e121c0637c99292018f8935652e423630f2001099a2410f_1790825327386675300_0.json","raw_sha256":"1a957289f56621bebd21cb45dd99baaedb2c3bc11cb28d700558e4bbcaa19695","source_api":"Stack Exchange API 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Iori","profile_url":"https://scicomp.stackexchange.com/users/54430/lorenzo-iori","user_type":"registered"},"created_at":"2025-07-28T09:04:03+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"AE3B9EFD-BDF2-4534-A36C-C0D2AB181A60","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/AE3B9EFD-BDF2-4534-A36C-C0D2AB181A60/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lorenzo 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Iori","profile_url":"https://scicomp.stackexchange.com/users/54430/lorenzo-iori","user_type":"registered"},"created_at":"2025-07-29T14:04:04+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"B35F7AAE-2953-45D0-AD16-97CC9997095D","revision_number":5,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/B35F7AAE-2953-45D0-AD16-97CC9997095D/view-source"}],"url":"https://scicomp.stackexchange.com/questions/45185/split-step-fourier-method-for-ultrashort-pulse-propagation-predicts-everything"},{"author":"Lorenzo Iori","author_url":"https://scicomp.stackexchange.com/users/54430/lorenzo-iori","content_license":"CC BY-SA 4.0","context_id":"45186","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lorenzo Iori","profile_url":"https://scicomp.stackexchange.com/users/54430/lorenzo-iori","user_type":"registered"},"created_at":"2025-07-29T14:07:20+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"163AA634-CBFB-456A-AD54-8FFDF16B1F6A","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/163AA634-CBFB-456A-AD54-8FFDF16B1F6A/view-source"}],"url":"https://scicomp.stackexchange.com/a/45186"}],"contexts":[{"context_id":"question","html":"<p>I'm implementing in Python the split-step Fourier method (SSFM) to solve the non-linear envelope propagation equation (NEE), and I'm including second and third order dispersion (GDD, TOD), self-phase modulation (SPM) and self-steepening. I'm pretty happy with the results of the simulation: I can predict, at least in the same order of magnitude, the transform-limited duration of the pulse, the output duration of the pulse (after the non-linear path I am simulating) and the shape of the output spectrum. However, when it comes to analyzing the spectral phase at the output, the values seem completely off (for example: I expect, from the experiments, the pulse to have positive dispersion, so that a negative GDD should compensate it, but the simulations tell me the opposite.</p>\n<p>The issue is that I'm having problems in picking the correct signs for the dispersion and non-linear operator: in fact the shape of the NEE depends on the Fourier transform convention adopted, and there are many factors +/-1, or even +/-i, of which I'm not sure. Also, regarding the factor gamma for SPM: I'm using the formula (omega_0 / c) * (n2 / Aeff), with Aeff = pi w^2 / 2 for a Gaussian beam, and I'm not completely sure about this either (I'm using a 1D model in which, regarding the spatial evolution of the laser pulse, I consider a Gaussian beam with a corrective M^2 factor).</p>\n<p>My question basically is if the implementation is correct or if there are any inconsistencies in the code below.</p>\n<p>Here are the fundamental cells of the notebook:</p>\n<pre><code># freq to time:\ndef ifft(A_w):\n    return np.fft.fftshift(np.fft.ifft(np.fft.ifftshift(A_w))) / dt\n\n# time to freq\ndef fft(A_t):\n    return np.fft.fftshift(np.fft.fft(np.fft.ifftshift(A_t))) * dt\n\n\n# Dispersion and absorption operators for air and fused silica\nD_op_fs = - 1j * 0.5 * beta2_fs * w**2 - 1j * (1/6) * beta3_fs * w**3\nAbs_op_fs = np.exp(- 0.5 * alfa_fs * dz_fs)\nD_op_air = - 1j * 0.5 * beta2_air * w**2 - 1j * (1/6) * beta3_air * w**3\n\n\n# Function to propagate pulse by distance dz in SSFM\ndef propagate_pulse(A, D_op, Abs_op, dz, eff_area, n2):\n    \n    A_w = fft(A)\n    A_w = A_w * np.exp(D_op*dz/2) * Abs_op\n    A = ifft(A_w)\n    \n    gamma = (w0 / c) * n2 / eff_area\n    I = abs(A)**2\n    # without self-steepening\n    A = A * np.exp(- 1j * gamma * dz * I)\n    # with self-steepening\n    # A = A * np.exp(- 1j * gamma * dz * (I - 1j / w0 * (2*ifft(1j*w*fft(A))*np.conj(A)+ifft(1j*w*fft(np.conj(A)))*A)))\n        \n    A_w = fft(A)\n    A_w = A_w * np.exp(D_op*dz/2) * Abs_op\n    A = ifft(A_w)\n    \n    return A\n</code></pre>\n<p>Moreover, when introducing GDD&lt;0 with chirped mirrors, I use the convention</p>\n<pre><code>GDD_mirror = -45e-30    # in fs^2\nE_w = fft(E)\nE_w = E_w * np.exp(- 1j * GDD_mirror / 2 * w**2)\nE = ifft(E_w)\n</code></pre>\n<p>Edit: I have also included a way to change the GDD and TOD at the input pulse so to match the transform-limited and actual pulse duration, and I have already made many trials in changing the relative signs of dispersion, SPM, GDD, ...</p>\n","text":"I'm implementing in Python the split-step Fourier method (SSFM) to solve the non-linear envelope propagation equation (NEE), and I'm including second and third order dispersion (GDD, TOD), self-phase modulation (SPM) and self-steepening. I'm pretty happy with the results of the simulation: I can predict, at least in the same order of magnitude, the transform-limited duration of the pulse, the output duration of the pulse (after the non-linear path I am simulating) and the shape of the output spectrum. However, when it comes to analyzing the spectral phase at the output, the values seem completely off (for example: I expect, from the experiments, the pulse to have positive dispersion, so that a negative GDD should compensate it, but the simulations tell me the opposite.\n\n\n\n\nThe issue is that I'm having problems in picking the correct signs for the dispersion and non-linear operator: in fact the shape of the NEE depends on the Fourier transform convention adopted, and there are many factors +/-1, or even +/-i, of which I'm not sure. Also, regarding the factor gamma for SPM: I'm using the formula (omega_0 / c) * (n2 / Aeff), with Aeff = pi w^2 / 2 for a Gaussian beam, and I'm not completely sure about this either (I'm using a 1D model in which, regarding the spatial evolution of the laser pulse, I consider a Gaussian beam with a corrective M^2 factor).\n\n\n\n\nMy question basically is if the implementation is correct or if there are any inconsistencies in the code below.\n\n\n\n\nHere are the fundamental cells of the notebook:\n\n\n\n\n# freq to time:\ndef ifft(A_w):\n    return np.fft.fftshift(np.fft.ifft(np.fft.ifftshift(A_w))) / dt\n\n# time to freq\ndef fft(A_t):\n    return np.fft.fftshift(np.fft.fft(np.fft.ifftshift(A_t))) * dt\n\n\n# Dispersion and absorption operators for air and fused silica\nD_op_fs = - 1j * 0.5 * beta2_fs * w**2 - 1j * (1/6) * beta3_fs * w**3\nAbs_op_fs = np.exp(- 0.5 * alfa_fs * dz_fs)\nD_op_air = - 1j * 0.5 * beta2_air * w**2 - 1j * (1/6) * beta3_air * w**3\n\n\n# Function to propagate pulse by distance dz in SSFM\ndef propagate_pulse(A, D_op, Abs_op, dz, eff_area, n2):\n    \n    A_w = fft(A)\n    A_w = A_w * np.exp(D_op*dz/2) * Abs_op\n    A = ifft(A_w)\n    \n    gamma = (w0 / c) * n2 / eff_area\n    I = abs(A)**2\n    # without self-steepening\n    A = A * np.exp(- 1j * gamma * dz * I)\n    # with self-steepening\n    # A = A * np.exp(- 1j * gamma * dz * (I - 1j / w0 * (2*ifft(1j*w*fft(A))*np.conj(A)+ifft(1j*w*fft(np.conj(A)))*A)))\n        \n    A_w = fft(A)\n    A_w = A_w * np.exp(D_op*dz/2) * Abs_op\n    A = ifft(A_w)\n    \n    return A\n\n\n\n\n\nMoreover, when introducing GDD<0 with chirped mirrors, I use the convention\n\n\n\n\nGDD_mirror = -45e-30    # in fs^2\nE_w = fft(E)\nE_w = E_w * np.exp(- 1j * GDD_mirror / 2 * w**2)\nE = ifft(E_w)\n\n\n\n\n\nEdit: I have also included a way to change the GDD and TOD at the input pulse so to match the transform-limited and actual pulse duration, and I have already made many trials in changing the relative signs of dispersion, SPM, GDD, ..."},{"context_id":"45186","html":"<p>I might have found the solution, of which I'm listing the main points/observations here below:</p>\n<ul>\n<li>the FFT/IFFT implementation in the code is consistent with the Fourier transform computed as <span class=\"math-container\">$\\tilde{F}(\\omega)=\\int^{+\\infty}_{-\\infty}f(t)e^{-i\\omega t}dt$</span> and correspondingly <span class=\"math-container\">$f(t)=\\frac{1}{2\\pi}\\int^{+\\infty}_{-\\infty}\\tilde{F}(\\omega)e^{i\\omega t}dt$</span>: to be sure about this I tried with the simple case of a Gaussian, but the multiplicative constants all turned out to be ok</li>\n<li>the dispersion operator should be written in the form <span class=\"math-container\">$D_{op}(\\omega)=-\\frac i2 \\beta_2 \\omega^2-\\frac i6 \\beta_3 \\omega^3$</span> to have the correct chirp sign at the output</li>\n<li>SPM should be taken into account with the factor <span class=\"math-container\">$e^{-i\\gamma \\Delta z I}$</span> (once again I made sure about this by just considering the SPM term and by computing the instantaneous frequency, which we know how it should look like)</li>\n<li>a spectral phase term <span class=\"math-container\">$\\varphi(\\omega)=-\\kappa \\omega^2, \\kappa&gt;0$</span> corresponds to a positive chirp, meaning that lower frequencies (shorter wavelengths) arrive later (just a note about the convention used, so that all signs are consistent now)</li>\n</ul>\n<p>Of course, if you have any further comments or observations let me know!</p>\n","text":"I might have found the solution, of which I'm listing the main points/observations here below:\n\n\n\n\n\nthe FFT/IFFT implementation in the code is consistent with the Fourier transform computed as $\\tilde{F}(\\omega)=\\int^{+\\infty}_{-\\infty}f(t)e^{-i\\omega t}dt$ and correspondingly $f(t)=\\frac{1}{2\\pi}\\int^{+\\infty}_{-\\infty}\\tilde{F}(\\omega)e^{i\\omega t}dt$: to be sure about this I tried with the simple case of a Gaussian, but the multiplicative constants all turned out to be ok\n\n\n\n\nthe dispersion operator should be written in the form $D_{op}(\\omega)=-\\frac i2 \\beta_2 \\omega^2-\\frac i6 \\beta_3 \\omega^3$ to have the correct chirp sign at the output\n\n\n\n\nSPM should be taken into account with the factor $e^{-i\\gamma \\Delta z I}$ (once again I made sure about this by just considering the SPM term and by computing the instantaneous frequency, which we know how it should look like)\n\n\n\n\na spectral phase term $\\varphi(\\omega)=-\\kappa \\omega^2, \\kappa>0$ corresponds to a positive chirp, meaning that lower frequencies (shorter wavelengths) arrive later (just a note about the convention used, so that all signs are consistent now)\n\n\n\n\n\nOf course, if you have any further comments or observations let me know!"}],"domain":"computational_science","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"bd5fd699490a197c46453cd6248b87ba2e8c956fa8b9f71ad9a2f50b5a440c08","hard_case_family":["no_accepted_answer"],"id":"RHM-906af7b675a6b310cac98ed7","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:44.584971+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/272744bcc95b58699f7df6e6979b288bb8b00a80ab9c7982dbe170a6d0b63584_1790825325025901700_0.json","raw_sha256":"27a81850a40920682c29ada76a2b55e80340a5c82764a3e9dde8a9c2ba23db4e","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lorenzo Iori","profile_url":"https://scicomp.stackexchange.com/users/54430/lorenzo-iori","user_type":"registered"},"created_at":"2025-07-28T09:04:03+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"AE3B9EFD-BDF2-4534-A36C-C0D2AB181A60","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/AE3B9EFD-BDF2-4534-A36C-C0D2AB181A60/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lorenzo Iori","profile_url":"https://scicomp.stackexchange.com/users/54430/lorenzo-iori","user_type":"registered"},"created_at":"2025-07-28T09:15:52+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"BE26735D-FCBC-47F1-A566-F341DD41F55C","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/BE26735D-FCBC-47F1-A566-F341DD41F55C/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lorenzo Iori","profile_url":"https://scicomp.stackexchange.com/users/54430/lorenzo-iori","user_type":"registered"},"created_at":"2025-07-28T14:07:20+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"67CC67B8-AC93-4C69-9C21-0E6BDBF43102","revision_number":3,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/67CC67B8-AC93-4C69-9C21-0E6BDBF43102/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lorenzo Iori","profile_url":"https://scicomp.stackexchange.com/users/54430/lorenzo-iori","user_type":"registered"},"created_at":"2025-07-28T14:32:46+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"3BBDD6A2-8D30-430A-8EAF-A458144119BA","revision_number":4,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/3BBDD6A2-8D30-430A-8EAF-A458144119BA/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lorenzo Iori","profile_url":"https://scicomp.stackexchange.com/users/54430/lorenzo-iori","user_type":"registered"},"created_at":"2025-07-29T14:04:04+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"B35F7AAE-2953-45D0-AD16-97CC9997095D","revision_number":5,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/B35F7AAE-2953-45D0-AD16-97CC9997095D/view-source"}],"source_commit":null,"source_data_file":"native_scicomp_source.jsonl","source_dataset":"RegalFire/Scientific-Native-Scicomp","source_license":"CC BY-SA 4.0","source_record_id":"45185","source_record_sha256":"5223204980616f3e7438fe5ec2e2fc70fc28a4270ef10902b49578dee783c8e3","source_url":"https://scicomp.stackexchange.com/questions/45185/split-step-fourier-method-for-ultrashort-pulse-propagation-predicts-everything","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Split-step Fourier method for ultrashort pulse propagation predicts everything, but not the spectral phase\nI'm implementing in Python the split-step Fourier method (SSFM) to solve the non-linear envelope propagation equation (NEE), and I'm including second and third order dispersion (GDD, TOD), self-phase modulation (SPM) and self-steepening. I'm pretty happy with the results of the simulation: I can predict, at least in the same order of magnitude, the transform-limited duration of the pulse, the output duration of the pulse (after the non-linear path I am simulating) and the shape of the output spectrum. However, when it comes to analyzing the spectral phase at the output, the values seem completely off (for example: I expect, from the experiments, the pulse to have positive dispersion, so that a negative GDD should compensate it, but the simulations tell me the opposite.\n\n\n\n\nThe issue is that I'm having problems in picking the correct signs for the dispersion and non-linear operator: in fact the shape of the NEE depends on the Fourier transform convention adopted, and there are many factors +/-1, or even +/-i, of which I'm not sure. Also, regarding the factor gamma for SPM: I'm using the formula (omega_0 / c) * (n2 / Aeff), with Aeff = pi w^2 / 2 for a Gaussian beam, and I'm not completely sure about this either (I'm using a 1D model in which, regarding the spatial evolution of the laser pulse, I consider a Gaussian beam with a corrective M^2 factor).\n\n\n\n\nMy question basically is if the implementation is correct or if there are any inconsistencies in the code below.\n\n\n\n\nHere are the fundamental cells of the notebook:\n\n\n\n\n# freq to time:\ndef ifft(A_w):\n    return np.fft.fftshift(np.fft.ifft(np.fft.ifftshift(A_w))) / dt\n\n# time to freq\ndef fft(A_t):\n    return np.fft.fftshift(np.fft.fft(np.fft.ifftshift(A_t))) * dt\n\n\n# Dispersion and absorption operators for air and fused silica\nD_op_fs = - 1j * 0.5 * beta2_fs * w**2 - 1j * (1/6) * beta3_fs * w**3\nAbs_op_fs = np.exp(- 0.5 * alfa_fs * dz_fs)\nD_op_air = - 1j * 0.5 * beta2_air * w**2 - 1j * (1/6) * beta3_air * w**3\n\n\n# Function to propagate pulse by distance dz in SSFM\ndef propagate_pulse(A, D_op, Abs_op, dz, eff_area, n2):\n    \n    A_w = fft(A)\n    A_w = A_w * np.exp(D_op*dz/2) * Abs_op\n    A = ifft(A_w)\n    \n    gamma = (w0 / c) * n2 / eff_area\n    I = abs(A)**2\n    # without self-steepening\n    A = A * np.exp(- 1j * gamma * dz * I)\n    # with self-steepening\n    # A = A * np.exp(- 1j * gamma * dz * (I - 1j / w0 * (2*ifft(1j*w*fft(A))*np.conj(A)+ifft(1j*w*fft(np.conj(A)))*A)))\n        \n    A_w = fft(A)\n    A_w = A_w * np.exp(D_op*dz/2) * Abs_op\n    A = ifft(A_w)\n    \n    return A\n\n\n\n\n\nMoreover, when introducing GDD<0 with chirped mirrors, I use the convention\n\n\n\n\nGDD_mirror = -45e-30    # in fs^2\nE_w = fft(E)\nE_w = E_w * np.exp(- 1j * GDD_mirror / 2 * w**2)\nE = ifft(E_w)\n\n\n\n\n\nEdit: I have also included a way to change the GDD and TOD at the input pulse so to match the transform-limited and actual pulse duration, and I have already made many trials in changing the relative signs of dispersion, SPM, GDD, ...","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45186,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":45203,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The problem is two-dimensional because it is posed on a two-dimensional manifold. Software such as deal.II (disclaimer: I'm one of the authors of this software) have no problem with solving PDEs on a manifold, making it essentially the same as if you had a flat domain. The discretization will look exactly the same, and you get a matrix that has the same properties and that consequently can be solved with the same methods.</p>\n","answer_id":45203,"answer_text":"The problem is two-dimensional because it is posed on a two-dimensional manifold. Software such as deal.II (disclaimer: I'm one of the authors of this software) have no problem with solving PDEs on a manifold, making it essentially the same as if you had a flat domain. The discretization will look exactly the same, and you get a matrix that has the same properties and that consequently can be solved with the same methods.","answer_url":"https://scicomp.stackexchange.com/a/45203","author":"Wolfgang Bangerth","author_url":"https://scicomp.stackexchange.com/users/393/wolfgang-bangerth","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2025-08-03T23:31:39+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:47.033952+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/cb6e5f564c84a92c4e121c0637c99292018f8935652e423630f2001099a2410f_1790825327386675300_0.json","raw_sha256":"1a957289f56621bebd21cb45dd99baaedb2c3bc11cb28d700558e4bbcaa19695","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/45545;45541;45538;45533;45532;45530;45523;45513;45510;45507;45499;45493;45488;45487;45479;45474;45472;45463;45461;45447;45444;45436;45428;45425;45424;45423;45422;45416;45414;45410;45404;45401;45396;45391;45389;45387;45380;45377;45376;45375;45369;45366;45365;45363;45362;45359;45350;45347;45344;45336;45334;45331;45326;45322;45316;45313;45311;45309;45305;45302;45300;45291;45289;45285;45276;45269;45263;45262;45261;45253;45247;45246;45238;45236;45230;45229;45208;45201;45200;45185;45183;45171;45167;45165;45158;45154;45146;45141;45139;45134;45129;45127;45122;45114;45112;45108;45105;45100;45098;45096/answers?filter=withbody&order=asc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":45200,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Wolfgang Bangerth","profile_url":"https://scicomp.stackexchange.com/users/393/wolfgang-bangerth","user_type":"registered"},"created_at":"2025-08-03T23:31:39+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"018E2F6B-212A-4D8F-A1E5-3F3882056126","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/018E2F6B-212A-4D8F-A1E5-3F3882056126/view-source"}],"score":5,"updated_at":"2025-08-03T23:31:39+00:00"},{"answer_html":"<p>The generalization of the Laplace operator on curved surfaces is called <a href=\"https://en.wikipedia.org/wiki/Laplace%E2%80%93Beltrami_operator\" rel=\"nofollow noreferrer\">Laplace-Beltrami operator</a>.</p>\n<p>When working with surfaces embedded in 3D space, you're essentially dealing with a 2D problem with added geometric complexity. The discretization yields an operator matrix similar to the 2D case, but the surface geometry introduces additional challenges. The surface curvature will affect the condition number and can make it harder(comparatively) to solve. The same solvers will likely work. Preconditioning will help.</p>\n","answer_id":45206,"answer_text":"The generalization of the Laplace operator on curved surfaces is called Laplace-Beltrami operator (https://en.wikipedia.org/wiki/Laplace%E2%80%93Beltrami_operator).\n\n\n\n\nWhen working with surfaces embedded in 3D space, you're essentially dealing with a 2D problem with added geometric complexity. The discretization yields an operator matrix similar to the 2D case, but the surface geometry introduces additional challenges. The surface curvature will affect the condition number and can make it harder(comparatively) to solve. The same solvers will likely work. Preconditioning will help.","answer_url":"https://scicomp.stackexchange.com/a/45206","author":"Abhilash Reddy M","author_url":"https://scicomp.stackexchange.com/users/16934/abhilash-reddy-m","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2025-08-04T13:57:28+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:47.033952+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/cb6e5f564c84a92c4e121c0637c99292018f8935652e423630f2001099a2410f_1790825327386675300_0.json","raw_sha256":"1a957289f56621bebd21cb45dd99baaedb2c3bc11cb28d700558e4bbcaa19695","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/45545;45541;45538;45533;45532;45530;45523;45513;45510;45507;45499;45493;45488;45487;45479;45474;45472;45463;45461;45447;45444;45436;45428;45425;45424;45423;45422;45416;45414;45410;45404;45401;45396;45391;45389;45387;45380;45377;45376;45375;45369;45366;45365;45363;45362;45359;45350;45347;45344;45336;45334;45331;45326;45322;45316;45313;45311;45309;45305;45302;45300;45291;45289;45285;45276;45269;45263;45262;45261;45253;45247;45246;45238;45236;45230;45229;45208;45201;45200;45185;45183;45171;45167;45165;45158;45154;45146;45141;45139;45134;45129;45127;45122;45114;45112;45108;45105;45100;45098;45096/answers?filter=withbody&order=asc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":45200,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Abhilash Reddy M","profile_url":"https://scicomp.stackexchange.com/users/16934/abhilash-reddy-m","user_type":"registered"},"created_at":"2025-08-04T13:57:28+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"AB2BEF21-CDE1-4978-95DB-DD3D903D2B83","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/AB2BEF21-CDE1-4978-95DB-DD3D903D2B83/view-source"}],"score":3,"updated_at":"2025-08-04T13:57:28+00:00"}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Researcher R","author_url":"https://scicomp.stackexchange.com/users/53321/researcher-r","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Researcher R","profile_url":"https://scicomp.stackexchange.com/users/53321/researcher-r","user_type":"registered"},"created_at":"2025-08-02T22:25:43+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"D756C7A0-4BE4-4E82-BC24-CE48DB6E4EFF","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/D756C7A0-4BE4-4E82-BC24-CE48DB6E4EFF/view-source"}],"url":"https://scicomp.stackexchange.com/questions/45200/what-would-be-the-correct-form-of-the-pde-for-a-plate-with-topography"},{"author":"Wolfgang Bangerth","author_url":"https://scicomp.stackexchange.com/users/393/wolfgang-bangerth","content_license":"CC BY-SA 4.0","context_id":"45203","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Wolfgang Bangerth","profile_url":"https://scicomp.stackexchange.com/users/393/wolfgang-bangerth","user_type":"registered"},"created_at":"2025-08-03T23:31:39+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"018E2F6B-212A-4D8F-A1E5-3F3882056126","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/018E2F6B-212A-4D8F-A1E5-3F3882056126/view-source"}],"url":"https://scicomp.stackexchange.com/a/45203"},{"author":"Abhilash Reddy M","author_url":"https://scicomp.stackexchange.com/users/16934/abhilash-reddy-m","content_license":"CC BY-SA 4.0","context_id":"45206","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Abhilash Reddy M","profile_url":"https://scicomp.stackexchange.com/users/16934/abhilash-reddy-m","user_type":"registered"},"created_at":"2025-08-04T13:57:28+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"AB2BEF21-CDE1-4978-95DB-DD3D903D2B83","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/AB2BEF21-CDE1-4978-95DB-DD3D903D2B83/view-source"}],"url":"https://scicomp.stackexchange.com/a/45206"}],"contexts":[{"context_id":"question","html":"<p>I've meshed the following thin plate with a wavy topography below</p>\n<p><a href=\"https://i.sstatic.net/MIJjgTpB.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/MIJjgTpB.png\" alt=\"enter image description here\" /></a></p>\n<p>Assume the plate has no thickness, it's effectively like a sheet of paper. I want to solve Poisson's Equation</p>\n<p><span class=\"math-container\">$$\\Delta u = -f \\\\ u|_{\\textbf{x}\\in \\partial \\Omega} = g$$</span></p>\n<p>on this plate. In order to do so, there are a couple things that I need to know:</p>\n<ol>\n<li><p>Would the Laplacian for this problem be 2D or 3D? The plate undulates in the z-direction, so I'd assume it would be 3D, but I'm not sure.</p>\n</li>\n<li><p>For this particular problem, would this require any special solver or would any standard solver like LU factorization work? If any solver works, is there one that would work best for problems with topography?</p>\n</li>\n</ol>\n<p>To help contextualize 1, I'm using Fenicsx to approximate the solution, and the package requires identifying the correct variational/weak form of the PDE, and that requires that I know the correct original form of the PDE. 2 relates to the solver that I would have the package use.</p>\n","text":"I've meshed the following thin plate with a wavy topography below\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/MIJjgTpB.png] (https://i.sstatic.net/MIJjgTpB.png)\n\n\n\n\nAssume the plate has no thickness, it's effectively like a sheet of paper. I want to solve Poisson's Equation\n\n\n\n\n$$\\Delta u = -f \\\\ u|_{\\textbf{x}\\in \\partial \\Omega} = g$$\n\n\n\n\non this plate. In order to do so, there are a couple things that I need to know:\n\n\n\n\n\n\n\nWould the Laplacian for this problem be 2D or 3D? The plate undulates in the z-direction, so I'd assume it would be 3D, but I'm not sure.\n\n\n\n\n\n\n\n\n\nFor this particular problem, would this require any special solver or would any standard solver like LU factorization work? If any solver works, is there one that would work best for problems with topography?\n\n\n\n\n\n\n\n\nTo help contextualize 1, I'm using Fenicsx to approximate the solution, and the package requires identifying the correct variational/weak form of the PDE, and that requires that I know the correct original form of the PDE. 2 relates to the solver that I would have the package use."},{"context_id":"45203","html":"<p>The problem is two-dimensional because it is posed on a two-dimensional manifold. Software such as deal.II (disclaimer: I'm one of the authors of this software) have no problem with solving PDEs on a manifold, making it essentially the same as if you had a flat domain. The discretization will look exactly the same, and you get a matrix that has the same properties and that consequently can be solved with the same methods.</p>\n","text":"The problem is two-dimensional because it is posed on a two-dimensional manifold. Software such as deal.II (disclaimer: I'm one of the authors of this software) have no problem with solving PDEs on a manifold, making it essentially the same as if you had a flat domain. The discretization will look exactly the same, and you get a matrix that has the same properties and that consequently can be solved with the same methods."},{"context_id":"45206","html":"<p>The generalization of the Laplace operator on curved surfaces is called <a href=\"https://en.wikipedia.org/wiki/Laplace%E2%80%93Beltrami_operator\" rel=\"nofollow noreferrer\">Laplace-Beltrami operator</a>.</p>\n<p>When working with surfaces embedded in 3D space, you're essentially dealing with a 2D problem with added geometric complexity. The discretization yields an operator matrix similar to the 2D case, but the surface geometry introduces additional challenges. The surface curvature will affect the condition number and can make it harder(comparatively) to solve. The same solvers will likely work. Preconditioning will help.</p>\n","text":"The generalization of the Laplace operator on curved surfaces is called Laplace-Beltrami operator (https://en.wikipedia.org/wiki/Laplace%E2%80%93Beltrami_operator).\n\n\n\n\nWhen working with surfaces embedded in 3D space, you're essentially dealing with a 2D problem with added geometric complexity. The discretization yields an operator matrix similar to the 2D case, but the surface geometry introduces additional challenges. The surface curvature will affect the condition number and can make it harder(comparatively) to solve. The same solvers will likely work. Preconditioning will help."}],"domain":"computational_science","external_citations":["https://en.wikipedia.org/wiki/Laplace%E2%80%93Beltrami_operator","https://i.sstatic.net/MIJjgTpB.png"],"ground_truth_type":"metadata_grounded","group_id":"8307f1ee75841ce20d9a1ff4401be9d7b3e409f87a0fef086938bc30c76982e2","hard_case_family":["multiple_sources","multiple_answer_candidates"],"id":"RHM-d143a557e779c60f0d45f15c","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:44.584971+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/272744bcc95b58699f7df6e6979b288bb8b00a80ab9c7982dbe170a6d0b63584_1790825325025901700_0.json","raw_sha256":"27a81850a40920682c29ada76a2b55e80340a5c82764a3e9dde8a9c2ba23db4e","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Researcher R","profile_url":"https://scicomp.stackexchange.com/users/53321/researcher-r","user_type":"registered"},"created_at":"2025-08-02T22:25:43+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"D756C7A0-4BE4-4E82-BC24-CE48DB6E4EFF","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/D756C7A0-4BE4-4E82-BC24-CE48DB6E4EFF/view-source"}],"source_commit":null,"source_data_file":"native_scicomp_source.jsonl","source_dataset":"RegalFire/Scientific-Native-Scicomp","source_license":"CC BY-SA 4.0","source_record_id":"45200","source_record_sha256":"54c47d31e53bf58a3c663f1c9287b9d98a6732551c3737d1aece4a1dc7cbe6ad","source_url":"https://scicomp.stackexchange.com/questions/45200/what-would-be-the-correct-form-of-the-pde-for-a-plate-with-topography","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What would be the correct form of the PDE for a plate with topography?\nI've meshed the following thin plate with a wavy topography below\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/MIJjgTpB.png] (https://i.sstatic.net/MIJjgTpB.png)\n\n\n\n\nAssume the plate has no thickness, it's effectively like a sheet of paper. I want to solve Poisson's Equation\n\n\n\n\n$$\\Delta u = -f \\\\ u|_{\\textbf{x}\\in \\partial \\Omega} = g$$\n\n\n\n\non this plate. In order to do so, there are a couple things that I need to know:\n\n\n\n\n\n\n\nWould the Laplacian for this problem be 2D or 3D? The plate undulates in the z-direction, so I'd assume it would be 3D, but I'm not sure.\n\n\n\n\n\n\n\n\n\nFor this particular problem, would this require any special solver or would any standard solver like LU factorization work? If any solver works, is there one that would work best for problems with topography?\n\n\n\n\n\n\n\n\nTo help contextualize 1, I'm using Fenicsx to approximate the solution, and the package requires identifying the correct variational/weak form of the PDE, and that requires that I know the correct original form of the PDE. 2 relates to the solver that I would have the package use.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45203,"score":5},{"answer_id":45206,"score":3}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>this is just Monte Carlo integration with cosine-weighted sampling. that’s why it works and the others don’t.</p>\n<p>cosine weighting enforces the correct solid-angle measure, so the flux gradient obeys Gauss’s law. uniform hemisphere or tangent-plane sampling breaks that, which is why the field comes out wrong. the 2/π factor is the usual cosine-hemisphere normalization.</p>\n<p>in physics terms, you’re doing a Monte Carlo solution of Poisson’s equation via flux sampling, and the Schwarzschild behavior drops out naturally when the sampling measure matches the geometry. not a single “owner”  it’s standard Monte Carlo done with the right weighting.</p>\n","answer_id":45329,"answer_text":"this is just Monte Carlo integration with cosine-weighted sampling. that’s why it works and the others don’t.\n\n\n\n\ncosine weighting enforces the correct solid-angle measure, so the flux gradient obeys Gauss’s law. uniform hemisphere or tangent-plane sampling breaks that, which is why the field comes out wrong. the 2/π factor is the usual cosine-hemisphere normalization.\n\n\n\n\nin physics terms, you’re doing a Monte Carlo solution of Poisson’s equation via flux sampling, and the Schwarzschild behavior drops out naturally when the sampling measure matches the geometry. not a single “owner”  it’s standard Monte Carlo done with the right weighting.","answer_url":"https://scicomp.stackexchange.com/a/45329","author":"Linda Anderson","author_url":"https://scicomp.stackexchange.com/users/56218/linda-anderson","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-01-05T09:26:54+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:47.033952+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/cb6e5f564c84a92c4e121c0637c99292018f8935652e423630f2001099a2410f_1790825327386675300_0.json","raw_sha256":"1a957289f56621bebd21cb45dd99baaedb2c3bc11cb28d700558e4bbcaa19695","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/45545;45541;45538;45533;45532;45530;45523;45513;45510;45507;45499;45493;45488;45487;45479;45474;45472;45463;45461;45447;45444;45436;45428;45425;45424;45423;45422;45416;45414;45410;45404;45401;45396;45391;45389;45387;45380;45377;45376;45375;45369;45366;45365;45363;45362;45359;45350;45347;45344;45336;45334;45331;45326;45322;45316;45313;45311;45309;45305;45302;45300;45291;45289;45285;45276;45269;45263;45262;45261;45253;45247;45246;45238;45236;45230;45229;45208;45201;45200;45185;45183;45171;45167;45165;45158;45154;45146;45141;45139;45134;45129;45127;45122;45114;45112;45108;45105;45100;45098;45096/answers?filter=withbody&order=asc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":45322,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Linda Anderson","profile_url":"https://scicomp.stackexchange.com/users/56218/linda-anderson","user_type":"registered"},"created_at":"2026-01-05T09:26:54+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"8F296337-1611-4B90-B028-6FDD3F098E8A","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/8F296337-1611-4B90-B028-6FDD3F098E8A/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Linda Anderson","profile_url":"https://scicomp.stackexchange.com/users/56218/linda-anderson","user_type":"registered"},"created_at":"2026-01-05T09:27:15+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"317C93D3-B055-47E3-8255-35BB56F95C1B","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/317C93D3-B055-47E3-8255-35BB56F95C1B/view-source"}],"score":5,"updated_at":"2026-01-05T09:27:15+00:00"},{"answer_html":"<p>The first answer fails to mention that there is a purely quantum method (labeled C)) -- the cosine weighting is only a classical approximation (labeled B)). The following is the important part of the C++ code (which uses standard multi-threading):</p>\n<pre class=\"lang-cpp prettyprint-override\"><code>void worker_thread(\n    long long unsigned int start_idx,\n    long long unsigned int end_idx,\n    unsigned int thread_seed,\n    const real_type emitter_radius,\n    const real_type receiver_distance,\n    const real_type receiver_distance_plus,\n    const real_type receiver_radius,\n    real_type&amp; result_count,\n    real_type&amp; result_count_plus)\n{\n    // Thread-local random number generator\n    std::mt19937 local_gen(thread_seed);\n    std::uniform_real_distribution&lt;real_type&gt; local_dis(0.0, 1.0);\n\n    real_type local_count = 0;\n    real_type local_count_plus = 0;\n\n    // Update progress every N iterations to reduce atomic overhead\n    const long long unsigned int progress_update_interval = 10000;\n    long long unsigned int local_progress = 0;\n\n    for (long long unsigned int i = start_idx; i &lt; end_idx; i++)\n    {\n        vector_3 location = random_unit_vector(local_gen, local_dis);\n        location.x *= emitter_radius;\n        location.y *= emitter_radius;\n        location.z *= emitter_radius;\n\n        vector_3 surface_normal = location;\n        surface_normal.normalize();\n\n\n        // A) Newtonian gravitation\n        //vector_3 normal =\n        //  surface_normal;\n\n        // B) Schwarzschild gravitation\n        //vector_3 normal = \n        //  random_cosine_weighted_hemisphere(\n        //      surface_normal, local_gen, local_dis);\n\n        // C) Quantum gravitation\n        vector_3 r = random_unit_vector(local_gen, local_dis);\n        r.x *= emitter_radius;\n        r.y *= emitter_radius;\n        r.z *= emitter_radius;\n        vector_3 normal = (location - r).normalize();\n\n\n        local_count += intersect(\n            location, normal,\n            receiver_distance, receiver_radius);\n\n        local_count_plus += intersect(\n            location, normal,\n            receiver_distance_plus, receiver_radius);\n\n        // Update global progress periodically\n        local_progress++;\n        if (local_progress &gt;= progress_update_interval)\n        {\n            global_progress.fetch_add(\n                local_progress, std::memory_order_relaxed);\n    \n            local_progress = 0;\n        }\n    }\n\n    // Add any remaining progress\n    if (local_progress &gt; 0)\n    {\n        global_progress.fetch_add(\n            local_progress, std::memory_order_relaxed);\n    }\n\n    result_count = local_count;\n    result_count_plus = local_count_plus;\n}\n</code></pre>\n","answer_id":45343,"answer_text":"The first answer fails to mention that there is a purely quantum method (labeled C)) -- the cosine weighting is only a classical approximation (labeled B)). The following is the important part of the C++ code (which uses standard multi-threading):\n\n\n\n\nvoid worker_thread(\n    long long unsigned int start_idx,\n    long long unsigned int end_idx,\n    unsigned int thread_seed,\n    const real_type emitter_radius,\n    const real_type receiver_distance,\n    const real_type receiver_distance_plus,\n    const real_type receiver_radius,\n    real_type& result_count,\n    real_type& result_count_plus)\n{\n    // Thread-local random number generator\n    std::mt19937 local_gen(thread_seed);\n    std::uniform_real_distribution<real_type> local_dis(0.0, 1.0);\n\n    real_type local_count = 0;\n    real_type local_count_plus = 0;\n\n    // Update progress every N iterations to reduce atomic overhead\n    const long long unsigned int progress_update_interval = 10000;\n    long long unsigned int local_progress = 0;\n\n    for (long long unsigned int i = start_idx; i < end_idx; i++)\n    {\n        vector_3 location = random_unit_vector(local_gen, local_dis);\n        location.x *= emitter_radius;\n        location.y *= emitter_radius;\n        location.z *= emitter_radius;\n\n        vector_3 surface_normal = location;\n        surface_normal.normalize();\n\n\n        // A) Newtonian gravitation\n        //vector_3 normal =\n        //  surface_normal;\n\n        // B) Schwarzschild gravitation\n        //vector_3 normal = \n        //  random_cosine_weighted_hemisphere(\n        //      surface_normal, local_gen, local_dis);\n\n        // C) Quantum gravitation\n        vector_3 r = random_unit_vector(local_gen, local_dis);\n        r.x *= emitter_radius;\n        r.y *= emitter_radius;\n        r.z *= emitter_radius;\n        vector_3 normal = (location - r).normalize();\n\n\n        local_count += intersect(\n            location, normal,\n            receiver_distance, receiver_radius);\n\n        local_count_plus += intersect(\n            location, normal,\n            receiver_distance_plus, receiver_radius);\n\n        // Update global progress periodically\n        local_progress++;\n        if (local_progress >= progress_update_interval)\n        {\n            global_progress.fetch_add(\n                local_progress, std::memory_order_relaxed);\n    \n            local_progress = 0;\n        }\n    }\n\n    // Add any remaining progress\n    if (local_progress > 0)\n    {\n        global_progress.fetch_add(\n            local_progress, std::memory_order_relaxed);\n    }\n\n    result_count = local_count;\n    result_count_plus = local_count_plus;\n}","answer_url":"https://scicomp.stackexchange.com/a/45343","author":"shawn_halayka","author_url":"https://scicomp.stackexchange.com/users/48649/shawn-halayka","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-01-18T14:29:37+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:47.033952+00:00","license":"CC BY-SA 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4.0","contributor":{"display_name":"shawn_halayka","profile_url":"https://scicomp.stackexchange.com/users/48649/shawn-halayka","user_type":"registered"},"created_at":"2026-03-19T21:29:13+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"F02DA395-BFED-4987-A4F2-199B2AA19C48","revision_number":5,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/F02DA395-BFED-4987-A4F2-199B2AA19C48/view-source"}],"url":"https://scicomp.stackexchange.com/a/45343"}],"contexts":[{"context_id":"question","html":"<h2>Question</h2>\n<p><strong>What is the name of the numerical technique used to generate the appropriate gravitational acceleration by using a set of gravitational field lines that are not necessarily normal to the surface of the emitter?</strong></p>\n<p>I have found that using cosine weighted pseudorandom field lines produces the result predicted by Schwarzschild's general relativity. It's a very simple calculation. Please help me identify its owner.</p>\n<h2>Introduction</h2>\n<p>In the past, I have written a short tutorial for C++ programmers on isotropic Newtonian gravitation.\nIn that old tutorial, I build an isotropic gravitational field through the use of pseudorandomly generated field lines.\nIn that old tutorial I use a sphere as the receiver.\nThe paper for that old tutorial is at <a href=\"https://www.techrxiv.org/users/685306/articles/1250456-newtonian-gravitation-from-scratch-for-c-programmers\" rel=\"noreferrer\">Newtonian gravitation from scratch, for C++ programmers</a>.</p>\n<p>In this question, I point out a match between the numerical gravitation and the gravitational time dilation from Schwarzschild's general relativity (see the book <a href=\"https://search.worldcat.org/title/585119\" rel=\"noreferrer\">Gravitation, by Misner et al</a>).\nHere, I use an axis-aligned bounding box (AABB) as the receiver.</p>\n<p>In this question I use Planck units, where <span class=\"math-container\">$c = G = \\hbar = k = 1$</span>.</p>\n<h2>Method</h2>\n<p>Where <span class=\"math-container\">$r_{e}$</span> is the emitter's Schwarzschild radius, <span class=\"math-container\">$r_{r}$</span> is the receiver AABB radius (e.g. half of the AABB side length), and <span class=\"math-container\">$1\\mathrm{e}11$</span> and <span class=\"math-container\">$0.01$</span> are arbitrary constants:\n<span class=\"math-container\">\\begin{equation}\nr_{e} = \\sqrt{\\frac{1\\mathrm{e}11 \\log(2)}{\\pi}},\n\\end{equation}</span>\n<span class=\"math-container\">\\begin{equation}\nr_{r} = r_{e} \\times 0.01.\n\\end{equation}</span>\nThe event horizon area is:\n<span class=\"math-container\">\\begin{equation}\nA_{e} = 4 \\pi r_{e}^2.\n\\end{equation}</span>\nThe binary entropy (e.g. field line count, see the papers about the holographic principle) is:\n<span class=\"math-container\">\\begin{equation}\nn_{e} = \\frac{A_{e}}{4 \\log(2)} = 1\\mathrm{e}11.\n\\end{equation}</span>\nWhere <span class=\"math-container\">$R$</span> is the distance from the emitter's centre, the derivative is:\n<span class=\"math-container\">\\begin{equation}\n\\alpha = \\frac{\\beta(R + \\epsilon) - \\beta(R)}{\\epsilon}.\n\\end{equation}</span>\nHere <span class=\"math-container\">$\\beta$</span> is the get intersecting line density function.\nThe gradient strength is:\n<span class=\"math-container\">\\begin{equation}\ng = \\frac{-\\alpha}{r_{r}^2}.% \\approx \\frac{n_e}{2 R^3}.\n\\end{equation}</span>\nFrom this I get the Newtonian acceleration <span class=\"math-container\">$a_N$</span>, where <span class=\"math-container\">$r_e \\ll R$</span>:\n<span class=\"math-container\">\\begin{equation}\na_N =\\frac{g R \\log 2}{8 M_{e}} =  \\sqrt{\\frac{n_e \\log 2}{4 \\pi R^4}} = \\frac{M_{e}}{R^2}.\n\\end{equation}</span>\nI can also get a general relativistic acceleration <span class=\"math-container\">$a_S$</span>, where <span class=\"math-container\">$r_e &lt; R$</span>:\n<span class=\"math-container\">\\begin{equation}\na_S = \\frac{g R \\log 2}{8 M_{e}},\n\\end{equation}</span>\nAt close proximity, where <span class=\"math-container\">$r_e \\approx R$</span>, the metric produced is related to the Schwarzschild metric -- curved space, curved time:\n<span class=\"math-container\">\\begin{equation}\nt = \\sqrt{1 - \\frac{r_e}{R}},\n\\end{equation}</span>\n<span class=\"math-container\">\\begin{equation}\n\\frac{dt}{dR} = \\frac{r_e}{2 t R^2}.\n\\end{equation}</span>\n<span class=\"math-container\">\\begin{equation}\na_S \\approx \\frac{dt}{dR} \\frac{2}{\\pi} = \\frac{r_e}{\\pi t R^2}.\n\\end{equation}</span>\nAt far proximity, where <span class=\"math-container\">$r_e \\ll R$</span>, <span class=\"math-container\">$t \\approx 1$</span>, and <span class=\"math-container\">$dt/dR \\approx 0$</span>, the metric produced is Newtonian -- curved space, practically flat time.</p>\n<p>Using numerical relativity, I tried pseudorandom hemisphere and pseudorandom tangent plane field lines, but they did not work.\nThe only technique that works is cosine weighted pseudorandom field lines.\nThat is to say, as per the code for this tutorial (<a href=\"https://github.com/sjhalayka/schwarzschild_falloff_field_lines\" rel=\"noreferrer\">https://github.com/sjhalayka/schwarzschild_falloff_field_lines</a>), the cosine weighted pseudorandom field lines produce the correct result, off by a factor of <span class=\"math-container\">$2 / \\pi$</span>.</p>\n<h2>Figure</h2>\n<p><a href=\"https://i.sstatic.net/XWbsh2qc.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/XWbsh2qc.png\" alt=\"axis-aligned bounding box\" /></a></p>\n<p>This figure shows an axis-aligned bounding box and an isotropic emitter, looking from slightly above.\nAn example field line (red) and intersecting line segment (green) are given.\nThe bounding box is filled with these green intersecting line segments.\nIt is the gradient of the density of these line segments that forms the gravitational acceleration.\nNote that the field line is normal to the surface of the emitter (producing Newtonian gravitation).</p>\n<h2>C++ code</h2>\n<pre class=\"lang-cpp prettyprint-override\"><code>double get_intersecting_line_density(\n    const long long unsigned int n,\n    const double emitter_radius,\n    const double receiver_distance,\n    const double receiver_distance_plus,\n    const double receiver_radius)\n{\n    double count = 0;\n    double count_plus = 0;\n\n    generator.seed(static_cast&lt;unsigned&gt;(0));\n\n    for (long long unsigned int i = 0; i &lt; n; i++)\n    {\n        vector_3 location = random_unit_vector();\n\n        location.x *= emitter_radius;\n        location.y *= emitter_radius;\n        location.z *= emitter_radius;\n\n        vector_3 surface_normal = location;\n        surface_normal.normalize();\n\n        vector_3 normal = \n                random_cosine_weighted_hemisphere(\n                surface_normal);\n\n        std::optional&lt;double&gt; i_hit = intersect(\n            location, normal, \n            receiver_distance, receiver_radius);\n\n        if (i_hit)\n            count += *i_hit / (2.0 * receiver_radius);\n    \n        i_hit = intersect(\n            location, normal,\n            receiver_distance_plus, receiver_radius);\n\n        if (i_hit)\n            count_plus += *i_hit / (2.0 * receiver_radius);\n    }\n\n    return count_plus - count;\n}\n</code></pre>\n<p>Thank you for your time!</p>\n","text":"Question\n\n\n\n\nWhat is the name of the numerical technique used to generate the appropriate gravitational acceleration by using a set of gravitational field lines that are not necessarily normal to the surface of the emitter?\n\n\n\n\nI have found that using cosine weighted pseudorandom field lines produces the result predicted by Schwarzschild's general relativity. It's a very simple calculation. Please help me identify its owner.\n\n\n\n\nIntroduction\n\n\n\n\nIn the past, I have written a short tutorial for C++ programmers on isotropic Newtonian gravitation.\nIn that old tutorial, I build an isotropic gravitational field through the use of pseudorandomly generated field lines.\nIn that old tutorial I use a sphere as the receiver.\nThe paper for that old tutorial is at Newtonian gravitation from scratch, for C++ programmers (https://www.techrxiv.org/users/685306/articles/1250456-newtonian-gravitation-from-scratch-for-c-programmers).\n\n\n\n\nIn this question, I point out a match between the numerical gravitation and the gravitational time dilation from Schwarzschild's general relativity (see the book Gravitation, by Misner et al (https://search.worldcat.org/title/585119)).\nHere, I use an axis-aligned bounding box (AABB) as the receiver.\n\n\n\n\nIn this question I use Planck units, where $c = G = \\hbar = k = 1$.\n\n\n\n\nMethod\n\n\n\n\nWhere $r_{e}$ is the emitter's Schwarzschild radius, $r_{r}$ is the receiver AABB radius (e.g. half of the AABB side length), and $1\\mathrm{e}11$ and $0.01$ are arbitrary constants:\n\\begin{equation}\nr_{e} = \\sqrt{\\frac{1\\mathrm{e}11 \\log(2)}{\\pi}},\n\\end{equation}\n\\begin{equation}\nr_{r} = r_{e} \\times 0.01.\n\\end{equation}\nThe event horizon area is:\n\\begin{equation}\nA_{e} = 4 \\pi r_{e}^2.\n\\end{equation}\nThe binary entropy (e.g. field line count, see the papers about the holographic principle) is:\n\\begin{equation}\nn_{e} = \\frac{A_{e}}{4 \\log(2)} = 1\\mathrm{e}11.\n\\end{equation}\nWhere $R$ is the distance from the emitter's centre, the derivative is:\n\\begin{equation}\n\\alpha = \\frac{\\beta(R + \\epsilon) - \\beta(R)}{\\epsilon}.\n\\end{equation}\nHere $\\beta$ is the get intersecting line density function.\nThe gradient strength is:\n\\begin{equation}\ng = \\frac{-\\alpha}{r_{r}^2}.% \\approx \\frac{n_e}{2 R^3}.\n\\end{equation}\nFrom this I get the Newtonian acceleration $a_N$, where $r_e \\ll R$:\n\\begin{equation}\na_N =\\frac{g R \\log 2}{8 M_{e}} =  \\sqrt{\\frac{n_e \\log 2}{4 \\pi R^4}} = \\frac{M_{e}}{R^2}.\n\\end{equation}\nI can also get a general relativistic acceleration $a_S$, where $r_e < R$:\n\\begin{equation}\na_S = \\frac{g R \\log 2}{8 M_{e}},\n\\end{equation}\nAt close proximity, where $r_e \\approx R$, the metric produced is related to the Schwarzschild metric -- curved space, curved time:\n\\begin{equation}\nt = \\sqrt{1 - \\frac{r_e}{R}},\n\\end{equation}\n\\begin{equation}\n\\frac{dt}{dR} = \\frac{r_e}{2 t R^2}.\n\\end{equation}\n\\begin{equation}\na_S \\approx \\frac{dt}{dR} \\frac{2}{\\pi} = \\frac{r_e}{\\pi t R^2}.\n\\end{equation}\nAt far proximity, where $r_e \\ll R$, $t \\approx 1$, and $dt/dR \\approx 0$, the metric produced is Newtonian -- curved space, practically flat time.\n\n\n\n\nUsing numerical relativity, I tried pseudorandom hemisphere and pseudorandom tangent plane field lines, but they did not work.\nThe only technique that works is cosine weighted pseudorandom field lines.\nThat is to say, as per the code for this tutorial (https://github.com/sjhalayka/schwarzschild_falloff_field_lines (https://github.com/sjhalayka/schwarzschild_falloff_field_lines)), the cosine weighted pseudorandom field lines produce the correct result, off by a factor of $2 / \\pi$.\n\n\n\n\nFigure\n\n\n\n\n[image: axis-aligned bounding box; source: https://i.sstatic.net/XWbsh2qc.png] (https://i.sstatic.net/XWbsh2qc.png)\n\n\n\n\nThis figure shows an axis-aligned bounding box and an isotropic emitter, looking from slightly above.\nAn example field line (red) and intersecting line segment (green) are given.\nThe bounding box is filled with these green intersecting line segments.\nIt is the gradient of the density of these line segments that forms the gravitational acceleration.\nNote that the field line is normal to the surface of the emitter (producing Newtonian gravitation).\n\n\n\n\nC++ code\n\n\n\n\ndouble get_intersecting_line_density(\n    const long long unsigned int n,\n    const double emitter_radius,\n    const double receiver_distance,\n    const double receiver_distance_plus,\n    const double receiver_radius)\n{\n    double count = 0;\n    double count_plus = 0;\n\n    generator.seed(static_cast<unsigned>(0));\n\n    for (long long unsigned int i = 0; i < n; i++)\n    {\n        vector_3 location = random_unit_vector();\n\n        location.x *= emitter_radius;\n        location.y *= emitter_radius;\n        location.z *= emitter_radius;\n\n        vector_3 surface_normal = location;\n        surface_normal.normalize();\n\n        vector_3 normal = \n                random_cosine_weighted_hemisphere(\n                surface_normal);\n\n        std::optional<double> i_hit = intersect(\n            location, normal, \n            receiver_distance, receiver_radius);\n\n        if (i_hit)\n            count += *i_hit / (2.0 * receiver_radius);\n    \n        i_hit = intersect(\n            location, normal,\n            receiver_distance_plus, receiver_radius);\n\n        if (i_hit)\n            count_plus += *i_hit / (2.0 * receiver_radius);\n    }\n\n    return count_plus - count;\n}\n\n\n\n\n\nThank you for your time!"},{"context_id":"45329","html":"<p>this is just Monte Carlo integration with cosine-weighted sampling. that’s why it works and the others don’t.</p>\n<p>cosine weighting enforces the correct solid-angle measure, so the flux gradient obeys Gauss’s law. uniform hemisphere or tangent-plane sampling breaks that, which is why the field comes out wrong. the 2/π factor is the usual cosine-hemisphere normalization.</p>\n<p>in physics terms, you’re doing a Monte Carlo solution of Poisson’s equation via flux sampling, and the Schwarzschild behavior drops out naturally when the sampling measure matches the geometry. not a single “owner”  it’s standard Monte Carlo done with the right weighting.</p>\n","text":"this is just Monte Carlo integration with cosine-weighted sampling. that’s why it works and the others don’t.\n\n\n\n\ncosine weighting enforces the correct solid-angle measure, so the flux gradient obeys Gauss’s law. uniform hemisphere or tangent-plane sampling breaks that, which is why the field comes out wrong. the 2/π factor is the usual cosine-hemisphere normalization.\n\n\n\n\nin physics terms, you’re doing a Monte Carlo solution of Poisson’s equation via flux sampling, and the Schwarzschild behavior drops out naturally when the sampling measure matches the geometry. not a single “owner”  it’s standard Monte Carlo done with the right weighting."},{"context_id":"45343","html":"<p>The first answer fails to mention that there is a purely quantum method (labeled C)) -- the cosine weighting is only a classical approximation (labeled B)). The following is the important part of the C++ code (which uses standard multi-threading):</p>\n<pre class=\"lang-cpp prettyprint-override\"><code>void worker_thread(\n    long long unsigned int start_idx,\n    long long unsigned int end_idx,\n    unsigned int thread_seed,\n    const real_type emitter_radius,\n    const real_type receiver_distance,\n    const real_type receiver_distance_plus,\n    const real_type receiver_radius,\n    real_type&amp; result_count,\n    real_type&amp; result_count_plus)\n{\n    // Thread-local random number generator\n    std::mt19937 local_gen(thread_seed);\n    std::uniform_real_distribution&lt;real_type&gt; local_dis(0.0, 1.0);\n\n    real_type local_count = 0;\n    real_type local_count_plus = 0;\n\n    // Update progress every N iterations to reduce atomic overhead\n    const long long unsigned int progress_update_interval = 10000;\n    long long unsigned int local_progress = 0;\n\n    for (long long unsigned int i = start_idx; i &lt; end_idx; i++)\n    {\n        vector_3 location = random_unit_vector(local_gen, local_dis);\n        location.x *= emitter_radius;\n        location.y *= emitter_radius;\n        location.z *= emitter_radius;\n\n        vector_3 surface_normal = location;\n        surface_normal.normalize();\n\n\n        // A) Newtonian gravitation\n        //vector_3 normal =\n        //  surface_normal;\n\n        // B) Schwarzschild gravitation\n        //vector_3 normal = \n        //  random_cosine_weighted_hemisphere(\n        //      surface_normal, local_gen, local_dis);\n\n        // C) Quantum gravitation\n        vector_3 r = random_unit_vector(local_gen, local_dis);\n        r.x *= emitter_radius;\n        r.y *= emitter_radius;\n        r.z *= emitter_radius;\n        vector_3 normal = (location - r).normalize();\n\n\n        local_count += intersect(\n            location, normal,\n            receiver_distance, receiver_radius);\n\n        local_count_plus += intersect(\n            location, normal,\n            receiver_distance_plus, receiver_radius);\n\n        // Update global progress periodically\n        local_progress++;\n        if (local_progress &gt;= progress_update_interval)\n        {\n            global_progress.fetch_add(\n                local_progress, std::memory_order_relaxed);\n    \n            local_progress = 0;\n        }\n    }\n\n    // Add any remaining progress\n    if (local_progress &gt; 0)\n    {\n        global_progress.fetch_add(\n            local_progress, std::memory_order_relaxed);\n    }\n\n    result_count = local_count;\n    result_count_plus = local_count_plus;\n}\n</code></pre>\n","text":"The first answer fails to mention that there is a purely quantum method (labeled C)) -- the cosine weighting is only a classical approximation (labeled B)). The following is the important part of the C++ code (which uses standard multi-threading):\n\n\n\n\nvoid worker_thread(\n    long long unsigned int start_idx,\n    long long unsigned int end_idx,\n    unsigned int thread_seed,\n    const real_type emitter_radius,\n    const real_type receiver_distance,\n    const real_type receiver_distance_plus,\n    const real_type receiver_radius,\n    real_type& result_count,\n    real_type& result_count_plus)\n{\n    // Thread-local random number generator\n    std::mt19937 local_gen(thread_seed);\n    std::uniform_real_distribution<real_type> local_dis(0.0, 1.0);\n\n    real_type local_count = 0;\n    real_type local_count_plus = 0;\n\n    // Update progress every N iterations to reduce atomic overhead\n    const long long unsigned int progress_update_interval = 10000;\n    long long unsigned int local_progress = 0;\n\n    for (long long unsigned int i = start_idx; i < end_idx; i++)\n    {\n        vector_3 location = random_unit_vector(local_gen, local_dis);\n        location.x *= emitter_radius;\n        location.y *= emitter_radius;\n        location.z *= emitter_radius;\n\n        vector_3 surface_normal = location;\n        surface_normal.normalize();\n\n\n        // A) Newtonian gravitation\n        //vector_3 normal =\n        //  surface_normal;\n\n        // B) Schwarzschild gravitation\n        //vector_3 normal = \n        //  random_cosine_weighted_hemisphere(\n        //      surface_normal, local_gen, local_dis);\n\n        // C) Quantum gravitation\n        vector_3 r = random_unit_vector(local_gen, local_dis);\n        r.x *= emitter_radius;\n        r.y *= emitter_radius;\n        r.z *= emitter_radius;\n        vector_3 normal = (location - r).normalize();\n\n\n        local_count += intersect(\n            location, normal,\n            receiver_distance, receiver_radius);\n\n        local_count_plus += intersect(\n            location, normal,\n            receiver_distance_plus, receiver_radius);\n\n        // Update global progress periodically\n        local_progress++;\n        if (local_progress >= progress_update_interval)\n        {\n            global_progress.fetch_add(\n                local_progress, std::memory_order_relaxed);\n    \n            local_progress = 0;\n        }\n    }\n\n    // Add any remaining progress\n    if (local_progress > 0)\n    {\n        global_progress.fetch_add(\n            local_progress, std::memory_order_relaxed);\n    }\n\n    result_count = local_count;\n    result_count_plus = local_count_plus;\n}"}],"domain":"computational_science","external_citations":["https://github.com/sjhalayka/schwarzschild_falloff_field_lines","https://i.sstatic.net/XWbsh2qc.png","https://search.worldcat.org/title/585119","https://www.techrxiv.org/users/685306/articles/1250456-newtonian-gravitation-from-scratch-for-c-programmers"],"ground_truth_type":"metadata_grounded","group_id":"493d8f724951311e95828c562fc3793d7d7131e7cc3efc2e287086abc61195fc","hard_case_family":["no_accepted_answer","multiple_sources","multiple_answer_candidates"],"id":"RHM-9b0dcf9a1e140879b5148763","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:44.584971+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/272744bcc95b58699f7df6e6979b288bb8b00a80ab9c7982dbe170a6d0b63584_1790825325025901700_0.json","raw_sha256":"27a81850a40920682c29ada76a2b55e80340a5c82764a3e9dde8a9c2ba23db4e","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"shawn_halayka","profile_url":"https://scicomp.stackexchange.com/users/48649/shawn-halayka","user_type":"registered"},"created_at":"2025-12-27T16:49:47+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"B772F06F-B869-413B-B8CD-DA295250BCD1","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/B772F06F-B869-413B-B8CD-DA295250BCD1/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Reinderien","profile_url":"https://scicomp.stackexchange.com/users/41212/reinderien","user_type":"registered"},"created_at":"2025-12-27T20:17:48+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"EE985562-6FE8-4FB6-A77E-D42F97D166EC","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/EE985562-6FE8-4FB6-A77E-D42F97D166EC/view-source"}],"source_commit":null,"source_data_file":"native_scicomp_source.jsonl","source_dataset":"RegalFire/Scientific-Native-Scicomp","source_license":"CC BY-SA 4.0","source_record_id":"45322","source_record_sha256":"71bb21ea86802a70e8d66ee51503b38cf0c0c7c2827e28417687c0e2d5875a8d","source_url":"https://scicomp.stackexchange.com/questions/45322/numerical-schwarzschild-gravity","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Numerical Schwarzschild gravity?\nQuestion\n\n\n\n\nWhat is the name of the numerical technique used to generate the appropriate gravitational acceleration by using a set of gravitational field lines that are not necessarily normal to the surface of the emitter?\n\n\n\n\nI have found that using cosine weighted pseudorandom field lines produces the result predicted by Schwarzschild's general relativity. It's a very simple calculation. Please help me identify its owner.\n\n\n\n\nIntroduction\n\n\n\n\nIn the past, I have written a short tutorial for C++ programmers on isotropic Newtonian gravitation.\nIn that old tutorial, I build an isotropic gravitational field through the use of pseudorandomly generated field lines.\nIn that old tutorial I use a sphere as the receiver.\nThe paper for that old tutorial is at Newtonian gravitation from scratch, for C++ programmers (https://www.techrxiv.org/users/685306/articles/1250456-newtonian-gravitation-from-scratch-for-c-programmers).\n\n\n\n\nIn this question, I point out a match between the numerical gravitation and the gravitational time dilation from Schwarzschild's general relativity (see the book Gravitation, by Misner et al (https://search.worldcat.org/title/585119)).\nHere, I use an axis-aligned bounding box (AABB) as the receiver.\n\n\n\n\nIn this question I use Planck units, where $c = G = \\hbar = k = 1$.\n\n\n\n\nMethod\n\n\n\n\nWhere $r_{e}$ is the emitter's Schwarzschild radius, $r_{r}$ is the receiver AABB radius (e.g. half of the AABB side length), and $1\\mathrm{e}11$ and $0.01$ are arbitrary constants:\n\\begin{equation}\nr_{e} = \\sqrt{\\frac{1\\mathrm{e}11 \\log(2)}{\\pi}},\n\\end{equation}\n\\begin{equation}\nr_{r} = r_{e} \\times 0.01.\n\\end{equation}\nThe event horizon area is:\n\\begin{equation}\nA_{e} = 4 \\pi r_{e}^2.\n\\end{equation}\nThe binary entropy (e.g. field line count, see the papers about the holographic principle) is:\n\\begin{equation}\nn_{e} = \\frac{A_{e}}{4 \\log(2)} = 1\\mathrm{e}11.\n\\end{equation}\nWhere $R$ is the distance from the emitter's centre, the derivative is:\n\\begin{equation}\n\\alpha = \\frac{\\beta(R + \\epsilon) - \\beta(R)}{\\epsilon}.\n\\end{equation}\nHere $\\beta$ is the get intersecting line density function.\nThe gradient strength is:\n\\begin{equation}\ng = \\frac{-\\alpha}{r_{r}^2}.% \\approx \\frac{n_e}{2 R^3}.\n\\end{equation}\nFrom this I get the Newtonian acceleration $a_N$, where $r_e \\ll R$:\n\\begin{equation}\na_N =\\frac{g R \\log 2}{8 M_{e}} =  \\sqrt{\\frac{n_e \\log 2}{4 \\pi R^4}} = \\frac{M_{e}}{R^2}.\n\\end{equation}\nI can also get a general relativistic acceleration $a_S$, where $r_e < R$:\n\\begin{equation}\na_S = \\frac{g R \\log 2}{8 M_{e}},\n\\end{equation}\nAt close proximity, where $r_e \\approx R$, the metric produced is related to the Schwarzschild metric -- curved space, curved time:\n\\begin{equation}\nt = \\sqrt{1 - \\frac{r_e}{R}},\n\\end{equation}\n\\begin{equation}\n\\frac{dt}{dR} = \\frac{r_e}{2 t R^2}.\n\\end{equation}\n\\begin{equation}\na_S \\approx \\frac{dt}{dR} \\frac{2}{\\pi} = \\frac{r_e}{\\pi t R^2}.\n\\end{equation}\nAt far proximity, where $r_e \\ll R$, $t \\approx 1$, and $dt/dR \\approx 0$, the metric produced is Newtonian -- curved space, practically flat time.\n\n\n\n\nUsing numerical relativity, I tried pseudorandom hemisphere and pseudorandom tangent plane field lines, but they did not work.\nThe only technique that works is cosine weighted pseudorandom field lines.\nThat is to say, as per the code for this tutorial (https://github.com/sjhalayka/schwarzschild_falloff_field_lines (https://github.com/sjhalayka/schwarzschild_falloff_field_lines)), the cosine weighted pseudorandom field lines produce the correct result, off by a factor of $2 / \\pi$.\n\n\n\n\nFigure\n\n\n\n\n[image: axis-aligned bounding box; source: https://i.sstatic.net/XWbsh2qc.png] (https://i.sstatic.net/XWbsh2qc.png)\n\n\n\n\nThis figure shows an axis-aligned bounding box and an isotropic emitter, looking from slightly above.\nAn example field line (red) and intersecting line segment (green) are given.\nThe bounding box is filled with these green intersecting line segments.\nIt is the gradient of the density of these line segments that forms the gravitational acceleration.\nNote that the field line is normal to the surface of the emitter (producing Newtonian gravitation).\n\n\n\n\nC++ code\n\n\n\n\ndouble get_intersecting_line_density(\n    const long long unsigned int n,\n    const double emitter_radius,\n    const double receiver_distance,\n    const double receiver_distance_plus,\n    const double receiver_radius)\n{\n    double count = 0;\n    double count_plus = 0;\n\n    generator.seed(static_cast<unsigned>(0));\n\n    for (long long unsigned int i = 0; i < n; i++)\n    {\n        vector_3 location = random_unit_vector();\n\n        location.x *= emitter_radius;\n        location.y *= emitter_radius;\n        location.z *= emitter_radius;\n\n        vector_3 surface_normal = location;\n        surface_normal.normalize();\n\n        vector_3 normal = \n                random_cosine_weighted_hemisphere(\n                surface_normal);\n\n        std::optional<double> i_hit = intersect(\n            location, normal, \n            receiver_distance, receiver_radius);\n\n        if (i_hit)\n            count += *i_hit / (2.0 * receiver_radius);\n    \n        i_hit = intersect(\n            location, normal,\n            receiver_distance_plus, receiver_radius);\n\n        if (i_hit)\n            count_plus += *i_hit / (2.0 * receiver_radius);\n    }\n\n    return count_plus - count;\n}\n\n\n\n\n\nThank you for your time!","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45329,"score":5},{"answer_id":45343,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<blockquote>\n<p>monothonic</p>\n</blockquote>\n<p>I'm sure you meant monotonic.</p>\n<blockquote>\n<p>I am looking for a fast way to solve the problem</p>\n</blockquote>\n<p>Are you actually? I think if you were, you would use something off-the-shelf. &quot;Simple iterative&quot; and &quot;fast&quot; don't particularly jive, here. Let's take a random stab at remodelling your problem to meet <em>some</em> of your criteria:</p>\n<ul>\n<li>Linear, not quadratic</li>\n<li>No manual iteration per se</li>\n<li>Enforce inter-reference monotonicity through simple linear constraints</li>\n<li>Model cost as being absolute error plus absolute second-order differential, the latter receiving your <span class=\"math-container\">$\\lambda$</span> weight</li>\n</ul>\n<p>A traditional LP would express the problem thus. Define the following decision vectors:</p>\n<ul>\n<li><span class=\"math-container\">$z \\in \\mathbb R^n$</span>, the fit points</li>\n<li><span class=\"math-container\">$z_p \\in \\mathbb R^n$</span>, <span class=\"math-container\">$z_p \\ge 0$</span>, positive-clipped fit error</li>\n<li><span class=\"math-container\">$z_n \\in \\mathbb R^n$</span>, <span class=\"math-container\">$z_n \\ge 0$</span>, negative-clipped fit error</li>\n<li><span class=\"math-container\">$d_p \\in \\mathbb R^{n-2}$</span>, <span class=\"math-container\">$d_p \\ge 0$</span>, positive-clipped second-order differentials</li>\n<li><span class=\"math-container\">$d_n \\in \\mathbb R^{n-2}$</span>, <span class=\"math-container\">$d_n \\ge 0$</span>, negative-clipped second-order differentials</li>\n</ul>\n<p>Find</p>\n<p><span class=\"math-container\">$$ \\min_z z_p + z_n + \\lambda ( d_p + d_n ) $$</span></p>\n<p>given the following constraints:</p>\n<p><span class=\"math-container\">$$ z_p \\ge z - y $$</span>\n<span class=\"math-container\">$$ z_n \\ge y - z $$</span>\n<span class=\"math-container\">$$ d_p \\ge \\frac {\\partial^2 z} {\\partial i^2} $$</span>\n<span class=\"math-container\">$$ d_n \\ge -\\frac {\\partial^2 z} {\\partial i^2} $$</span>\n<span class=\"math-container\">$ (z_{i+1} - z_i) \\text{sgn}( y_1 - y_0 ) \\ge 0 $</span> for every index <span class=\"math-container\">$i$</span> between every anchor point <span class=\"math-container\">$y_0$</span>, <span class=\"math-container\">$y_1$</span></p>\n<p><span class=\"math-container\">$ \\frac {\\partial^2 z} {\\partial i^2} $</span> discretised by:\n<span class=\"math-container\">$$ \\begin{bmatrix}\n1 &amp; -2 &amp; 1 \\\\\n  &amp; 1  &amp; -2 &amp; 1 \\\\\n  &amp;    &amp;    &amp;   &amp; \\ddots\n\\end{bmatrix} z $$</span></p>\n<p>The problem is very sparse, and I trust that essentially no LP solvers would have any difficulty with it. HiGHS completes it quickly.</p>\n<pre class=\"lang-py prettyprint-override\"><code>import matplotlib.pyplot as plt\nimport numpy as np\nimport scipy.sparse as sp\nfrom scipy.optimize import milp, LinearConstraint\n\n\ndef sample_data(rand: np.random.Generator, n: int = 1501) -&gt; tuple[\n    np.ndarray, np.ndarray, np.ndarray,\n]:\n    x = np.linspace(start=0, stop=10, num=n)\n    y = rand.uniform(low=-0.1, high=0.1, size=x.size).cumsum()\n    iref = np.array((2, 6, 9))*(n//10)\n    return x, y, iref\n\n\ndef cost(n: int, nd: int, smoothing: float) -&gt; np.ndarray:\n    return np.concatenate((\n        np.zeros(n),   # z does not incur a cost directly\n        np.ones(2*n),  # zerr cost\n        np.full(2*nd, fill_value=smoothing),\n    ))\n\n\ndef bounds(iref: np.ndarray, n: int, nd: int, y: np.ndarray) -&gt; np.ndarray:\n    lbound, ubound = bounds = np.zeros((2, 3*n + 2*nd))\n    lbound[:n] = -np.inf\n    ubound[:] = np.inf\n\n    iprev = iref[:-1]\n    inext = iref[1:]\n    pprev = y[iprev]\n    pnext = y[inext]\n    pfloor = np.minimum(pprev, pnext)\n    pceil = np.maximum(pprev, pnext)\n\n    for i0, i1, plo, phi in zip(iprev, inext, pfloor, pceil):\n        lbound[i0] = y[i0]\n        ubound[i0] = y[i0]\n        inner = slice(i0 + 1, i1)\n        lbound[inner] = plo\n        ubound[inner] = phi\n    lbound[iref[-1]] = y[iref[-1]]\n    ubound[iref[-1]] = y[iref[-1]]\n\n    return bounds\n\n\ndef zerror_constraints(n: int, nd: int, y: np.ndarray) -&gt; tuple[LinearConstraint, ...]:\n    # zep &gt;= z - y:  z - zep &lt;= y\n    # zen &gt;= y - z:  z + zen &gt;= y\n    eye = sp.eye_array(n)\n    zero = sp.csc_array((n, n))\n    zerond = sp.csc_array((n, 2*nd))\n    pos = LinearConstraint(\n        A=sp.hstack((eye, -eye, zero, zerond), format='csc'), ub=y)\n    neg = LinearConstraint(\n        A=sp.hstack((eye, zero, eye, zerond), format='csc'), lb=y)\n    return pos, neg\n\n\ndef d2_constraints(n: int, nd: int) -&gt; tuple[LinearConstraint, ...]:\n    # d2z/dt2 = z[i+2] - 2z[i+1] + z[i]\n    # d2p &gt;=  d2z/dt2: -z[i] + 2z[i+1] - z[i+2] +0 +0 + d2p &gt;= 0\n    # d2n &gt;= -d2z/dt2:  z[i] - 2z[i+1] + z[i+2] +0 +0 +   0 + d2n &gt;= 0\n    data = np.broadcast_to(\n        np.array(([1], [-2], [1]), dtype=np.float32),  # don't bother with /dt**2\n        shape=(3, n))\n    offsets = np.array((0, 1, 2), dtype=np.int32)\n    kernel = sp.dia_array((data, offsets), shape=(nd, n))\n    err_zero = sp.csc_array((nd, 2*n))\n    eye = sp.eye_array(nd)\n    zero = sp.csc_array((nd, nd))\n    pos = LinearConstraint(\n        A=sp.hstack((-kernel, err_zero, eye, zero), format='csc'), lb=0)\n    neg = LinearConstraint(\n        A=sp.hstack(( kernel, err_zero, zero, eye), format='csc'), lb=0)\n    return pos, neg\n\n\ndef monotone_constraints(n: int, nd: int, y: np.ndarray, iref: np.ndarray) -&gt; tuple[LinearConstraint, ...]:\n    iprev = iref[:-1]\n    inext = iref[1:]\n    yprev = y[iprev]\n    ynext = y[inext]\n    blocks = []\n\n    for i0, i1, y0, y1 in zip(iprev, inext, yprev, ynext):\n        sign = np.sign(y1 - y0)\n        if sign == 0:\n            continue  # the entire segment will already have lower and upper bounds equal to each other\n        block = sp.eye_array(\n            m=i1 - i0, n=3*n + 2*nd, k=i0 + 1,\n        ) - sp.eye_array(\n            m=i1 - i0, n=3*n + 2*nd, k=i0)\n        blocks.append(sign*block)\n    constraint = LinearConstraint(A=sp.vstack(blocks, format='csc'), lb=0)\n    return constraint,\n\n\ndef solve(y: np.ndarray, iref: np.ndarray, smoothing: float = 1.) -&gt; tuple[\n    np.ndarray, tuple[LinearConstraint, ...],\n]:\n    '''\n    Variables:\n        z, continuous unbounded (outside of ref points)\n        zep, continuous, &gt;= 0, &gt;= z-y\n        zen, continuous, &gt;= 0, &gt;= y-z\n        d2p, n-2, continuous, &gt;= 0, &gt;= d2z/dt2\n        d2n, n-2, continuous, &gt;= 0, &gt;= -d2z/dt2\n    '''\n    n = y.size\n    nd = n - 2\n    constraints = (\n        zerror_constraints(n, nd, y) + d2_constraints(n, nd) + monotone_constraints(n, nd, y, iref)\n    )\n\n    result = milp(\n        c=cost(n, nd, smoothing), integrality=0, bounds=bounds(iref, n, nd, y),\n        constraints=constraints,\n    )\n    if not result.success:\n        raise result.message\n    z, zep, zen, d2p, d2n = np.split(result.x, (n, 2*n, 3*n, 3*n+nd))\n    return z, constraints\n\n\ndef demo() -&gt; None:\n    rand = np.random.default_rng(seed=0)\n    x, y, iref = sample_data(rand, n=801)\n\n    fig, ax = plt.subplots()\n    ax.plot(x, y, label='orig')\n    ax.scatter(x[iref], y[iref], color='red', label='ref point')\n\n    for smoothing in (0.5, 3):\n        z, constraints = solve(y, iref, smoothing)\n        ax.plot(x, z, label=f'smooth={smoothing}')\n    ax.legend()\n\n    sparsity = sp.vstack([c.A for c in constraints]).sign().toarray()\n    fig, ax = plt.subplots()\n    ax.set_title(f'Constraint sparsity, n={y.size}')\n    ax.imshow(sparsity)\n\n    plt.show()\n\n\nif __name__ == '__main__':\n    demo()\n</code></pre>\n<p>Here we see that the solution does exactly what we tell it to:</p>\n<p><a href=\"https://i.sstatic.net/oTyX0oWA.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/oTyX0oWA.png\" alt=\"example solution\" /></a></p>\n<p>Outside of the reference points, monotonicity is not enforced so the smoothed curve follows the input curve. Within the reference points, monotonicity is preserved, and the solver does its best to balance smoothing and fitting; a finer-scale depiction of this behaviour:</p>\n<p><a href=\"https://i.sstatic.net/cW1t1avg.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/cW1t1avg.png\" alt=\"smoothing\" /></a></p>\n<p>The sparsity pattern for the problem looks like this (size reduced for visibility):</p>\n<p><a href=\"https://i.sstatic.net/UmVF5qyE.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/UmVF5qyE.png\" alt=\"sparsity\" /></a></p>\n<p>Though the performance will vary based on hardware and dataset content and size, for n=1501 I see execution times of ~80 ms.</p>\n","answer_id":45335,"answer_text":"monothonic\n\n\n\n\n\n\n\nI'm sure you meant monotonic.\n\n\n\n\n\n\n\nI am looking for a fast way to solve the problem\n\n\n\n\n\n\n\nAre you actually? I think if you were, you would use something off-the-shelf. \"Simple iterative\" and \"fast\" don't particularly jive, here. Let's take a random stab at remodelling your problem to meet some of your criteria:\n\n\n\n\n\nLinear, not quadratic\n\n\n\n\nNo manual iteration per se\n\n\n\n\nEnforce inter-reference monotonicity through simple linear constraints\n\n\n\n\nModel cost as being absolute error plus absolute second-order differential, the latter receiving your $\\lambda$ weight\n\n\n\n\n\nA traditional LP would express the problem thus. Define the following decision vectors:\n\n\n\n\n\n$z \\in \\mathbb R^n$, the fit points\n\n\n\n\n$z_p \\in \\mathbb R^n$, $z_p \\ge 0$, positive-clipped fit error\n\n\n\n\n$z_n \\in \\mathbb R^n$, $z_n \\ge 0$, negative-clipped fit error\n\n\n\n\n$d_p \\in \\mathbb R^{n-2}$, $d_p \\ge 0$, positive-clipped second-order differentials\n\n\n\n\n$d_n \\in \\mathbb R^{n-2}$, $d_n \\ge 0$, negative-clipped second-order differentials\n\n\n\n\n\nFind\n\n\n\n\n$$ \\min_z z_p + z_n + \\lambda ( d_p + d_n ) $$\n\n\n\n\ngiven the following constraints:\n\n\n\n\n$$ z_p \\ge z - y $$\n$$ z_n \\ge y - z $$\n$$ d_p \\ge \\frac {\\partial^2 z} {\\partial i^2} $$\n$$ d_n \\ge -\\frac {\\partial^2 z} {\\partial i^2} $$\n$ (z_{i+1} - z_i) \\text{sgn}( y_1 - y_0 ) \\ge 0 $ for every index $i$ between every anchor point $y_0$, $y_1$\n\n\n\n\n$ \\frac {\\partial^2 z} {\\partial i^2} $ discretised by:\n$$ \\begin{bmatrix}\n1 & -2 & 1 \\\\\n  & 1  & -2 & 1 \\\\\n  &    &    &   & \\ddots\n\\end{bmatrix} z $$\n\n\n\n\nThe problem is very sparse, and I trust that essentially no LP solvers would have any difficulty with it. HiGHS completes it quickly.\n\n\n\n\nimport matplotlib.pyplot as plt\nimport numpy as np\nimport scipy.sparse as sp\nfrom scipy.optimize import milp, LinearConstraint\n\n\ndef sample_data(rand: np.random.Generator, n: int = 1501) -> tuple[\n    np.ndarray, np.ndarray, np.ndarray,\n]:\n    x = np.linspace(start=0, stop=10, num=n)\n    y = rand.uniform(low=-0.1, high=0.1, size=x.size).cumsum()\n    iref = np.array((2, 6, 9))*(n//10)\n    return x, y, iref\n\n\ndef cost(n: int, nd: int, smoothing: float) -> np.ndarray:\n    return np.concatenate((\n        np.zeros(n),   # z does not incur a cost directly\n        np.ones(2*n),  # zerr cost\n        np.full(2*nd, fill_value=smoothing),\n    ))\n\n\ndef bounds(iref: np.ndarray, n: int, nd: int, y: np.ndarray) -> np.ndarray:\n    lbound, ubound = bounds = np.zeros((2, 3*n + 2*nd))\n    lbound[:n] = -np.inf\n    ubound[:] = np.inf\n\n    iprev = iref[:-1]\n    inext = iref[1:]\n    pprev = y[iprev]\n    pnext = y[inext]\n    pfloor = np.minimum(pprev, pnext)\n    pceil = np.maximum(pprev, pnext)\n\n    for i0, i1, plo, phi in zip(iprev, inext, pfloor, pceil):\n        lbound[i0] = y[i0]\n        ubound[i0] = y[i0]\n        inner = slice(i0 + 1, i1)\n        lbound[inner] = plo\n        ubound[inner] = phi\n    lbound[iref[-1]] = y[iref[-1]]\n    ubound[iref[-1]] = y[iref[-1]]\n\n    return bounds\n\n\ndef zerror_constraints(n: int, nd: int, y: np.ndarray) -> tuple[LinearConstraint, ...]:\n    # zep >= z - y:  z - zep <= y\n    # zen >= y - z:  z + zen >= y\n    eye = sp.eye_array(n)\n    zero = sp.csc_array((n, n))\n    zerond = sp.csc_array((n, 2*nd))\n    pos = LinearConstraint(\n        A=sp.hstack((eye, -eye, zero, zerond), format='csc'), ub=y)\n    neg = LinearConstraint(\n        A=sp.hstack((eye, zero, eye, zerond), format='csc'), lb=y)\n    return pos, neg\n\n\ndef d2_constraints(n: int, nd: int) -> tuple[LinearConstraint, ...]:\n    # d2z/dt2 = z[i+2] - 2z[i+1] + z[i]\n    # d2p >=  d2z/dt2: -z[i] + 2z[i+1] - z[i+2] +0 +0 + d2p >= 0\n    # d2n >= -d2z/dt2:  z[i] - 2z[i+1] + z[i+2] +0 +0 +   0 + d2n >= 0\n    data = np.broadcast_to(\n        np.array(([1], [-2], [1]), dtype=np.float32),  # don't bother with /dt**2\n        shape=(3, n))\n    offsets = np.array((0, 1, 2), dtype=np.int32)\n    kernel = sp.dia_array((data, offsets), shape=(nd, n))\n    err_zero = sp.csc_array((nd, 2*n))\n    eye = sp.eye_array(nd)\n    zero = sp.csc_array((nd, nd))\n    pos = LinearConstraint(\n        A=sp.hstack((-kernel, err_zero, eye, zero), format='csc'), lb=0)\n    neg = LinearConstraint(\n        A=sp.hstack(( kernel, err_zero, zero, eye), format='csc'), lb=0)\n    return pos, neg\n\n\ndef monotone_constraints(n: int, nd: int, y: np.ndarray, iref: np.ndarray) -> tuple[LinearConstraint, ...]:\n    iprev = iref[:-1]\n    inext = iref[1:]\n    yprev = y[iprev]\n    ynext = y[inext]\n    blocks = []\n\n    for i0, i1, y0, y1 in zip(iprev, inext, yprev, ynext):\n        sign = np.sign(y1 - y0)\n        if sign == 0:\n            continue  # the entire segment will already have lower and upper bounds equal to each other\n        block = sp.eye_array(\n            m=i1 - i0, n=3*n + 2*nd, k=i0 + 1,\n        ) - sp.eye_array(\n            m=i1 - i0, n=3*n + 2*nd, k=i0)\n        blocks.append(sign*block)\n    constraint = LinearConstraint(A=sp.vstack(blocks, format='csc'), lb=0)\n    return constraint,\n\n\ndef solve(y: np.ndarray, iref: np.ndarray, smoothing: float = 1.) -> tuple[\n    np.ndarray, tuple[LinearConstraint, ...],\n]:\n    '''\n    Variables:\n        z, continuous unbounded (outside of ref points)\n        zep, continuous, >= 0, >= z-y\n        zen, continuous, >= 0, >= y-z\n        d2p, n-2, continuous, >= 0, >= d2z/dt2\n        d2n, n-2, continuous, >= 0, >= -d2z/dt2\n    '''\n    n = y.size\n    nd = n - 2\n    constraints = (\n        zerror_constraints(n, nd, y) + d2_constraints(n, nd) + monotone_constraints(n, nd, y, iref)\n    )\n\n    result = milp(\n        c=cost(n, nd, smoothing), integrality=0, bounds=bounds(iref, n, nd, y),\n        constraints=constraints,\n    )\n    if not result.success:\n        raise result.message\n    z, zep, zen, d2p, d2n = np.split(result.x, (n, 2*n, 3*n, 3*n+nd))\n    return z, constraints\n\n\ndef demo() -> None:\n    rand = np.random.default_rng(seed=0)\n    x, y, iref = sample_data(rand, n=801)\n\n    fig, ax = plt.subplots()\n    ax.plot(x, y, label='orig')\n    ax.scatter(x[iref], y[iref], color='red', label='ref point')\n\n    for smoothing in (0.5, 3):\n        z, constraints = solve(y, iref, smoothing)\n        ax.plot(x, z, label=f'smooth={smoothing}')\n    ax.legend()\n\n    sparsity = sp.vstack([c.A for c in constraints]).sign().toarray()\n    fig, ax = plt.subplots()\n    ax.set_title(f'Constraint sparsity, n={y.size}')\n    ax.imshow(sparsity)\n\n    plt.show()\n\n\nif __name__ == '__main__':\n    demo()\n\n\n\n\n\nHere we see that the solution does exactly what we tell it to:\n\n\n\n\n[image: example solution; source: https://i.sstatic.net/oTyX0oWA.png] (https://i.sstatic.net/oTyX0oWA.png)\n\n\n\n\nOutside of the reference points, monotonicity is not enforced so the smoothed curve follows the input curve. Within the reference points, monotonicity is preserved, and the solver does its best to balance smoothing and fitting; a finer-scale depiction of this behaviour:\n\n\n\n\n[image: smoothing; source: https://i.sstatic.net/cW1t1avg.png] (https://i.sstatic.net/cW1t1avg.png)\n\n\n\n\nThe sparsity pattern for the problem looks like this (size reduced for visibility):\n\n\n\n\n[image: sparsity; source: https://i.sstatic.net/UmVF5qyE.png] (https://i.sstatic.net/UmVF5qyE.png)\n\n\n\n\nThough the performance will vary based on hardware and dataset content and size, for n=1501 I see execution times of ~80 ms.","answer_url":"https://scicomp.stackexchange.com/a/45335","author":"Reinderien","author_url":"https://scicomp.stackexchange.com/users/41212/reinderien","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-01-10T07:56:42+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:47.033952+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/cb6e5f564c84a92c4e121c0637c99292018f8935652e423630f2001099a2410f_1790825327386675300_0.json","raw_sha256":"1a957289f56621bebd21cb45dd99baaedb2c3bc11cb28d700558e4bbcaa19695","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/45545;45541;45538;45533;45532;45530;45523;45513;45510;45507;45499;45493;45488;45487;45479;45474;45472;45463;45461;45447;45444;45436;45428;45425;45424;45423;45422;45416;45414;45410;45404;45401;45396;45391;45389;45387;45380;45377;45376;45375;45369;45366;45365;45363;45362;45359;45350;45347;45344;45336;45334;45331;45326;45322;45316;45313;45311;45309;45305;45302;45300;45291;45289;45285;45276;45269;45263;45262;45261;45253;45247;45246;45238;45236;45230;45229;45208;45201;45200;45185;45183;45171;45167;45165;45158;45154;45146;45141;45139;45134;45129;45127;45122;45114;45112;45108;45105;45100;45098;45096/answers?filter=withbody&order=asc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":45334,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Reinderien","profile_url":"https://scicomp.stackexchange.com/users/41212/reinderien","user_type":"registered"},"created_at":"2026-01-10T07:56:42+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"49224026-A98C-4DFC-B187-28324764F758","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/49224026-A98C-4DFC-B187-28324764F758/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Reinderien","profile_url":"https://scicomp.stackexchange.com/users/41212/reinderien","user_type":"registered"},"created_at":"2026-01-10T15:16:37+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"0462867C-327F-469E-957B-1FE451F4CE5C","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/0462867C-327F-469E-957B-1FE451F4CE5C/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Reinderien","profile_url":"https://scicomp.stackexchange.com/users/41212/reinderien","user_type":"registered"},"created_at":"2026-01-10T20:00:35+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"302EF20B-4729-4185-A059-5377ED4B7555","revision_number":3,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/302EF20B-4729-4185-A059-5377ED4B7555/view-source"}],"score":3,"updated_at":"2026-01-10T20:00:35+00:00"},{"answer_html":"<p>I managed to create a prototype solver based on ADMM in MATLAB:</p>\n<pre class=\"lang-matlab prettyprint-override\"><code>function [ vX, isConv ] = SplineQPSmooth( vY, mD, paramLambda, vI, mA, sParams )\n\narguments(Input)\n    vY (:, 1) {mustBeNumeric, mustBeFinite, mustBeReal}\n    mD (:, :) {mustBeNumeric, mustBeFinite, mustBeReal}\n    paramLambda (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBeNonnegative}\n    vI (:, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBeInteger}\n    mA (:, :) {mustBeNumeric, mustBeFinite, mustBeReal}\n    sParams.paramRho (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 1.0\n    sParams.numIter (1, 1) {mustBeNumeric, mustBeFinite, mustBeInteger, mustBePositive} = 5000\n    sParams.epsAbs (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 1e-5\n    sParams.epsRel (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 1e-5\n    sParams.convInterval (1, 1) {mustBeNumeric, mustBeFinite, mustBeInteger, mustBePositive} = 25\n    sParams.paramTau (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 10\nend\n\narguments(Output)\n    vX (:, 1) {mustBeNumeric, mustBeFinite, mustBeReal}\n    isConv (1, 1) {mustBeA(isConv, 'logical')}\nend\n\nnumSamples = length(vY);\nnumEq      = length(vI);\nnumInEq    = size(mA, 1);\n\n% Quadratic Terms\nmQ = sparse(eye(numSamples)) + paramLambda * (mD' * mD);\nvQ = -vY;\n\n% Equality Constraints\nmE = sparse(1:numEq, vI, 1, numEq, numSamples);\nvD = vY(vI);\n\nparamRho     = sParams.paramRho;\nparamRhoInv  = inv(paramRho);\nnumIter      = sParams.numIter;\nepsAbs       = sParams.epsAbs;\nepsRel       = sParams.epsRel;\nconvInterval = sParams.convInterval;\nparamTau     = sParams.paramTau;\n\n% ADMM Variables\nvX  = vY;                %&lt;! Optimization variable\nvS  = zeros(numInEq, 1); %&lt;! Slack variable for inequality\nvS1 = zeros(numInEq, 1); %&lt;! Preious iteration buffer\nvMu = zeros(numInEq, 1); %&lt;! Dual variable for inequality\nvNu = zeros(numEq, 1);   %&lt;! Dual variabe for equality\n\n% Factorize the KKT System\n% (Q + rho * A' * A + rho * E' * E) * z = r\nmK = mQ + paramRho * (mA.' * mA) + paramRho * (mE.' * mE);\nsK = decomposition(mK, 'chol', 'CheckCondition', false);\n\nisConv     = false;\nupdatedRho = false;\n\nfor ii = 1:numIter\n    vS1(:) = vS; %&lt;! Previous iteration\n\n    % Solve the Linear System\n    vR = -vQ - mA.' * (paramRho * vS + vMu) + mE.' * (paramRho * vD - vNu); %&lt;! Right hand vector\n    vX = sK \\ vR;\n\n    % Proximal / Projection Step\n    % s = -A * z with s &gt;= 0\n    vS = max(0, -(mA * vX + paramRhoInv * vMu));\n\n    % Update Dual Variables\n    vMu = vMu + paramRho * (mA * vX + vS);\n    vNu = vNu + paramRho * (mE * vX - vD);\n\n    % Check Convergence\n    if mod(ii, convInterval) == 0\n        primRes = norm(mA * vX + vS, 'inf');\n        dualRes = norm(paramRho * mA' * (vS - vS1), 'inf');\n        if ((primRes &lt; epsAbs) &amp;&amp; (dualRes &lt; epsAbs))\n            isConv = true;\n            break;\n        end\n\n        % Adpat `paramRho`\n        resRatio = primRes / dualRes;\n        % fprintf('Primal Residual: %0.7f, Dual Residual: %0.7f\\n', primRes, dualRes);\n        % fprintf('Residual Ratio: %0.2f, ρ = %0.3f\\n', resRatio, paramRho);\n        if (resRatio &gt; paramTau) || (inv(resRatio) &gt; paramTau)\n            updatedRho = true;\n        else\n            updatedRho = false;\n        end\n        if updatedRho\n            paramRho = paramRho * sqrt(resRatio);\n            paramRho = clip(paramRho, 1e-5, 1e5);\n            paramRhoInv  = inv(paramRho);\n            mK = mQ + paramRho * (mA.' * mA) + paramRho * (mE.' * mE);\n            sK = decomposition(mK, 'chol', 'CheckCondition', false);\n        end\n    end\n\nend\n\nend\n</code></pre>\n<p>I has convergence check and adaptation of the ADMM's step size parameter <span class=\"math-container\">$\\rho$</span>.<br />\nI will add mathematical formulation and a memory optimized version using Julia.</p>\n<p>On MATLAB with this naive code I could beat <code>quadprog()</code> by 30% with the same output:</p>\n<p><a href=\"https://i.sstatic.net/VC8uzUSt.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/VC8uzUSt.png\" alt=\"enter image description here\" /></a></p>\n\n","answer_id":45337,"answer_text":"I managed to create a prototype solver based on ADMM in MATLAB:\n\n\n\n\nfunction [ vX, isConv ] = SplineQPSmooth( vY, mD, paramLambda, vI, mA, sParams )\n\narguments(Input)\n    vY (:, 1) {mustBeNumeric, mustBeFinite, mustBeReal}\n    mD (:, :) {mustBeNumeric, mustBeFinite, mustBeReal}\n    paramLambda (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBeNonnegative}\n    vI (:, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBeInteger}\n    mA (:, :) {mustBeNumeric, mustBeFinite, mustBeReal}\n    sParams.paramRho (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 1.0\n    sParams.numIter (1, 1) {mustBeNumeric, mustBeFinite, mustBeInteger, mustBePositive} = 5000\n    sParams.epsAbs (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 1e-5\n    sParams.epsRel (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 1e-5\n    sParams.convInterval (1, 1) {mustBeNumeric, mustBeFinite, mustBeInteger, mustBePositive} = 25\n    sParams.paramTau (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 10\nend\n\narguments(Output)\n    vX (:, 1) {mustBeNumeric, mustBeFinite, mustBeReal}\n    isConv (1, 1) {mustBeA(isConv, 'logical')}\nend\n\nnumSamples = length(vY);\nnumEq      = length(vI);\nnumInEq    = size(mA, 1);\n\n% Quadratic Terms\nmQ = sparse(eye(numSamples)) + paramLambda * (mD' * mD);\nvQ = -vY;\n\n% Equality Constraints\nmE = sparse(1:numEq, vI, 1, numEq, numSamples);\nvD = vY(vI);\n\nparamRho     = sParams.paramRho;\nparamRhoInv  = inv(paramRho);\nnumIter      = sParams.numIter;\nepsAbs       = sParams.epsAbs;\nepsRel       = sParams.epsRel;\nconvInterval = sParams.convInterval;\nparamTau     = sParams.paramTau;\n\n% ADMM Variables\nvX  = vY;                %<! Optimization variable\nvS  = zeros(numInEq, 1); %<! Slack variable for inequality\nvS1 = zeros(numInEq, 1); %<! Preious iteration buffer\nvMu = zeros(numInEq, 1); %<! Dual variable for inequality\nvNu = zeros(numEq, 1);   %<! Dual variabe for equality\n\n% Factorize the KKT System\n% (Q + rho * A' * A + rho * E' * E) * z = r\nmK = mQ + paramRho * (mA.' * mA) + paramRho * (mE.' * mE);\nsK = decomposition(mK, 'chol', 'CheckCondition', false);\n\nisConv     = false;\nupdatedRho = false;\n\nfor ii = 1:numIter\n    vS1(:) = vS; %<! Previous iteration\n\n    % Solve the Linear System\n    vR = -vQ - mA.' * (paramRho * vS + vMu) + mE.' * (paramRho * vD - vNu); %<! Right hand vector\n    vX = sK \\ vR;\n\n    % Proximal / Projection Step\n    % s = -A * z with s >= 0\n    vS = max(0, -(mA * vX + paramRhoInv * vMu));\n\n    % Update Dual Variables\n    vMu = vMu + paramRho * (mA * vX + vS);\n    vNu = vNu + paramRho * (mE * vX - vD);\n\n    % Check Convergence\n    if mod(ii, convInterval) == 0\n        primRes = norm(mA * vX + vS, 'inf');\n        dualRes = norm(paramRho * mA' * (vS - vS1), 'inf');\n        if ((primRes < epsAbs) && (dualRes < epsAbs))\n            isConv = true;\n            break;\n        end\n\n        % Adpat `paramRho`\n        resRatio = primRes / dualRes;\n        % fprintf('Primal Residual: %0.7f, Dual Residual: %0.7f\\n', primRes, dualRes);\n        % fprintf('Residual Ratio: %0.2f, ρ = %0.3f\\n', resRatio, paramRho);\n        if (resRatio > paramTau) || (inv(resRatio) > paramTau)\n            updatedRho = true;\n        else\n            updatedRho = false;\n        end\n        if updatedRho\n            paramRho = paramRho * sqrt(resRatio);\n            paramRho = clip(paramRho, 1e-5, 1e5);\n            paramRhoInv  = inv(paramRho);\n            mK = mQ + paramRho * (mA.' * mA) + paramRho * (mE.' * mE);\n            sK = decomposition(mK, 'chol', 'CheckCondition', false);\n        end\n    end\n\nend\n\nend\n\n\n\n\n\nI has convergence check and adaptation of the ADMM's step size parameter $\\rho$.\n\nI will add mathematical formulation and a memory optimized version using Julia.\n\n\n\n\nOn MATLAB with this naive code I could beat quadprog() by 30% with the same output:\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/VC8uzUSt.png] (https://i.sstatic.net/VC8uzUSt.png)","answer_url":"https://scicomp.stackexchange.com/a/45337","author":"Royi","author_url":"https://scicomp.stackexchange.com/users/7951/royi","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-01-10T16:53:59+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:47.033952+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/cb6e5f564c84a92c4e121c0637c99292018f8935652e423630f2001099a2410f_1790825327386675300_0.json","raw_sha256":"1a957289f56621bebd21cb45dd99baaedb2c3bc11cb28d700558e4bbcaa19695","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/45545;45541;45538;45533;45532;45530;45523;45513;45510;45507;45499;45493;45488;45487;45479;45474;45472;45463;45461;45447;45444;45436;45428;45425;45424;45423;45422;45416;45414;45410;45404;45401;45396;45391;45389;45387;45380;45377;45376;45375;45369;45366;45365;45363;45362;45359;45350;45347;45344;45336;45334;45331;45326;45322;45316;45313;45311;45309;45305;45302;45300;45291;45289;45285;45276;45269;45263;45262;45261;45253;45247;45246;45238;45236;45230;45229;45208;45201;45200;45185;45183;45171;45167;45165;45158;45154;45146;45141;45139;45134;45129;45127;45122;45114;45112;45108;45105;45100;45098;45096/answers?filter=withbody&order=asc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":45334,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Royi","profile_url":"https://scicomp.stackexchange.com/users/7951/royi","user_type":"registered"},"created_at":"2026-01-10T16:53:59+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"62C943AA-9B1D-4A55-BEE1-9F975532FF13","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/62C943AA-9B1D-4A55-BEE1-9F975532FF13/view-source"}],"score":0,"updated_at":"2026-01-10T16:53:59+00:00"},{"answer_html":"<p>I produced an ADMM based solver which I found very efficient.</p>\n<p>The problem is given by:</p>\n<p><span class=\"math-container\">$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } &amp; \\quad &amp; \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D}^{m} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} &amp; \\quad &amp; {x}_{i} = {y}_{i} \\; \\forall i \\in \\mathcal{I} \\\\\n&amp; \\quad &amp; \\boldsymbol{A} \\boldsymbol{x} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$</span></p>\n<p>I will use <span class=\"math-container\">$\\boldsymbol{D} = \\boldsymbol{D}^{m}$</span> to simplify notations.<br />\nThe equality constraints can be turned into matrix form and the problem becomes:</p>\n<p><span class=\"math-container\">$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } &amp; \\quad &amp; \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} &amp; \\quad &amp; \\boldsymbol{E} \\boldsymbol{x} = \\boldsymbol{d} \\\\\n&amp; \\quad &amp; \\boldsymbol{A} \\boldsymbol{x} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$</span></p>\n<p>The trick to utilize the ADMM framework is to introduce a slack variable to handle the inequality constraint:</p>\n<p><span class=\"math-container\">$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } &amp; \\quad &amp; \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} &amp; \\quad &amp; \\boldsymbol{E} \\boldsymbol{x} = \\boldsymbol{d} \\\\\n&amp; \\quad &amp; \\boldsymbol{A} \\boldsymbol{x} + \\boldsymbol{s} = \\boldsymbol{0} \\\\\n&amp; \\quad &amp; \\boldsymbol{s} \\geq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$</span></p>\n<p>The equality constraints are introduced by the Augmented Lagrangian:</p>\n<p><span class=\"math-container\">$$\n{\\ell}_{\\rho} \\left( \\boldsymbol{x}, \\boldsymbol{s}, \\boldsymbol{\\mu}, \\boldsymbol{\\nu} \\right) = \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2} + \\frac{\\rho}{2} {\\left\\| \\boldsymbol{A} \\boldsymbol{x} + \\boldsymbol{s} + {\\rho}^{-1} \\boldsymbol{\\mu} \\right\\|}_{2}^{2} + \\frac{\\rho}{2} {\\left\\| \\boldsymbol{E} \\boldsymbol{x} - \\boldsymbol{d} + {\\rho}^{-1} \\boldsymbol{\\nu} \\right\\|}_{2}^{2} + {I}_{\\mathbb{R}_{+}} \\left( \\boldsymbol{s} \\right)\n$$</span></p>\n<p>The steps to solve:</p>\n<ul>\n<li>Primal Update (Solve Linear System): <span class=\"math-container\">$\\boldsymbol{x}^{ \\left( k + 1 \\right)} = {\\left( \\boldsymbol{I} + \\lambda \\boldsymbol{D}^{\\top} \\boldsymbol{D} + \\rho \\boldsymbol{A}^{\\top} \\boldsymbol{A} + \\rho\\boldsymbol{E}^{\\top} \\boldsymbol{E} \\right)}^{-1} \\left( \\boldsymbol{y} - \\boldsymbol{A}^{\\top} \\left( \\rho \\boldsymbol{s}^{\\left( k \\right)} + \\boldsymbol{\\mu}^{\\left( k \\right)} \\right) + \\boldsymbol{E}^{\\top} \\left( \\rho \\boldsymbol{d} - \\boldsymbol{\\nu}^{\\left( k \\right)} \\right) \\right)$</span>.</li>\n<li>Slack Update (Non Negative LS): <span class=\"math-container\">$\\boldsymbol{s}^{ \\left( k + 1 \\right)} = \\max \\left( \\boldsymbol{0}, - \\boldsymbol{A} \\boldsymbol{x}^{\\left( k + 1 \\right)} - {\\rho}^{-1} \\boldsymbol{\\mu}^{\\left( k \\right)} \\right)$</span>.</li>\n<li>Dual Update (Gradient Ascent) for <span class=\"math-container\">$\\boldsymbol{\\mu}$</span>: <span class=\"math-container\">$\\boldsymbol{\\mu}^{\\left( k + 1 \\right)} = \\boldsymbol{\\mu}^{\\left( k \\right)} + \\rho \\left( \\boldsymbol{A} \\boldsymbol{x}^{\\left( k + 1 \\right)} + \\boldsymbol{s}^{\\left( k + 1 \\right)} \\right)$</span>.</li>\n<li>Dual Update (Gradient Ascent) for <span class=\"math-container\">$\\boldsymbol{\\nu}$</span>: <span class=\"math-container\">$\\boldsymbol{\\nu}^{\\left( k + 1 \\right)} = \\boldsymbol{\\nu}^{\\left( k \\right)} + \\rho \\left( \\boldsymbol{E} \\boldsymbol{x}^{\\left( k + 1 \\right)} - \\boldsymbol{d} \\right)$</span>.</li>\n</ul>\n<p>The stopping condition is when both residuals are below a threshold:</p>\n<ul>\n<li>Primal Residual: <span class=\"math-container\">${r}^{\\left( k \\right)} = {\\left\\| \\boldsymbol{A} \\boldsymbol{x}^{\\left( k \\right)} + \\boldsymbol{s}^{\\left( k \\right)} \\right\\|}_{\\infty}$</span>.</li>\n<li>Dual Residual (OSQP Style): <span class=\"math-container\">${s}^{\\left( k \\right)} = {\\left\\| \\rho \\boldsymbol{A} \\left( \\boldsymbol{s}^{\\left( k \\right)} - \\boldsymbol{s}^{\\left( k - 1 \\right)} \\right) \\right\\|}_{\\infty}$</span>.</li>\n</ul>\n<p>The use of the infinity norm decouples the dimension of the problem from the thresholds.</p>\n<p>I also used OSQP style update of the <span class=\"math-container\">$\\rho$</span> parameter to accelerate convergence: <span class=\"math-container\">${\\rho}^{\\left( k \\right)} = {\\rho}^{\\left( k - 1 \\right)} \\sqrt{ \\frac{ {r}^{\\left( k \\right)} }{ {s}^{\\left( k \\right)} } }$</span>.</p>\n<p>I implemented all in Julia and compared to the <a href=\"https://github.com/embotech/ecos\" rel=\"nofollow noreferrer\">ECOS</a> / <a href=\"https://github.com/cvxgrp/scs\" rel=\"nofollow noreferrer\">SCS</a> solvers wrapped by <a href=\"https://github.com/jump-dev/Convex.jl\" rel=\"nofollow noreferrer\"><code>Convex.jl</code></a>.</p>\n<p><a href=\"https://i.sstatic.net/f5YcjFm6.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/f5YcjFm6.png\" alt=\"enter image description here\" /></a></p>\n<p>Run Times:</p>\n<ul>\n<li>ECOS</li>\n</ul>\n<pre><code>BenchmarkTools.Trial: 1227 samples with 1 evaluation per sample.\n Range (min … max):  3.412 ms …  18.615 ms  ┊ GC (min … max): 0.00% … 60.46%\n Time  (median):     3.807 ms               ┊ GC (median):    0.00%\n Time  (mean ± σ):   4.061 ms ± 859.845 μs  ┊ GC (mean ± σ):  1.67% ±  5.36%\n\n   ▅█▇▄▃ ▁\n  ▄████████▇▆▇▅▆▅▅▄▄▃▃▃▃▄▃▄▄▄▃▃▃▃▃▃▂▂▂▂▃▃▂▂▂▃▂▂▂▂▂▂▂▂▂▂▂▂▁▂▂▂ ▃\n  3.41 ms         Histogram: frequency by time        6.54 ms &lt;\n\n Memory estimate: 806.21 KiB, allocs estimate: 7886.\n</code></pre>\n<ul>\n<li>SCS</li>\n</ul>\n<pre><code>BenchmarkTools.Trial: 98 samples with 1 evaluation per sample.\n Range (min … max):  49.280 ms …  53.704 ms  ┊ GC (min … max): 0.00% … 0.00%\n Time  (median):     50.892 ms               ┊ GC (median):    0.00%\n Time  (mean ± σ):   51.055 ms ± 918.217 μs  ┊ GC (mean ± σ):  0.00% ± 0.00%\n\n       ▁        ▃ ▁▁▁█ █▃ ▁ ▃ ▁   ▆   ▁           ▁\n  ▄▁▁▇▁█▁▁▄▄▇▄▄▇█▇████▇██▄█▇█▄█▄▁▄█▄▇▇█▁▇▄▄▄▄▁▇▇▄▄█▄▁▄▄▁▄▁▁▁▁▇ ▁\n  49.3 ms         Histogram: frequency by time         53.2 ms &lt;\n\n Memory estimate: 694.24 KiB, allocs estimate: 7998.\n</code></pre>\n<ul>\n<li>ADMM (My code):</li>\n</ul>\n<pre><code>BenchmarkTools.Trial: 7569 samples with 1 evaluation per sample.\n Range (min … max):  447.700 μs …  23.329 ms  ┊ GC (min … max): 0.00% … 70.82%\n Time  (median):     651.300 μs               ┊ GC (median):    0.00%\n Time  (mean ± σ):   656.690 μs ± 412.333 μs  ┊ GC (mean ± σ):  1.30% ±  2.26%\n\n   ▁▄▄▁            ▁▃▅▅▆▆█▇▇▆▅▄▂▁▁\n  ▃████▆▄▃▂▂▂▂▂▁▂▃▅███████████████▇▆▆▄▅▄▄▄▃▃▂▂▂▂▂▂▂▂▂▁▁▂▁▁▁▁▁▁▁ ▄\n  448 μs           Histogram: frequency by time          970 μs &lt;\n\n Memory estimate: 874.89 KiB, allocs estimate: 1089.\n</code></pre>\n<p>The ADMM method is an order of magnitude faster than the generic solvers.<br />\nIt can be greatly improved as it designed for arbitrary matrix <span class=\"math-container\">$\\boldsymbol{E}$</span>. It can be farther optimized for the case of equality.</p>\n<hr />\n<p>The code is available on my <a href=\"https://github.com/RoyiAvital/StackExchangeCodes\" rel=\"nofollow noreferrer\">StackExchange Code GitHub Repository</a> (Look at the <code>ComputationalScience\\Q45334</code> folder).</p>\n","answer_id":45341,"answer_text":"I produced an ADMM based solver which I found very efficient.\n\n\n\n\nThe problem is given by:\n\n\n\n\n$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } & \\quad & \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D}^{m} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} & \\quad & {x}_{i} = {y}_{i} \\; \\forall i \\in \\mathcal{I} \\\\\n& \\quad & \\boldsymbol{A} \\boldsymbol{x} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$\n\n\n\n\nI will use $\\boldsymbol{D} = \\boldsymbol{D}^{m}$ to simplify notations.\n\nThe equality constraints can be turned into matrix form and the problem becomes:\n\n\n\n\n$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } & \\quad & \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} & \\quad & \\boldsymbol{E} \\boldsymbol{x} = \\boldsymbol{d} \\\\\n& \\quad & \\boldsymbol{A} \\boldsymbol{x} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$\n\n\n\n\nThe trick to utilize the ADMM framework is to introduce a slack variable to handle the inequality constraint:\n\n\n\n\n$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } & \\quad & \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} & \\quad & \\boldsymbol{E} \\boldsymbol{x} = \\boldsymbol{d} \\\\\n& \\quad & \\boldsymbol{A} \\boldsymbol{x} + \\boldsymbol{s} = \\boldsymbol{0} \\\\\n& \\quad & \\boldsymbol{s} \\geq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$\n\n\n\n\nThe equality constraints are introduced by the Augmented Lagrangian:\n\n\n\n\n$$\n{\\ell}_{\\rho} \\left( \\boldsymbol{x}, \\boldsymbol{s}, \\boldsymbol{\\mu}, \\boldsymbol{\\nu} \\right) = \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2} + \\frac{\\rho}{2} {\\left\\| \\boldsymbol{A} \\boldsymbol{x} + \\boldsymbol{s} + {\\rho}^{-1} \\boldsymbol{\\mu} \\right\\|}_{2}^{2} + \\frac{\\rho}{2} {\\left\\| \\boldsymbol{E} \\boldsymbol{x} - \\boldsymbol{d} + {\\rho}^{-1} \\boldsymbol{\\nu} \\right\\|}_{2}^{2} + {I}_{\\mathbb{R}_{+}} \\left( \\boldsymbol{s} \\right)\n$$\n\n\n\n\nThe steps to solve:\n\n\n\n\n\nPrimal Update (Solve Linear System): $\\boldsymbol{x}^{ \\left( k + 1 \\right)} = {\\left( \\boldsymbol{I} + \\lambda \\boldsymbol{D}^{\\top} \\boldsymbol{D} + \\rho \\boldsymbol{A}^{\\top} \\boldsymbol{A} + \\rho\\boldsymbol{E}^{\\top} \\boldsymbol{E} \\right)}^{-1} \\left( \\boldsymbol{y} - \\boldsymbol{A}^{\\top} \\left( \\rho \\boldsymbol{s}^{\\left( k \\right)} + \\boldsymbol{\\mu}^{\\left( k \\right)} \\right) + \\boldsymbol{E}^{\\top} \\left( \\rho \\boldsymbol{d} - \\boldsymbol{\\nu}^{\\left( k \\right)} \\right) \\right)$.\n\n\n\n\nSlack Update (Non Negative LS): $\\boldsymbol{s}^{ \\left( k + 1 \\right)} = \\max \\left( \\boldsymbol{0}, - \\boldsymbol{A} \\boldsymbol{x}^{\\left( k + 1 \\right)} - {\\rho}^{-1} \\boldsymbol{\\mu}^{\\left( k \\right)} \\right)$.\n\n\n\n\nDual Update (Gradient Ascent) for $\\boldsymbol{\\mu}$: $\\boldsymbol{\\mu}^{\\left( k + 1 \\right)} = \\boldsymbol{\\mu}^{\\left( k \\right)} + \\rho \\left( \\boldsymbol{A} \\boldsymbol{x}^{\\left( k + 1 \\right)} + \\boldsymbol{s}^{\\left( k + 1 \\right)} \\right)$.\n\n\n\n\nDual Update (Gradient Ascent) for $\\boldsymbol{\\nu}$: $\\boldsymbol{\\nu}^{\\left( k + 1 \\right)} = \\boldsymbol{\\nu}^{\\left( k \\right)} + \\rho \\left( \\boldsymbol{E} \\boldsymbol{x}^{\\left( k + 1 \\right)} - \\boldsymbol{d} \\right)$.\n\n\n\n\n\nThe stopping condition is when both residuals are below a threshold:\n\n\n\n\n\nPrimal Residual: ${r}^{\\left( k \\right)} = {\\left\\| \\boldsymbol{A} \\boldsymbol{x}^{\\left( k \\right)} + \\boldsymbol{s}^{\\left( k \\right)} \\right\\|}_{\\infty}$.\n\n\n\n\nDual Residual (OSQP Style): ${s}^{\\left( k \\right)} = {\\left\\| \\rho \\boldsymbol{A} \\left( \\boldsymbol{s}^{\\left( k \\right)} - \\boldsymbol{s}^{\\left( k - 1 \\right)} \\right) \\right\\|}_{\\infty}$.\n\n\n\n\n\nThe use of the infinity norm decouples the dimension of the problem from the thresholds.\n\n\n\n\nI also used OSQP style update of the $\\rho$ parameter to accelerate convergence: ${\\rho}^{\\left( k \\right)} = {\\rho}^{\\left( k - 1 \\right)} \\sqrt{ \\frac{ {r}^{\\left( k \\right)} }{ {s}^{\\left( k \\right)} } }$.\n\n\n\n\nI implemented all in Julia and compared to the ECOS (https://github.com/embotech/ecos) / SCS (https://github.com/cvxgrp/scs) solvers wrapped by Convex.jl (https://github.com/jump-dev/Convex.jl).\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/f5YcjFm6.png] (https://i.sstatic.net/f5YcjFm6.png)\n\n\n\n\nRun Times:\n\n\n\n\n\nECOS\n\n\n\n\n\nBenchmarkTools.Trial: 1227 samples with 1 evaluation per sample.\n Range (min … max):  3.412 ms …  18.615 ms  ┊ GC (min … max): 0.00% … 60.46%\n Time  (median):     3.807 ms               ┊ GC (median):    0.00%\n Time  (mean ± σ):   4.061 ms ± 859.845 μs  ┊ GC (mean ± σ):  1.67% ±  5.36%\n\n   ▅█▇▄▃ ▁\n  ▄████████▇▆▇▅▆▅▅▄▄▃▃▃▃▄▃▄▄▄▃▃▃▃▃▃▂▂▂▂▃▃▂▂▂▃▂▂▂▂▂▂▂▂▂▂▂▂▁▂▂▂ ▃\n  3.41 ms         Histogram: frequency by time        6.54 ms <\n\n Memory estimate: 806.21 KiB, allocs estimate: 7886.\n\n\n\n\n\n\nSCS\n\n\n\n\n\nBenchmarkTools.Trial: 98 samples with 1 evaluation per sample.\n Range (min … max):  49.280 ms …  53.704 ms  ┊ GC (min … max): 0.00% … 0.00%\n Time  (median):     50.892 ms               ┊ GC (median):    0.00%\n Time  (mean ± σ):   51.055 ms ± 918.217 μs  ┊ GC (mean ± σ):  0.00% ± 0.00%\n\n       ▁        ▃ ▁▁▁█ █▃ ▁ ▃ ▁   ▆   ▁           ▁\n  ▄▁▁▇▁█▁▁▄▄▇▄▄▇█▇████▇██▄█▇█▄█▄▁▄█▄▇▇█▁▇▄▄▄▄▁▇▇▄▄█▄▁▄▄▁▄▁▁▁▁▇ ▁\n  49.3 ms         Histogram: frequency by time         53.2 ms <\n\n Memory estimate: 694.24 KiB, allocs estimate: 7998.\n\n\n\n\n\n\nADMM (My code):\n\n\n\n\n\nBenchmarkTools.Trial: 7569 samples with 1 evaluation per sample.\n Range (min … max):  447.700 μs …  23.329 ms  ┊ GC (min … max): 0.00% … 70.82%\n Time  (median):     651.300 μs               ┊ GC (median):    0.00%\n Time  (mean ± σ):   656.690 μs ± 412.333 μs  ┊ GC (mean ± σ):  1.30% ±  2.26%\n\n   ▁▄▄▁            ▁▃▅▅▆▆█▇▇▆▅▄▂▁▁\n  ▃████▆▄▃▂▂▂▂▂▁▂▃▅███████████████▇▆▆▄▅▄▄▄▃▃▂▂▂▂▂▂▂▂▂▁▁▂▁▁▁▁▁▁▁ ▄\n  448 μs           Histogram: frequency by time          970 μs <\n\n Memory estimate: 874.89 KiB, allocs estimate: 1089.\n\n\n\n\n\nThe ADMM method is an order of magnitude faster than the generic solvers.\n\nIt can be greatly improved as it designed for arbitrary matrix $\\boldsymbol{E}$. It can be farther optimized for the case of equality.\n\n\n\n\n\n\n\nThe code is available on my StackExchange Code GitHub Repository (https://github.com/RoyiAvital/StackExchangeCodes) (Look at the ComputationalScience\\Q45334 folder).","answer_url":"https://scicomp.stackexchange.com/a/45341","author":"Royi","author_url":"https://scicomp.stackexchange.com/users/7951/royi","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-01-17T09:49:49+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:47.033952+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/cb6e5f564c84a92c4e121c0637c99292018f8935652e423630f2001099a2410f_1790825327386675300_0.json","raw_sha256":"1a957289f56621bebd21cb45dd99baaedb2c3bc11cb28d700558e4bbcaa19695","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/45545;45541;45538;45533;45532;45530;45523;45513;45510;45507;45499;45493;45488;45487;45479;45474;45472;45463;45461;45447;45444;45436;45428;45425;45424;45423;45422;45416;45414;45410;45404;45401;45396;45391;45389;45387;45380;45377;45376;45375;45369;45366;45365;45363;45362;45359;45350;45347;45344;45336;45334;45331;45326;45322;45316;45313;45311;45309;45305;45302;45300;45291;45289;45285;45276;45269;45263;45262;45261;45253;45247;45246;45238;45236;45230;45229;45208;45201;45200;45185;45183;45171;45167;45165;45158;45154;45146;45141;45139;45134;45129;45127;45122;45114;45112;45108;45105;45100;45098;45096/answers?filter=withbody&order=asc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":45334,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Royi","profile_url":"https://scicomp.stackexchange.com/users/7951/royi","user_type":"registered"},"created_at":"2026-01-17T09:49:49+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"00755B30-2CCE-4266-8BA0-1A21879D0A39","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/00755B30-2CCE-4266-8BA0-1A21879D0A39/view-source"}],"score":2,"updated_at":"2026-01-17T09:49:49+00:00"},{"answer_html":"<p>Another formulation take advantage of the equality constraint to make the problem formulation smaller.</p>\n<p>The problem is given by:</p>\n<p><span class=\"math-container\">$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } &amp; \\quad &amp; \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} &amp; \\quad &amp; {x}_{i} = {y}_{i} \\; \\forall i \\in \\mathcal{I} \\\\\n&amp; \\quad &amp; \\boldsymbol{A} \\boldsymbol{x} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$</span></p>\n<p>Let <span class=\"math-container\">$\\mathcal{J} = \\left\\{ 1, 2, \\ldots, n \\right\\} \\setminus \\mathcal{I}$</span> then define:</p>\n<p><span class=\"math-container\">$$ \\boldsymbol{x} = \\begin{bmatrix} \\boldsymbol{x}_{\\mathcal{J}} \\\\ \\boldsymbol{x}_{\\mathcal{I}} \\end{bmatrix}, \\; \\boldsymbol{A} = \\begin{bmatrix} \\boldsymbol{A}_{\\mathcal{J}} &amp;&amp; \\boldsymbol{A}_{\\mathcal{I}} \\end{bmatrix}, \\boldsymbol{D} = \\begin{bmatrix} \\boldsymbol{D}_{\\mathcal{J}} &amp;&amp; \\boldsymbol{D}_{\\mathcal{I}} \\end{bmatrix}$$</span></p>\n<p>Then the above can be formulated as:</p>\n<p><span class=\"math-container\">$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x}_{\\mathcal{J}} } &amp; \\quad &amp; \\frac{1}{2} \\boldsymbol{x}_{\\mathcal{J}}^{\\top} \\boldsymbol{P} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{q}^{\\top} \\boldsymbol{x}_{\\mathcal{J}}  \\\\\n\\text{subject to} &amp; \\quad &amp; \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}} \\leq \\boldsymbol{b} \\\\\n\\end{alignat*}\n$$</span></p>\n<p>Where <span class=\"math-container\">$\\boldsymbol{P} = \\boldsymbol{I} + \\lambda \\boldsymbol{D}_{\\mathcal{J}}^{\\top} \\boldsymbol{D}_{\\mathcal{J}}, \\; \\boldsymbol{q} = - \\boldsymbol{y}_{\\mathcal{J}} + \\lambda \\boldsymbol{D}_{\\mathcal{J}}^{\\top} \\boldsymbol{D}_{\\mathcal{I}} \\boldsymbol{y}_{\\mathcal{I}}, \\; \\boldsymbol{b} = \\boldsymbol{A}_{\\mathcal{I}} \\boldsymbol{y}_{\\mathcal{I}}$</span>.</p>\n<p>This formulation reduces the number of constraints to handle.<br />\nThe inequality is treated by introducing a slack variable <span class=\"math-container\">$\\boldsymbol{s} \\geq \\boldsymbol{0}$</span> such that <span class=\"math-container\">$\\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{s} = \\boldsymbol{b}$</span>.</p>\n<p>The Augmented Lagrangian (Scaled form) is given by:</p>\n<p><span class=\"math-container\">$$\n{\\ell}_{\\rho} \\left( \\boldsymbol{x}_{\\mathcal{J}}, \\boldsymbol{s}, \\boldsymbol{\\mu} \\right) = \\frac{1}{2} \\boldsymbol{x}_{\\mathcal{J}}^{\\top} \\boldsymbol{P} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{q}^{\\top} \\boldsymbol{x}_{\\mathcal{J}} + \\frac{\\rho}{2} {\\left\\| \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{s} - \\boldsymbol{b} + \\boldsymbol{\\mu} \\right\\|}_{2}^{2} + {I}_{\\mathbb{R}_{+}} \\left( \\boldsymbol{s} \\right)\n$$</span></p>\n<p>The steps to solve:</p>\n<ul>\n<li>Primal Update (Solve Linear System): <span class=\"math-container\">$\\boldsymbol{x}_{\\mathcal{J}}^{\\left( k + 1 \\right)} = {\\left( \\boldsymbol{P} + \\rho \\boldsymbol{A}_{\\mathcal{J}}^{\\top} \\boldsymbol{A}_{\\mathcal{J}} \\right)}^{-1} \\left( - \\boldsymbol{q} + \\rho \\boldsymbol{A}_{\\mathcal{J}} \\left( \\boldsymbol{b} - \\boldsymbol{s}^{\\left( k \\right)} - \\boldsymbol{\\mu}^{\\left( k \\right)} \\right) \\right)$</span>.</li>\n<li>Slack Update (Non Negative LS / Projection): <span class=\"math-container\">$\\boldsymbol{s}^{\\left( k + 1 \\right)} = \\max \\left(\\boldsymbol{0}, \\boldsymbol{b} - \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}}^{\\left( k + 1 \\right)} - \\boldsymbol{\\mu}^{\\left( k \\right)} \\right)$</span>.</li>\n<li>Dual Update (Gradient Ascent): <span class=\"math-container\">$\\boldsymbol{\\mu}^{\\left( k + 1 \\right)} = \\boldsymbol{\\mu}^{\\left( k \\right)} + \\left( \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}}^{\\left( k + 1 \\right)} + \\boldsymbol{s}^{\\left( k + 1 \\right)} - \\boldsymbol{b} \\right)$</span>.</li>\n</ul>\n<p>The rest is similar to above with the needed adjustments for the residuals calculations.</p>\n<p>This implementation reduced another 40 [Micro Sec] of the run time.</p>\n","answer_id":45342,"answer_text":"Another formulation take advantage of the equality constraint to make the problem formulation smaller.\n\n\n\n\nThe problem is given by:\n\n\n\n\n$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } & \\quad & \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} & \\quad & {x}_{i} = {y}_{i} \\; \\forall i \\in \\mathcal{I} \\\\\n& \\quad & \\boldsymbol{A} \\boldsymbol{x} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$\n\n\n\n\nLet $\\mathcal{J} = \\left\\{ 1, 2, \\ldots, n \\right\\} \\setminus \\mathcal{I}$ then define:\n\n\n\n\n$$ \\boldsymbol{x} = \\begin{bmatrix} \\boldsymbol{x}_{\\mathcal{J}} \\\\ \\boldsymbol{x}_{\\mathcal{I}} \\end{bmatrix}, \\; \\boldsymbol{A} = \\begin{bmatrix} \\boldsymbol{A}_{\\mathcal{J}} && \\boldsymbol{A}_{\\mathcal{I}} \\end{bmatrix}, \\boldsymbol{D} = \\begin{bmatrix} \\boldsymbol{D}_{\\mathcal{J}} && \\boldsymbol{D}_{\\mathcal{I}} \\end{bmatrix}$$\n\n\n\n\nThen the above can be formulated as:\n\n\n\n\n$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x}_{\\mathcal{J}} } & \\quad & \\frac{1}{2} \\boldsymbol{x}_{\\mathcal{J}}^{\\top} \\boldsymbol{P} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{q}^{\\top} \\boldsymbol{x}_{\\mathcal{J}}  \\\\\n\\text{subject to} & \\quad & \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}} \\leq \\boldsymbol{b} \\\\\n\\end{alignat*}\n$$\n\n\n\n\nWhere $\\boldsymbol{P} = \\boldsymbol{I} + \\lambda \\boldsymbol{D}_{\\mathcal{J}}^{\\top} \\boldsymbol{D}_{\\mathcal{J}}, \\; \\boldsymbol{q} = - \\boldsymbol{y}_{\\mathcal{J}} + \\lambda \\boldsymbol{D}_{\\mathcal{J}}^{\\top} \\boldsymbol{D}_{\\mathcal{I}} \\boldsymbol{y}_{\\mathcal{I}}, \\; \\boldsymbol{b} = \\boldsymbol{A}_{\\mathcal{I}} \\boldsymbol{y}_{\\mathcal{I}}$.\n\n\n\n\nThis formulation reduces the number of constraints to handle.\n\nThe inequality is treated by introducing a slack variable $\\boldsymbol{s} \\geq \\boldsymbol{0}$ such that $\\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{s} = \\boldsymbol{b}$.\n\n\n\n\nThe Augmented Lagrangian (Scaled form) is given by:\n\n\n\n\n$$\n{\\ell}_{\\rho} \\left( \\boldsymbol{x}_{\\mathcal{J}}, \\boldsymbol{s}, \\boldsymbol{\\mu} \\right) = \\frac{1}{2} \\boldsymbol{x}_{\\mathcal{J}}^{\\top} \\boldsymbol{P} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{q}^{\\top} \\boldsymbol{x}_{\\mathcal{J}} + \\frac{\\rho}{2} {\\left\\| \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{s} - \\boldsymbol{b} + \\boldsymbol{\\mu} \\right\\|}_{2}^{2} + {I}_{\\mathbb{R}_{+}} \\left( \\boldsymbol{s} \\right)\n$$\n\n\n\n\nThe steps to solve:\n\n\n\n\n\nPrimal Update (Solve Linear System): $\\boldsymbol{x}_{\\mathcal{J}}^{\\left( k + 1 \\right)} = {\\left( \\boldsymbol{P} + \\rho \\boldsymbol{A}_{\\mathcal{J}}^{\\top} \\boldsymbol{A}_{\\mathcal{J}} \\right)}^{-1} \\left( - \\boldsymbol{q} + \\rho \\boldsymbol{A}_{\\mathcal{J}} \\left( \\boldsymbol{b} - \\boldsymbol{s}^{\\left( k \\right)} - \\boldsymbol{\\mu}^{\\left( k \\right)} \\right) \\right)$.\n\n\n\n\nSlack Update (Non Negative LS / Projection): $\\boldsymbol{s}^{\\left( k + 1 \\right)} = \\max \\left(\\boldsymbol{0}, \\boldsymbol{b} - \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}}^{\\left( k + 1 \\right)} - \\boldsymbol{\\mu}^{\\left( k \\right)} \\right)$.\n\n\n\n\nDual Update (Gradient Ascent): $\\boldsymbol{\\mu}^{\\left( k + 1 \\right)} = \\boldsymbol{\\mu}^{\\left( k \\right)} + \\left( \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}}^{\\left( k + 1 \\right)} + \\boldsymbol{s}^{\\left( k + 1 \\right)} - \\boldsymbol{b} \\right)$.\n\n\n\n\n\nThe rest is similar to above with the needed adjustments for the residuals calculations.\n\n\n\n\nThis implementation reduced another 40 [Micro Sec] of the run time.","answer_url":"https://scicomp.stackexchange.com/a/45342","author":"Royi","author_url":"https://scicomp.stackexchange.com/users/7951/royi","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-01-17T12:18:23+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:47.033952+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/cb6e5f564c84a92c4e121c0637c99292018f8935652e423630f2001099a2410f_1790825327386675300_0.json","raw_sha256":"1a957289f56621bebd21cb45dd99baaedb2c3bc11cb28d700558e4bbcaa19695","source_api":"Stack Exchange API 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4.0","contributor":{"display_name":"Royi","profile_url":"https://scicomp.stackexchange.com/users/7951/royi","user_type":"registered"},"created_at":"2026-01-17T12:18:23+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"9FE8A84D-E3F5-41A7-B296-8A0BBB5EB8BB","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/9FE8A84D-E3F5-41A7-B296-8A0BBB5EB8BB/view-source"}],"score":1,"updated_at":"2026-01-17T12:18:23+00:00"}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Royi","author_url":"https://scicomp.stackexchange.com/users/7951/royi","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 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4.0","contributor":{"display_name":"Royi","profile_url":"https://scicomp.stackexchange.com/users/7951/royi","user_type":"registered"},"created_at":"2026-01-17T12:18:23+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"9FE8A84D-E3F5-41A7-B296-8A0BBB5EB8BB","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/9FE8A84D-E3F5-41A7-B296-8A0BBB5EB8BB/view-source"}],"url":"https://scicomp.stackexchange.com/a/45342"}],"contexts":[{"context_id":"question","html":"<p>Let a 1D curve defined by <span class=\"math-container\">$\\left\\{ {y}_{1}, {y}_{2}, \\ldots, {y}_{n} \\right\\}$</span> sampled on a uniform grid.</p>\n<p>I want to smooth the curve with the following properties:</p>\n<ol>\n<li>The result, <span class=\"math-container\">$\\left\\{ {z}_{1}, {z}_{2}, \\ldots {z}_{n} \\right\\}$</span> should be smooth like Spline based method.</li>\n<li>For a set of indices <span class=\"math-container\">$\\mathcal{I}$</span> the smoothed curve must go through the reference point, namely <span class=\"math-container\">${z}_{i} = {y}_{i} \\; \\forall i \\in \\mathcal{I}$</span>.</li>\n<li>The smoothed values between 2 reference points must be monotonic.</li>\n</ol>\n<p>I came up with the following model:</p>\n<p><span class=\"math-container\">$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{z} } &amp; \\quad &amp; \\frac{1}{2} \\left\\| \\boldsymbol{z} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\lambda {\\left\\| \\boldsymbol{D}^{m} \\boldsymbol{z} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} &amp; \\quad &amp; {z}_{i} = {y}_{i} \\; \\forall i \\in \\mathcal{I} \\\\\n&amp; \\quad &amp; \\boldsymbol{A} \\boldsymbol{z} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$</span></p>\n<p>Where <span class=\"math-container\">$\\boldsymbol{D}^{m}$</span> is the <span class=\"math-container\">$m$</span> -th derivative operator.</p>\n<p>I am looking for a fast way to solve the problem for the case of 50-1500 samples.</p>\n<p>I rather not use black box Quadratic Programming solvers but design a simple to implement iterative method.</p>\n","text":"Let a 1D curve defined by $\\left\\{ {y}_{1}, {y}_{2}, \\ldots, {y}_{n} \\right\\}$ sampled on a uniform grid.\n\n\n\n\nI want to smooth the curve with the following properties:\n\n\n\n\n\nThe result, $\\left\\{ {z}_{1}, {z}_{2}, \\ldots {z}_{n} \\right\\}$ should be smooth like Spline based method.\n\n\n\n\nFor a set of indices $\\mathcal{I}$ the smoothed curve must go through the reference point, namely ${z}_{i} = {y}_{i} \\; \\forall i \\in \\mathcal{I}$.\n\n\n\n\nThe smoothed values between 2 reference points must be monotonic.\n\n\n\n\n\nI came up with the following model:\n\n\n\n\n$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{z} } & \\quad & \\frac{1}{2} \\left\\| \\boldsymbol{z} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\lambda {\\left\\| \\boldsymbol{D}^{m} \\boldsymbol{z} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} & \\quad & {z}_{i} = {y}_{i} \\; \\forall i \\in \\mathcal{I} \\\\\n& \\quad & \\boldsymbol{A} \\boldsymbol{z} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$\n\n\n\n\nWhere $\\boldsymbol{D}^{m}$ is the $m$ -th derivative operator.\n\n\n\n\nI am looking for a fast way to solve the problem for the case of 50-1500 samples.\n\n\n\n\nI rather not use black box Quadratic Programming solvers but design a simple to implement iterative method."},{"context_id":"45335","html":"<blockquote>\n<p>monothonic</p>\n</blockquote>\n<p>I'm sure you meant monotonic.</p>\n<blockquote>\n<p>I am looking for a fast way to solve the problem</p>\n</blockquote>\n<p>Are you actually? I think if you were, you would use something off-the-shelf. &quot;Simple iterative&quot; and &quot;fast&quot; don't particularly jive, here. Let's take a random stab at remodelling your problem to meet <em>some</em> of your criteria:</p>\n<ul>\n<li>Linear, not quadratic</li>\n<li>No manual iteration per se</li>\n<li>Enforce inter-reference monotonicity through simple linear constraints</li>\n<li>Model cost as being absolute error plus absolute second-order differential, the latter receiving your <span class=\"math-container\">$\\lambda$</span> weight</li>\n</ul>\n<p>A traditional LP would express the problem thus. Define the following decision vectors:</p>\n<ul>\n<li><span class=\"math-container\">$z \\in \\mathbb R^n$</span>, the fit points</li>\n<li><span class=\"math-container\">$z_p \\in \\mathbb R^n$</span>, <span class=\"math-container\">$z_p \\ge 0$</span>, positive-clipped fit error</li>\n<li><span class=\"math-container\">$z_n \\in \\mathbb R^n$</span>, <span class=\"math-container\">$z_n \\ge 0$</span>, negative-clipped fit error</li>\n<li><span class=\"math-container\">$d_p \\in \\mathbb R^{n-2}$</span>, <span class=\"math-container\">$d_p \\ge 0$</span>, positive-clipped second-order differentials</li>\n<li><span class=\"math-container\">$d_n \\in \\mathbb R^{n-2}$</span>, <span class=\"math-container\">$d_n \\ge 0$</span>, negative-clipped second-order differentials</li>\n</ul>\n<p>Find</p>\n<p><span class=\"math-container\">$$ \\min_z z_p + z_n + \\lambda ( d_p + d_n ) $$</span></p>\n<p>given the following constraints:</p>\n<p><span class=\"math-container\">$$ z_p \\ge z - y $$</span>\n<span class=\"math-container\">$$ z_n \\ge y - z $$</span>\n<span class=\"math-container\">$$ d_p \\ge \\frac {\\partial^2 z} {\\partial i^2} $$</span>\n<span class=\"math-container\">$$ d_n \\ge -\\frac {\\partial^2 z} {\\partial i^2} $$</span>\n<span class=\"math-container\">$ (z_{i+1} - z_i) \\text{sgn}( y_1 - y_0 ) \\ge 0 $</span> for every index <span class=\"math-container\">$i$</span> between every anchor point <span class=\"math-container\">$y_0$</span>, <span class=\"math-container\">$y_1$</span></p>\n<p><span class=\"math-container\">$ \\frac {\\partial^2 z} {\\partial i^2} $</span> discretised by:\n<span class=\"math-container\">$$ \\begin{bmatrix}\n1 &amp; -2 &amp; 1 \\\\\n  &amp; 1  &amp; -2 &amp; 1 \\\\\n  &amp;    &amp;    &amp;   &amp; \\ddots\n\\end{bmatrix} z $$</span></p>\n<p>The problem is very sparse, and I trust that essentially no LP solvers would have any difficulty with it. HiGHS completes it quickly.</p>\n<pre class=\"lang-py prettyprint-override\"><code>import matplotlib.pyplot as plt\nimport numpy as np\nimport scipy.sparse as sp\nfrom scipy.optimize import milp, LinearConstraint\n\n\ndef sample_data(rand: np.random.Generator, n: int = 1501) -&gt; tuple[\n    np.ndarray, np.ndarray, np.ndarray,\n]:\n    x = np.linspace(start=0, stop=10, num=n)\n    y = rand.uniform(low=-0.1, high=0.1, size=x.size).cumsum()\n    iref = np.array((2, 6, 9))*(n//10)\n    return x, y, iref\n\n\ndef cost(n: int, nd: int, smoothing: float) -&gt; np.ndarray:\n    return np.concatenate((\n        np.zeros(n),   # z does not incur a cost directly\n        np.ones(2*n),  # zerr cost\n        np.full(2*nd, fill_value=smoothing),\n    ))\n\n\ndef bounds(iref: np.ndarray, n: int, nd: int, y: np.ndarray) -&gt; np.ndarray:\n    lbound, ubound = bounds = np.zeros((2, 3*n + 2*nd))\n    lbound[:n] = -np.inf\n    ubound[:] = np.inf\n\n    iprev = iref[:-1]\n    inext = iref[1:]\n    pprev = y[iprev]\n    pnext = y[inext]\n    pfloor = np.minimum(pprev, pnext)\n    pceil = np.maximum(pprev, pnext)\n\n    for i0, i1, plo, phi in zip(iprev, inext, pfloor, pceil):\n        lbound[i0] = y[i0]\n        ubound[i0] = y[i0]\n        inner = slice(i0 + 1, i1)\n        lbound[inner] = plo\n        ubound[inner] = phi\n    lbound[iref[-1]] = y[iref[-1]]\n    ubound[iref[-1]] = y[iref[-1]]\n\n    return bounds\n\n\ndef zerror_constraints(n: int, nd: int, y: np.ndarray) -&gt; tuple[LinearConstraint, ...]:\n    # zep &gt;= z - y:  z - zep &lt;= y\n    # zen &gt;= y - z:  z + zen &gt;= y\n    eye = sp.eye_array(n)\n    zero = sp.csc_array((n, n))\n    zerond = sp.csc_array((n, 2*nd))\n    pos = LinearConstraint(\n        A=sp.hstack((eye, -eye, zero, zerond), format='csc'), ub=y)\n    neg = LinearConstraint(\n        A=sp.hstack((eye, zero, eye, zerond), format='csc'), lb=y)\n    return pos, neg\n\n\ndef d2_constraints(n: int, nd: int) -&gt; tuple[LinearConstraint, ...]:\n    # d2z/dt2 = z[i+2] - 2z[i+1] + z[i]\n    # d2p &gt;=  d2z/dt2: -z[i] + 2z[i+1] - z[i+2] +0 +0 + d2p &gt;= 0\n    # d2n &gt;= -d2z/dt2:  z[i] - 2z[i+1] + z[i+2] +0 +0 +   0 + d2n &gt;= 0\n    data = np.broadcast_to(\n        np.array(([1], [-2], [1]), dtype=np.float32),  # don't bother with /dt**2\n        shape=(3, n))\n    offsets = np.array((0, 1, 2), dtype=np.int32)\n    kernel = sp.dia_array((data, offsets), shape=(nd, n))\n    err_zero = sp.csc_array((nd, 2*n))\n    eye = sp.eye_array(nd)\n    zero = sp.csc_array((nd, nd))\n    pos = LinearConstraint(\n        A=sp.hstack((-kernel, err_zero, eye, zero), format='csc'), lb=0)\n    neg = LinearConstraint(\n        A=sp.hstack(( kernel, err_zero, zero, eye), format='csc'), lb=0)\n    return pos, neg\n\n\ndef monotone_constraints(n: int, nd: int, y: np.ndarray, iref: np.ndarray) -&gt; tuple[LinearConstraint, ...]:\n    iprev = iref[:-1]\n    inext = iref[1:]\n    yprev = y[iprev]\n    ynext = y[inext]\n    blocks = []\n\n    for i0, i1, y0, y1 in zip(iprev, inext, yprev, ynext):\n        sign = np.sign(y1 - y0)\n        if sign == 0:\n            continue  # the entire segment will already have lower and upper bounds equal to each other\n        block = sp.eye_array(\n            m=i1 - i0, n=3*n + 2*nd, k=i0 + 1,\n        ) - sp.eye_array(\n            m=i1 - i0, n=3*n + 2*nd, k=i0)\n        blocks.append(sign*block)\n    constraint = LinearConstraint(A=sp.vstack(blocks, format='csc'), lb=0)\n    return constraint,\n\n\ndef solve(y: np.ndarray, iref: np.ndarray, smoothing: float = 1.) -&gt; tuple[\n    np.ndarray, tuple[LinearConstraint, ...],\n]:\n    '''\n    Variables:\n        z, continuous unbounded (outside of ref points)\n        zep, continuous, &gt;= 0, &gt;= z-y\n        zen, continuous, &gt;= 0, &gt;= y-z\n        d2p, n-2, continuous, &gt;= 0, &gt;= d2z/dt2\n        d2n, n-2, continuous, &gt;= 0, &gt;= -d2z/dt2\n    '''\n    n = y.size\n    nd = n - 2\n    constraints = (\n        zerror_constraints(n, nd, y) + d2_constraints(n, nd) + monotone_constraints(n, nd, y, iref)\n    )\n\n    result = milp(\n        c=cost(n, nd, smoothing), integrality=0, bounds=bounds(iref, n, nd, y),\n        constraints=constraints,\n    )\n    if not result.success:\n        raise result.message\n    z, zep, zen, d2p, d2n = np.split(result.x, (n, 2*n, 3*n, 3*n+nd))\n    return z, constraints\n\n\ndef demo() -&gt; None:\n    rand = np.random.default_rng(seed=0)\n    x, y, iref = sample_data(rand, n=801)\n\n    fig, ax = plt.subplots()\n    ax.plot(x, y, label='orig')\n    ax.scatter(x[iref], y[iref], color='red', label='ref point')\n\n    for smoothing in (0.5, 3):\n        z, constraints = solve(y, iref, smoothing)\n        ax.plot(x, z, label=f'smooth={smoothing}')\n    ax.legend()\n\n    sparsity = sp.vstack([c.A for c in constraints]).sign().toarray()\n    fig, ax = plt.subplots()\n    ax.set_title(f'Constraint sparsity, n={y.size}')\n    ax.imshow(sparsity)\n\n    plt.show()\n\n\nif __name__ == '__main__':\n    demo()\n</code></pre>\n<p>Here we see that the solution does exactly what we tell it to:</p>\n<p><a href=\"https://i.sstatic.net/oTyX0oWA.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/oTyX0oWA.png\" alt=\"example solution\" /></a></p>\n<p>Outside of the reference points, monotonicity is not enforced so the smoothed curve follows the input curve. Within the reference points, monotonicity is preserved, and the solver does its best to balance smoothing and fitting; a finer-scale depiction of this behaviour:</p>\n<p><a href=\"https://i.sstatic.net/cW1t1avg.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/cW1t1avg.png\" alt=\"smoothing\" /></a></p>\n<p>The sparsity pattern for the problem looks like this (size reduced for visibility):</p>\n<p><a href=\"https://i.sstatic.net/UmVF5qyE.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/UmVF5qyE.png\" alt=\"sparsity\" /></a></p>\n<p>Though the performance will vary based on hardware and dataset content and size, for n=1501 I see execution times of ~80 ms.</p>\n","text":"monothonic\n\n\n\n\n\n\n\nI'm sure you meant monotonic.\n\n\n\n\n\n\n\nI am looking for a fast way to solve the problem\n\n\n\n\n\n\n\nAre you actually? I think if you were, you would use something off-the-shelf. \"Simple iterative\" and \"fast\" don't particularly jive, here. Let's take a random stab at remodelling your problem to meet some of your criteria:\n\n\n\n\n\nLinear, not quadratic\n\n\n\n\nNo manual iteration per se\n\n\n\n\nEnforce inter-reference monotonicity through simple linear constraints\n\n\n\n\nModel cost as being absolute error plus absolute second-order differential, the latter receiving your $\\lambda$ weight\n\n\n\n\n\nA traditional LP would express the problem thus. Define the following decision vectors:\n\n\n\n\n\n$z \\in \\mathbb R^n$, the fit points\n\n\n\n\n$z_p \\in \\mathbb R^n$, $z_p \\ge 0$, positive-clipped fit error\n\n\n\n\n$z_n \\in \\mathbb R^n$, $z_n \\ge 0$, negative-clipped fit error\n\n\n\n\n$d_p \\in \\mathbb R^{n-2}$, $d_p \\ge 0$, positive-clipped second-order differentials\n\n\n\n\n$d_n \\in \\mathbb R^{n-2}$, $d_n \\ge 0$, negative-clipped second-order differentials\n\n\n\n\n\nFind\n\n\n\n\n$$ \\min_z z_p + z_n + \\lambda ( d_p + d_n ) $$\n\n\n\n\ngiven the following constraints:\n\n\n\n\n$$ z_p \\ge z - y $$\n$$ z_n \\ge y - z $$\n$$ d_p \\ge \\frac {\\partial^2 z} {\\partial i^2} $$\n$$ d_n \\ge -\\frac {\\partial^2 z} {\\partial i^2} $$\n$ (z_{i+1} - z_i) \\text{sgn}( y_1 - y_0 ) \\ge 0 $ for every index $i$ between every anchor point $y_0$, $y_1$\n\n\n\n\n$ \\frac {\\partial^2 z} {\\partial i^2} $ discretised by:\n$$ \\begin{bmatrix}\n1 & -2 & 1 \\\\\n  & 1  & -2 & 1 \\\\\n  &    &    &   & \\ddots\n\\end{bmatrix} z $$\n\n\n\n\nThe problem is very sparse, and I trust that essentially no LP solvers would have any difficulty with it. HiGHS completes it quickly.\n\n\n\n\nimport matplotlib.pyplot as plt\nimport numpy as np\nimport scipy.sparse as sp\nfrom scipy.optimize import milp, LinearConstraint\n\n\ndef sample_data(rand: np.random.Generator, n: int = 1501) -> tuple[\n    np.ndarray, np.ndarray, np.ndarray,\n]:\n    x = np.linspace(start=0, stop=10, num=n)\n    y = rand.uniform(low=-0.1, high=0.1, size=x.size).cumsum()\n    iref = np.array((2, 6, 9))*(n//10)\n    return x, y, iref\n\n\ndef cost(n: int, nd: int, smoothing: float) -> np.ndarray:\n    return np.concatenate((\n        np.zeros(n),   # z does not incur a cost directly\n        np.ones(2*n),  # zerr cost\n        np.full(2*nd, fill_value=smoothing),\n    ))\n\n\ndef bounds(iref: np.ndarray, n: int, nd: int, y: np.ndarray) -> np.ndarray:\n    lbound, ubound = bounds = np.zeros((2, 3*n + 2*nd))\n    lbound[:n] = -np.inf\n    ubound[:] = np.inf\n\n    iprev = iref[:-1]\n    inext = iref[1:]\n    pprev = y[iprev]\n    pnext = y[inext]\n    pfloor = np.minimum(pprev, pnext)\n    pceil = np.maximum(pprev, pnext)\n\n    for i0, i1, plo, phi in zip(iprev, inext, pfloor, pceil):\n        lbound[i0] = y[i0]\n        ubound[i0] = y[i0]\n        inner = slice(i0 + 1, i1)\n        lbound[inner] = plo\n        ubound[inner] = phi\n    lbound[iref[-1]] = y[iref[-1]]\n    ubound[iref[-1]] = y[iref[-1]]\n\n    return bounds\n\n\ndef zerror_constraints(n: int, nd: int, y: np.ndarray) -> tuple[LinearConstraint, ...]:\n    # zep >= z - y:  z - zep <= y\n    # zen >= y - z:  z + zen >= y\n    eye = sp.eye_array(n)\n    zero = sp.csc_array((n, n))\n    zerond = sp.csc_array((n, 2*nd))\n    pos = LinearConstraint(\n        A=sp.hstack((eye, -eye, zero, zerond), format='csc'), ub=y)\n    neg = LinearConstraint(\n        A=sp.hstack((eye, zero, eye, zerond), format='csc'), lb=y)\n    return pos, neg\n\n\ndef d2_constraints(n: int, nd: int) -> tuple[LinearConstraint, ...]:\n    # d2z/dt2 = z[i+2] - 2z[i+1] + z[i]\n    # d2p >=  d2z/dt2: -z[i] + 2z[i+1] - z[i+2] +0 +0 + d2p >= 0\n    # d2n >= -d2z/dt2:  z[i] - 2z[i+1] + z[i+2] +0 +0 +   0 + d2n >= 0\n    data = np.broadcast_to(\n        np.array(([1], [-2], [1]), dtype=np.float32),  # don't bother with /dt**2\n        shape=(3, n))\n    offsets = np.array((0, 1, 2), dtype=np.int32)\n    kernel = sp.dia_array((data, offsets), shape=(nd, n))\n    err_zero = sp.csc_array((nd, 2*n))\n    eye = sp.eye_array(nd)\n    zero = sp.csc_array((nd, nd))\n    pos = LinearConstraint(\n        A=sp.hstack((-kernel, err_zero, eye, zero), format='csc'), lb=0)\n    neg = LinearConstraint(\n        A=sp.hstack(( kernel, err_zero, zero, eye), format='csc'), lb=0)\n    return pos, neg\n\n\ndef monotone_constraints(n: int, nd: int, y: np.ndarray, iref: np.ndarray) -> tuple[LinearConstraint, ...]:\n    iprev = iref[:-1]\n    inext = iref[1:]\n    yprev = y[iprev]\n    ynext = y[inext]\n    blocks = []\n\n    for i0, i1, y0, y1 in zip(iprev, inext, yprev, ynext):\n        sign = np.sign(y1 - y0)\n        if sign == 0:\n            continue  # the entire segment will already have lower and upper bounds equal to each other\n        block = sp.eye_array(\n            m=i1 - i0, n=3*n + 2*nd, k=i0 + 1,\n        ) - sp.eye_array(\n            m=i1 - i0, n=3*n + 2*nd, k=i0)\n        blocks.append(sign*block)\n    constraint = LinearConstraint(A=sp.vstack(blocks, format='csc'), lb=0)\n    return constraint,\n\n\ndef solve(y: np.ndarray, iref: np.ndarray, smoothing: float = 1.) -> tuple[\n    np.ndarray, tuple[LinearConstraint, ...],\n]:\n    '''\n    Variables:\n        z, continuous unbounded (outside of ref points)\n        zep, continuous, >= 0, >= z-y\n        zen, continuous, >= 0, >= y-z\n        d2p, n-2, continuous, >= 0, >= d2z/dt2\n        d2n, n-2, continuous, >= 0, >= -d2z/dt2\n    '''\n    n = y.size\n    nd = n - 2\n    constraints = (\n        zerror_constraints(n, nd, y) + d2_constraints(n, nd) + monotone_constraints(n, nd, y, iref)\n    )\n\n    result = milp(\n        c=cost(n, nd, smoothing), integrality=0, bounds=bounds(iref, n, nd, y),\n        constraints=constraints,\n    )\n    if not result.success:\n        raise result.message\n    z, zep, zen, d2p, d2n = np.split(result.x, (n, 2*n, 3*n, 3*n+nd))\n    return z, constraints\n\n\ndef demo() -> None:\n    rand = np.random.default_rng(seed=0)\n    x, y, iref = sample_data(rand, n=801)\n\n    fig, ax = plt.subplots()\n    ax.plot(x, y, label='orig')\n    ax.scatter(x[iref], y[iref], color='red', label='ref point')\n\n    for smoothing in (0.5, 3):\n        z, constraints = solve(y, iref, smoothing)\n        ax.plot(x, z, label=f'smooth={smoothing}')\n    ax.legend()\n\n    sparsity = sp.vstack([c.A for c in constraints]).sign().toarray()\n    fig, ax = plt.subplots()\n    ax.set_title(f'Constraint sparsity, n={y.size}')\n    ax.imshow(sparsity)\n\n    plt.show()\n\n\nif __name__ == '__main__':\n    demo()\n\n\n\n\n\nHere we see that the solution does exactly what we tell it to:\n\n\n\n\n[image: example solution; source: https://i.sstatic.net/oTyX0oWA.png] (https://i.sstatic.net/oTyX0oWA.png)\n\n\n\n\nOutside of the reference points, monotonicity is not enforced so the smoothed curve follows the input curve. Within the reference points, monotonicity is preserved, and the solver does its best to balance smoothing and fitting; a finer-scale depiction of this behaviour:\n\n\n\n\n[image: smoothing; source: https://i.sstatic.net/cW1t1avg.png] (https://i.sstatic.net/cW1t1avg.png)\n\n\n\n\nThe sparsity pattern for the problem looks like this (size reduced for visibility):\n\n\n\n\n[image: sparsity; source: https://i.sstatic.net/UmVF5qyE.png] (https://i.sstatic.net/UmVF5qyE.png)\n\n\n\n\nThough the performance will vary based on hardware and dataset content and size, for n=1501 I see execution times of ~80 ms."},{"context_id":"45337","html":"<p>I managed to create a prototype solver based on ADMM in MATLAB:</p>\n<pre class=\"lang-matlab prettyprint-override\"><code>function [ vX, isConv ] = SplineQPSmooth( vY, mD, paramLambda, vI, mA, sParams )\n\narguments(Input)\n    vY (:, 1) {mustBeNumeric, mustBeFinite, mustBeReal}\n    mD (:, :) {mustBeNumeric, mustBeFinite, mustBeReal}\n    paramLambda (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBeNonnegative}\n    vI (:, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBeInteger}\n    mA (:, :) {mustBeNumeric, mustBeFinite, mustBeReal}\n    sParams.paramRho (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 1.0\n    sParams.numIter (1, 1) {mustBeNumeric, mustBeFinite, mustBeInteger, mustBePositive} = 5000\n    sParams.epsAbs (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 1e-5\n    sParams.epsRel (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 1e-5\n    sParams.convInterval (1, 1) {mustBeNumeric, mustBeFinite, mustBeInteger, mustBePositive} = 25\n    sParams.paramTau (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 10\nend\n\narguments(Output)\n    vX (:, 1) {mustBeNumeric, mustBeFinite, mustBeReal}\n    isConv (1, 1) {mustBeA(isConv, 'logical')}\nend\n\nnumSamples = length(vY);\nnumEq      = length(vI);\nnumInEq    = size(mA, 1);\n\n% Quadratic Terms\nmQ = sparse(eye(numSamples)) + paramLambda * (mD' * mD);\nvQ = -vY;\n\n% Equality Constraints\nmE = sparse(1:numEq, vI, 1, numEq, numSamples);\nvD = vY(vI);\n\nparamRho     = sParams.paramRho;\nparamRhoInv  = inv(paramRho);\nnumIter      = sParams.numIter;\nepsAbs       = sParams.epsAbs;\nepsRel       = sParams.epsRel;\nconvInterval = sParams.convInterval;\nparamTau     = sParams.paramTau;\n\n% ADMM Variables\nvX  = vY;                %&lt;! Optimization variable\nvS  = zeros(numInEq, 1); %&lt;! Slack variable for inequality\nvS1 = zeros(numInEq, 1); %&lt;! Preious iteration buffer\nvMu = zeros(numInEq, 1); %&lt;! Dual variable for inequality\nvNu = zeros(numEq, 1);   %&lt;! Dual variabe for equality\n\n% Factorize the KKT System\n% (Q + rho * A' * A + rho * E' * E) * z = r\nmK = mQ + paramRho * (mA.' * mA) + paramRho * (mE.' * mE);\nsK = decomposition(mK, 'chol', 'CheckCondition', false);\n\nisConv     = false;\nupdatedRho = false;\n\nfor ii = 1:numIter\n    vS1(:) = vS; %&lt;! Previous iteration\n\n    % Solve the Linear System\n    vR = -vQ - mA.' * (paramRho * vS + vMu) + mE.' * (paramRho * vD - vNu); %&lt;! Right hand vector\n    vX = sK \\ vR;\n\n    % Proximal / Projection Step\n    % s = -A * z with s &gt;= 0\n    vS = max(0, -(mA * vX + paramRhoInv * vMu));\n\n    % Update Dual Variables\n    vMu = vMu + paramRho * (mA * vX + vS);\n    vNu = vNu + paramRho * (mE * vX - vD);\n\n    % Check Convergence\n    if mod(ii, convInterval) == 0\n        primRes = norm(mA * vX + vS, 'inf');\n        dualRes = norm(paramRho * mA' * (vS - vS1), 'inf');\n        if ((primRes &lt; epsAbs) &amp;&amp; (dualRes &lt; epsAbs))\n            isConv = true;\n            break;\n        end\n\n        % Adpat `paramRho`\n        resRatio = primRes / dualRes;\n        % fprintf('Primal Residual: %0.7f, Dual Residual: %0.7f\\n', primRes, dualRes);\n        % fprintf('Residual Ratio: %0.2f, ρ = %0.3f\\n', resRatio, paramRho);\n        if (resRatio &gt; paramTau) || (inv(resRatio) &gt; paramTau)\n            updatedRho = true;\n        else\n            updatedRho = false;\n        end\n        if updatedRho\n            paramRho = paramRho * sqrt(resRatio);\n            paramRho = clip(paramRho, 1e-5, 1e5);\n            paramRhoInv  = inv(paramRho);\n            mK = mQ + paramRho * (mA.' * mA) + paramRho * (mE.' * mE);\n            sK = decomposition(mK, 'chol', 'CheckCondition', false);\n        end\n    end\n\nend\n\nend\n</code></pre>\n<p>I has convergence check and adaptation of the ADMM's step size parameter <span class=\"math-container\">$\\rho$</span>.<br />\nI will add mathematical formulation and a memory optimized version using Julia.</p>\n<p>On MATLAB with this naive code I could beat <code>quadprog()</code> by 30% with the same output:</p>\n<p><a href=\"https://i.sstatic.net/VC8uzUSt.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/VC8uzUSt.png\" alt=\"enter image description here\" /></a></p>\n\n","text":"I managed to create a prototype solver based on ADMM in MATLAB:\n\n\n\n\nfunction [ vX, isConv ] = SplineQPSmooth( vY, mD, paramLambda, vI, mA, sParams )\n\narguments(Input)\n    vY (:, 1) {mustBeNumeric, mustBeFinite, mustBeReal}\n    mD (:, :) {mustBeNumeric, mustBeFinite, mustBeReal}\n    paramLambda (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBeNonnegative}\n    vI (:, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBeInteger}\n    mA (:, :) {mustBeNumeric, mustBeFinite, mustBeReal}\n    sParams.paramRho (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 1.0\n    sParams.numIter (1, 1) {mustBeNumeric, mustBeFinite, mustBeInteger, mustBePositive} = 5000\n    sParams.epsAbs (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 1e-5\n    sParams.epsRel (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 1e-5\n    sParams.convInterval (1, 1) {mustBeNumeric, mustBeFinite, mustBeInteger, mustBePositive} = 25\n    sParams.paramTau (1, 1) {mustBeNumeric, mustBeFinite, mustBeReal, mustBePositive} = 10\nend\n\narguments(Output)\n    vX (:, 1) {mustBeNumeric, mustBeFinite, mustBeReal}\n    isConv (1, 1) {mustBeA(isConv, 'logical')}\nend\n\nnumSamples = length(vY);\nnumEq      = length(vI);\nnumInEq    = size(mA, 1);\n\n% Quadratic Terms\nmQ = sparse(eye(numSamples)) + paramLambda * (mD' * mD);\nvQ = -vY;\n\n% Equality Constraints\nmE = sparse(1:numEq, vI, 1, numEq, numSamples);\nvD = vY(vI);\n\nparamRho     = sParams.paramRho;\nparamRhoInv  = inv(paramRho);\nnumIter      = sParams.numIter;\nepsAbs       = sParams.epsAbs;\nepsRel       = sParams.epsRel;\nconvInterval = sParams.convInterval;\nparamTau     = sParams.paramTau;\n\n% ADMM Variables\nvX  = vY;                %<! Optimization variable\nvS  = zeros(numInEq, 1); %<! Slack variable for inequality\nvS1 = zeros(numInEq, 1); %<! Preious iteration buffer\nvMu = zeros(numInEq, 1); %<! Dual variable for inequality\nvNu = zeros(numEq, 1);   %<! Dual variabe for equality\n\n% Factorize the KKT System\n% (Q + rho * A' * A + rho * E' * E) * z = r\nmK = mQ + paramRho * (mA.' * mA) + paramRho * (mE.' * mE);\nsK = decomposition(mK, 'chol', 'CheckCondition', false);\n\nisConv     = false;\nupdatedRho = false;\n\nfor ii = 1:numIter\n    vS1(:) = vS; %<! Previous iteration\n\n    % Solve the Linear System\n    vR = -vQ - mA.' * (paramRho * vS + vMu) + mE.' * (paramRho * vD - vNu); %<! Right hand vector\n    vX = sK \\ vR;\n\n    % Proximal / Projection Step\n    % s = -A * z with s >= 0\n    vS = max(0, -(mA * vX + paramRhoInv * vMu));\n\n    % Update Dual Variables\n    vMu = vMu + paramRho * (mA * vX + vS);\n    vNu = vNu + paramRho * (mE * vX - vD);\n\n    % Check Convergence\n    if mod(ii, convInterval) == 0\n        primRes = norm(mA * vX + vS, 'inf');\n        dualRes = norm(paramRho * mA' * (vS - vS1), 'inf');\n        if ((primRes < epsAbs) && (dualRes < epsAbs))\n            isConv = true;\n            break;\n        end\n\n        % Adpat `paramRho`\n        resRatio = primRes / dualRes;\n        % fprintf('Primal Residual: %0.7f, Dual Residual: %0.7f\\n', primRes, dualRes);\n        % fprintf('Residual Ratio: %0.2f, ρ = %0.3f\\n', resRatio, paramRho);\n        if (resRatio > paramTau) || (inv(resRatio) > paramTau)\n            updatedRho = true;\n        else\n            updatedRho = false;\n        end\n        if updatedRho\n            paramRho = paramRho * sqrt(resRatio);\n            paramRho = clip(paramRho, 1e-5, 1e5);\n            paramRhoInv  = inv(paramRho);\n            mK = mQ + paramRho * (mA.' * mA) + paramRho * (mE.' * mE);\n            sK = decomposition(mK, 'chol', 'CheckCondition', false);\n        end\n    end\n\nend\n\nend\n\n\n\n\n\nI has convergence check and adaptation of the ADMM's step size parameter $\\rho$.\n\nI will add mathematical formulation and a memory optimized version using Julia.\n\n\n\n\nOn MATLAB with this naive code I could beat quadprog() by 30% with the same output:\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/VC8uzUSt.png] (https://i.sstatic.net/VC8uzUSt.png)"},{"context_id":"45341","html":"<p>I produced an ADMM based solver which I found very efficient.</p>\n<p>The problem is given by:</p>\n<p><span class=\"math-container\">$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } &amp; \\quad &amp; \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D}^{m} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} &amp; \\quad &amp; {x}_{i} = {y}_{i} \\; \\forall i \\in \\mathcal{I} \\\\\n&amp; \\quad &amp; \\boldsymbol{A} \\boldsymbol{x} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$</span></p>\n<p>I will use <span class=\"math-container\">$\\boldsymbol{D} = \\boldsymbol{D}^{m}$</span> to simplify notations.<br />\nThe equality constraints can be turned into matrix form and the problem becomes:</p>\n<p><span class=\"math-container\">$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } &amp; \\quad &amp; \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} &amp; \\quad &amp; \\boldsymbol{E} \\boldsymbol{x} = \\boldsymbol{d} \\\\\n&amp; \\quad &amp; \\boldsymbol{A} \\boldsymbol{x} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$</span></p>\n<p>The trick to utilize the ADMM framework is to introduce a slack variable to handle the inequality constraint:</p>\n<p><span class=\"math-container\">$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } &amp; \\quad &amp; \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} &amp; \\quad &amp; \\boldsymbol{E} \\boldsymbol{x} = \\boldsymbol{d} \\\\\n&amp; \\quad &amp; \\boldsymbol{A} \\boldsymbol{x} + \\boldsymbol{s} = \\boldsymbol{0} \\\\\n&amp; \\quad &amp; \\boldsymbol{s} \\geq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$</span></p>\n<p>The equality constraints are introduced by the Augmented Lagrangian:</p>\n<p><span class=\"math-container\">$$\n{\\ell}_{\\rho} \\left( \\boldsymbol{x}, \\boldsymbol{s}, \\boldsymbol{\\mu}, \\boldsymbol{\\nu} \\right) = \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2} + \\frac{\\rho}{2} {\\left\\| \\boldsymbol{A} \\boldsymbol{x} + \\boldsymbol{s} + {\\rho}^{-1} \\boldsymbol{\\mu} \\right\\|}_{2}^{2} + \\frac{\\rho}{2} {\\left\\| \\boldsymbol{E} \\boldsymbol{x} - \\boldsymbol{d} + {\\rho}^{-1} \\boldsymbol{\\nu} \\right\\|}_{2}^{2} + {I}_{\\mathbb{R}_{+}} \\left( \\boldsymbol{s} \\right)\n$$</span></p>\n<p>The steps to solve:</p>\n<ul>\n<li>Primal Update (Solve Linear System): <span class=\"math-container\">$\\boldsymbol{x}^{ \\left( k + 1 \\right)} = {\\left( \\boldsymbol{I} + \\lambda \\boldsymbol{D}^{\\top} \\boldsymbol{D} + \\rho \\boldsymbol{A}^{\\top} \\boldsymbol{A} + \\rho\\boldsymbol{E}^{\\top} \\boldsymbol{E} \\right)}^{-1} \\left( \\boldsymbol{y} - \\boldsymbol{A}^{\\top} \\left( \\rho \\boldsymbol{s}^{\\left( k \\right)} + \\boldsymbol{\\mu}^{\\left( k \\right)} \\right) + \\boldsymbol{E}^{\\top} \\left( \\rho \\boldsymbol{d} - \\boldsymbol{\\nu}^{\\left( k \\right)} \\right) \\right)$</span>.</li>\n<li>Slack Update (Non Negative LS): <span class=\"math-container\">$\\boldsymbol{s}^{ \\left( k + 1 \\right)} = \\max \\left( \\boldsymbol{0}, - \\boldsymbol{A} \\boldsymbol{x}^{\\left( k + 1 \\right)} - {\\rho}^{-1} \\boldsymbol{\\mu}^{\\left( k \\right)} \\right)$</span>.</li>\n<li>Dual Update (Gradient Ascent) for <span class=\"math-container\">$\\boldsymbol{\\mu}$</span>: <span class=\"math-container\">$\\boldsymbol{\\mu}^{\\left( k + 1 \\right)} = \\boldsymbol{\\mu}^{\\left( k \\right)} + \\rho \\left( \\boldsymbol{A} \\boldsymbol{x}^{\\left( k + 1 \\right)} + \\boldsymbol{s}^{\\left( k + 1 \\right)} \\right)$</span>.</li>\n<li>Dual Update (Gradient Ascent) for <span class=\"math-container\">$\\boldsymbol{\\nu}$</span>: <span class=\"math-container\">$\\boldsymbol{\\nu}^{\\left( k + 1 \\right)} = \\boldsymbol{\\nu}^{\\left( k \\right)} + \\rho \\left( \\boldsymbol{E} \\boldsymbol{x}^{\\left( k + 1 \\right)} - \\boldsymbol{d} \\right)$</span>.</li>\n</ul>\n<p>The stopping condition is when both residuals are below a threshold:</p>\n<ul>\n<li>Primal Residual: <span class=\"math-container\">${r}^{\\left( k \\right)} = {\\left\\| \\boldsymbol{A} \\boldsymbol{x}^{\\left( k \\right)} + \\boldsymbol{s}^{\\left( k \\right)} \\right\\|}_{\\infty}$</span>.</li>\n<li>Dual Residual (OSQP Style): <span class=\"math-container\">${s}^{\\left( k \\right)} = {\\left\\| \\rho \\boldsymbol{A} \\left( \\boldsymbol{s}^{\\left( k \\right)} - \\boldsymbol{s}^{\\left( k - 1 \\right)} \\right) \\right\\|}_{\\infty}$</span>.</li>\n</ul>\n<p>The use of the infinity norm decouples the dimension of the problem from the thresholds.</p>\n<p>I also used OSQP style update of the <span class=\"math-container\">$\\rho$</span> parameter to accelerate convergence: <span class=\"math-container\">${\\rho}^{\\left( k \\right)} = {\\rho}^{\\left( k - 1 \\right)} \\sqrt{ \\frac{ {r}^{\\left( k \\right)} }{ {s}^{\\left( k \\right)} } }$</span>.</p>\n<p>I implemented all in Julia and compared to the <a href=\"https://github.com/embotech/ecos\" rel=\"nofollow noreferrer\">ECOS</a> / <a href=\"https://github.com/cvxgrp/scs\" rel=\"nofollow noreferrer\">SCS</a> solvers wrapped by <a href=\"https://github.com/jump-dev/Convex.jl\" rel=\"nofollow noreferrer\"><code>Convex.jl</code></a>.</p>\n<p><a href=\"https://i.sstatic.net/f5YcjFm6.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/f5YcjFm6.png\" alt=\"enter image description here\" /></a></p>\n<p>Run Times:</p>\n<ul>\n<li>ECOS</li>\n</ul>\n<pre><code>BenchmarkTools.Trial: 1227 samples with 1 evaluation per sample.\n Range (min … max):  3.412 ms …  18.615 ms  ┊ GC (min … max): 0.00% … 60.46%\n Time  (median):     3.807 ms               ┊ GC (median):    0.00%\n Time  (mean ± σ):   4.061 ms ± 859.845 μs  ┊ GC (mean ± σ):  1.67% ±  5.36%\n\n   ▅█▇▄▃ ▁\n  ▄████████▇▆▇▅▆▅▅▄▄▃▃▃▃▄▃▄▄▄▃▃▃▃▃▃▂▂▂▂▃▃▂▂▂▃▂▂▂▂▂▂▂▂▂▂▂▂▁▂▂▂ ▃\n  3.41 ms         Histogram: frequency by time        6.54 ms &lt;\n\n Memory estimate: 806.21 KiB, allocs estimate: 7886.\n</code></pre>\n<ul>\n<li>SCS</li>\n</ul>\n<pre><code>BenchmarkTools.Trial: 98 samples with 1 evaluation per sample.\n Range (min … max):  49.280 ms …  53.704 ms  ┊ GC (min … max): 0.00% … 0.00%\n Time  (median):     50.892 ms               ┊ GC (median):    0.00%\n Time  (mean ± σ):   51.055 ms ± 918.217 μs  ┊ GC (mean ± σ):  0.00% ± 0.00%\n\n       ▁        ▃ ▁▁▁█ █▃ ▁ ▃ ▁   ▆   ▁           ▁\n  ▄▁▁▇▁█▁▁▄▄▇▄▄▇█▇████▇██▄█▇█▄█▄▁▄█▄▇▇█▁▇▄▄▄▄▁▇▇▄▄█▄▁▄▄▁▄▁▁▁▁▇ ▁\n  49.3 ms         Histogram: frequency by time         53.2 ms &lt;\n\n Memory estimate: 694.24 KiB, allocs estimate: 7998.\n</code></pre>\n<ul>\n<li>ADMM (My code):</li>\n</ul>\n<pre><code>BenchmarkTools.Trial: 7569 samples with 1 evaluation per sample.\n Range (min … max):  447.700 μs …  23.329 ms  ┊ GC (min … max): 0.00% … 70.82%\n Time  (median):     651.300 μs               ┊ GC (median):    0.00%\n Time  (mean ± σ):   656.690 μs ± 412.333 μs  ┊ GC (mean ± σ):  1.30% ±  2.26%\n\n   ▁▄▄▁            ▁▃▅▅▆▆█▇▇▆▅▄▂▁▁\n  ▃████▆▄▃▂▂▂▂▂▁▂▃▅███████████████▇▆▆▄▅▄▄▄▃▃▂▂▂▂▂▂▂▂▂▁▁▂▁▁▁▁▁▁▁ ▄\n  448 μs           Histogram: frequency by time          970 μs &lt;\n\n Memory estimate: 874.89 KiB, allocs estimate: 1089.\n</code></pre>\n<p>The ADMM method is an order of magnitude faster than the generic solvers.<br />\nIt can be greatly improved as it designed for arbitrary matrix <span class=\"math-container\">$\\boldsymbol{E}$</span>. It can be farther optimized for the case of equality.</p>\n<hr />\n<p>The code is available on my <a href=\"https://github.com/RoyiAvital/StackExchangeCodes\" rel=\"nofollow noreferrer\">StackExchange Code GitHub Repository</a> (Look at the <code>ComputationalScience\\Q45334</code> folder).</p>\n","text":"I produced an ADMM based solver which I found very efficient.\n\n\n\n\nThe problem is given by:\n\n\n\n\n$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } & \\quad & \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D}^{m} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} & \\quad & {x}_{i} = {y}_{i} \\; \\forall i \\in \\mathcal{I} \\\\\n& \\quad & \\boldsymbol{A} \\boldsymbol{x} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$\n\n\n\n\nI will use $\\boldsymbol{D} = \\boldsymbol{D}^{m}$ to simplify notations.\n\nThe equality constraints can be turned into matrix form and the problem becomes:\n\n\n\n\n$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } & \\quad & \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} & \\quad & \\boldsymbol{E} \\boldsymbol{x} = \\boldsymbol{d} \\\\\n& \\quad & \\boldsymbol{A} \\boldsymbol{x} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$\n\n\n\n\nThe trick to utilize the ADMM framework is to introduce a slack variable to handle the inequality constraint:\n\n\n\n\n$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } & \\quad & \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} & \\quad & \\boldsymbol{E} \\boldsymbol{x} = \\boldsymbol{d} \\\\\n& \\quad & \\boldsymbol{A} \\boldsymbol{x} + \\boldsymbol{s} = \\boldsymbol{0} \\\\\n& \\quad & \\boldsymbol{s} \\geq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$\n\n\n\n\nThe equality constraints are introduced by the Augmented Lagrangian:\n\n\n\n\n$$\n{\\ell}_{\\rho} \\left( \\boldsymbol{x}, \\boldsymbol{s}, \\boldsymbol{\\mu}, \\boldsymbol{\\nu} \\right) = \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2} + \\frac{\\rho}{2} {\\left\\| \\boldsymbol{A} \\boldsymbol{x} + \\boldsymbol{s} + {\\rho}^{-1} \\boldsymbol{\\mu} \\right\\|}_{2}^{2} + \\frac{\\rho}{2} {\\left\\| \\boldsymbol{E} \\boldsymbol{x} - \\boldsymbol{d} + {\\rho}^{-1} \\boldsymbol{\\nu} \\right\\|}_{2}^{2} + {I}_{\\mathbb{R}_{+}} \\left( \\boldsymbol{s} \\right)\n$$\n\n\n\n\nThe steps to solve:\n\n\n\n\n\nPrimal Update (Solve Linear System): $\\boldsymbol{x}^{ \\left( k + 1 \\right)} = {\\left( \\boldsymbol{I} + \\lambda \\boldsymbol{D}^{\\top} \\boldsymbol{D} + \\rho \\boldsymbol{A}^{\\top} \\boldsymbol{A} + \\rho\\boldsymbol{E}^{\\top} \\boldsymbol{E} \\right)}^{-1} \\left( \\boldsymbol{y} - \\boldsymbol{A}^{\\top} \\left( \\rho \\boldsymbol{s}^{\\left( k \\right)} + \\boldsymbol{\\mu}^{\\left( k \\right)} \\right) + \\boldsymbol{E}^{\\top} \\left( \\rho \\boldsymbol{d} - \\boldsymbol{\\nu}^{\\left( k \\right)} \\right) \\right)$.\n\n\n\n\nSlack Update (Non Negative LS): $\\boldsymbol{s}^{ \\left( k + 1 \\right)} = \\max \\left( \\boldsymbol{0}, - \\boldsymbol{A} \\boldsymbol{x}^{\\left( k + 1 \\right)} - {\\rho}^{-1} \\boldsymbol{\\mu}^{\\left( k \\right)} \\right)$.\n\n\n\n\nDual Update (Gradient Ascent) for $\\boldsymbol{\\mu}$: $\\boldsymbol{\\mu}^{\\left( k + 1 \\right)} = \\boldsymbol{\\mu}^{\\left( k \\right)} + \\rho \\left( \\boldsymbol{A} \\boldsymbol{x}^{\\left( k + 1 \\right)} + \\boldsymbol{s}^{\\left( k + 1 \\right)} \\right)$.\n\n\n\n\nDual Update (Gradient Ascent) for $\\boldsymbol{\\nu}$: $\\boldsymbol{\\nu}^{\\left( k + 1 \\right)} = \\boldsymbol{\\nu}^{\\left( k \\right)} + \\rho \\left( \\boldsymbol{E} \\boldsymbol{x}^{\\left( k + 1 \\right)} - \\boldsymbol{d} \\right)$.\n\n\n\n\n\nThe stopping condition is when both residuals are below a threshold:\n\n\n\n\n\nPrimal Residual: ${r}^{\\left( k \\right)} = {\\left\\| \\boldsymbol{A} \\boldsymbol{x}^{\\left( k \\right)} + \\boldsymbol{s}^{\\left( k \\right)} \\right\\|}_{\\infty}$.\n\n\n\n\nDual Residual (OSQP Style): ${s}^{\\left( k \\right)} = {\\left\\| \\rho \\boldsymbol{A} \\left( \\boldsymbol{s}^{\\left( k \\right)} - \\boldsymbol{s}^{\\left( k - 1 \\right)} \\right) \\right\\|}_{\\infty}$.\n\n\n\n\n\nThe use of the infinity norm decouples the dimension of the problem from the thresholds.\n\n\n\n\nI also used OSQP style update of the $\\rho$ parameter to accelerate convergence: ${\\rho}^{\\left( k \\right)} = {\\rho}^{\\left( k - 1 \\right)} \\sqrt{ \\frac{ {r}^{\\left( k \\right)} }{ {s}^{\\left( k \\right)} } }$.\n\n\n\n\nI implemented all in Julia and compared to the ECOS (https://github.com/embotech/ecos) / SCS (https://github.com/cvxgrp/scs) solvers wrapped by Convex.jl (https://github.com/jump-dev/Convex.jl).\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/f5YcjFm6.png] (https://i.sstatic.net/f5YcjFm6.png)\n\n\n\n\nRun Times:\n\n\n\n\n\nECOS\n\n\n\n\n\nBenchmarkTools.Trial: 1227 samples with 1 evaluation per sample.\n Range (min … max):  3.412 ms …  18.615 ms  ┊ GC (min … max): 0.00% … 60.46%\n Time  (median):     3.807 ms               ┊ GC (median):    0.00%\n Time  (mean ± σ):   4.061 ms ± 859.845 μs  ┊ GC (mean ± σ):  1.67% ±  5.36%\n\n   ▅█▇▄▃ ▁\n  ▄████████▇▆▇▅▆▅▅▄▄▃▃▃▃▄▃▄▄▄▃▃▃▃▃▃▂▂▂▂▃▃▂▂▂▃▂▂▂▂▂▂▂▂▂▂▂▂▁▂▂▂ ▃\n  3.41 ms         Histogram: frequency by time        6.54 ms <\n\n Memory estimate: 806.21 KiB, allocs estimate: 7886.\n\n\n\n\n\n\nSCS\n\n\n\n\n\nBenchmarkTools.Trial: 98 samples with 1 evaluation per sample.\n Range (min … max):  49.280 ms …  53.704 ms  ┊ GC (min … max): 0.00% … 0.00%\n Time  (median):     50.892 ms               ┊ GC (median):    0.00%\n Time  (mean ± σ):   51.055 ms ± 918.217 μs  ┊ GC (mean ± σ):  0.00% ± 0.00%\n\n       ▁        ▃ ▁▁▁█ █▃ ▁ ▃ ▁   ▆   ▁           ▁\n  ▄▁▁▇▁█▁▁▄▄▇▄▄▇█▇████▇██▄█▇█▄█▄▁▄█▄▇▇█▁▇▄▄▄▄▁▇▇▄▄█▄▁▄▄▁▄▁▁▁▁▇ ▁\n  49.3 ms         Histogram: frequency by time         53.2 ms <\n\n Memory estimate: 694.24 KiB, allocs estimate: 7998.\n\n\n\n\n\n\nADMM (My code):\n\n\n\n\n\nBenchmarkTools.Trial: 7569 samples with 1 evaluation per sample.\n Range (min … max):  447.700 μs …  23.329 ms  ┊ GC (min … max): 0.00% … 70.82%\n Time  (median):     651.300 μs               ┊ GC (median):    0.00%\n Time  (mean ± σ):   656.690 μs ± 412.333 μs  ┊ GC (mean ± σ):  1.30% ±  2.26%\n\n   ▁▄▄▁            ▁▃▅▅▆▆█▇▇▆▅▄▂▁▁\n  ▃████▆▄▃▂▂▂▂▂▁▂▃▅███████████████▇▆▆▄▅▄▄▄▃▃▂▂▂▂▂▂▂▂▂▁▁▂▁▁▁▁▁▁▁ ▄\n  448 μs           Histogram: frequency by time          970 μs <\n\n Memory estimate: 874.89 KiB, allocs estimate: 1089.\n\n\n\n\n\nThe ADMM method is an order of magnitude faster than the generic solvers.\n\nIt can be greatly improved as it designed for arbitrary matrix $\\boldsymbol{E}$. It can be farther optimized for the case of equality.\n\n\n\n\n\n\n\nThe code is available on my StackExchange Code GitHub Repository (https://github.com/RoyiAvital/StackExchangeCodes) (Look at the ComputationalScience\\Q45334 folder)."},{"context_id":"45342","html":"<p>Another formulation take advantage of the equality constraint to make the problem formulation smaller.</p>\n<p>The problem is given by:</p>\n<p><span class=\"math-container\">$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } &amp; \\quad &amp; \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} &amp; \\quad &amp; {x}_{i} = {y}_{i} \\; \\forall i \\in \\mathcal{I} \\\\\n&amp; \\quad &amp; \\boldsymbol{A} \\boldsymbol{x} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$</span></p>\n<p>Let <span class=\"math-container\">$\\mathcal{J} = \\left\\{ 1, 2, \\ldots, n \\right\\} \\setminus \\mathcal{I}$</span> then define:</p>\n<p><span class=\"math-container\">$$ \\boldsymbol{x} = \\begin{bmatrix} \\boldsymbol{x}_{\\mathcal{J}} \\\\ \\boldsymbol{x}_{\\mathcal{I}} \\end{bmatrix}, \\; \\boldsymbol{A} = \\begin{bmatrix} \\boldsymbol{A}_{\\mathcal{J}} &amp;&amp; \\boldsymbol{A}_{\\mathcal{I}} \\end{bmatrix}, \\boldsymbol{D} = \\begin{bmatrix} \\boldsymbol{D}_{\\mathcal{J}} &amp;&amp; \\boldsymbol{D}_{\\mathcal{I}} \\end{bmatrix}$$</span></p>\n<p>Then the above can be formulated as:</p>\n<p><span class=\"math-container\">$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x}_{\\mathcal{J}} } &amp; \\quad &amp; \\frac{1}{2} \\boldsymbol{x}_{\\mathcal{J}}^{\\top} \\boldsymbol{P} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{q}^{\\top} \\boldsymbol{x}_{\\mathcal{J}}  \\\\\n\\text{subject to} &amp; \\quad &amp; \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}} \\leq \\boldsymbol{b} \\\\\n\\end{alignat*}\n$$</span></p>\n<p>Where <span class=\"math-container\">$\\boldsymbol{P} = \\boldsymbol{I} + \\lambda \\boldsymbol{D}_{\\mathcal{J}}^{\\top} \\boldsymbol{D}_{\\mathcal{J}}, \\; \\boldsymbol{q} = - \\boldsymbol{y}_{\\mathcal{J}} + \\lambda \\boldsymbol{D}_{\\mathcal{J}}^{\\top} \\boldsymbol{D}_{\\mathcal{I}} \\boldsymbol{y}_{\\mathcal{I}}, \\; \\boldsymbol{b} = \\boldsymbol{A}_{\\mathcal{I}} \\boldsymbol{y}_{\\mathcal{I}}$</span>.</p>\n<p>This formulation reduces the number of constraints to handle.<br />\nThe inequality is treated by introducing a slack variable <span class=\"math-container\">$\\boldsymbol{s} \\geq \\boldsymbol{0}$</span> such that <span class=\"math-container\">$\\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{s} = \\boldsymbol{b}$</span>.</p>\n<p>The Augmented Lagrangian (Scaled form) is given by:</p>\n<p><span class=\"math-container\">$$\n{\\ell}_{\\rho} \\left( \\boldsymbol{x}_{\\mathcal{J}}, \\boldsymbol{s}, \\boldsymbol{\\mu} \\right) = \\frac{1}{2} \\boldsymbol{x}_{\\mathcal{J}}^{\\top} \\boldsymbol{P} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{q}^{\\top} \\boldsymbol{x}_{\\mathcal{J}} + \\frac{\\rho}{2} {\\left\\| \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{s} - \\boldsymbol{b} + \\boldsymbol{\\mu} \\right\\|}_{2}^{2} + {I}_{\\mathbb{R}_{+}} \\left( \\boldsymbol{s} \\right)\n$$</span></p>\n<p>The steps to solve:</p>\n<ul>\n<li>Primal Update (Solve Linear System): <span class=\"math-container\">$\\boldsymbol{x}_{\\mathcal{J}}^{\\left( k + 1 \\right)} = {\\left( \\boldsymbol{P} + \\rho \\boldsymbol{A}_{\\mathcal{J}}^{\\top} \\boldsymbol{A}_{\\mathcal{J}} \\right)}^{-1} \\left( - \\boldsymbol{q} + \\rho \\boldsymbol{A}_{\\mathcal{J}} \\left( \\boldsymbol{b} - \\boldsymbol{s}^{\\left( k \\right)} - \\boldsymbol{\\mu}^{\\left( k \\right)} \\right) \\right)$</span>.</li>\n<li>Slack Update (Non Negative LS / Projection): <span class=\"math-container\">$\\boldsymbol{s}^{\\left( k + 1 \\right)} = \\max \\left(\\boldsymbol{0}, \\boldsymbol{b} - \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}}^{\\left( k + 1 \\right)} - \\boldsymbol{\\mu}^{\\left( k \\right)} \\right)$</span>.</li>\n<li>Dual Update (Gradient Ascent): <span class=\"math-container\">$\\boldsymbol{\\mu}^{\\left( k + 1 \\right)} = \\boldsymbol{\\mu}^{\\left( k \\right)} + \\left( \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}}^{\\left( k + 1 \\right)} + \\boldsymbol{s}^{\\left( k + 1 \\right)} - \\boldsymbol{b} \\right)$</span>.</li>\n</ul>\n<p>The rest is similar to above with the needed adjustments for the residuals calculations.</p>\n<p>This implementation reduced another 40 [Micro Sec] of the run time.</p>\n","text":"Another formulation take advantage of the equality constraint to make the problem formulation smaller.\n\n\n\n\nThe problem is given by:\n\n\n\n\n$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x} } & \\quad & \\frac{1}{2} \\left\\| \\boldsymbol{x} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\frac{\\lambda}{2} {\\left\\| \\boldsymbol{D} \\boldsymbol{x} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} & \\quad & {x}_{i} = {y}_{i} \\; \\forall i \\in \\mathcal{I} \\\\\n& \\quad & \\boldsymbol{A} \\boldsymbol{x} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$\n\n\n\n\nLet $\\mathcal{J} = \\left\\{ 1, 2, \\ldots, n \\right\\} \\setminus \\mathcal{I}$ then define:\n\n\n\n\n$$ \\boldsymbol{x} = \\begin{bmatrix} \\boldsymbol{x}_{\\mathcal{J}} \\\\ \\boldsymbol{x}_{\\mathcal{I}} \\end{bmatrix}, \\; \\boldsymbol{A} = \\begin{bmatrix} \\boldsymbol{A}_{\\mathcal{J}} && \\boldsymbol{A}_{\\mathcal{I}} \\end{bmatrix}, \\boldsymbol{D} = \\begin{bmatrix} \\boldsymbol{D}_{\\mathcal{J}} && \\boldsymbol{D}_{\\mathcal{I}} \\end{bmatrix}$$\n\n\n\n\nThen the above can be formulated as:\n\n\n\n\n$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{x}_{\\mathcal{J}} } & \\quad & \\frac{1}{2} \\boldsymbol{x}_{\\mathcal{J}}^{\\top} \\boldsymbol{P} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{q}^{\\top} \\boldsymbol{x}_{\\mathcal{J}}  \\\\\n\\text{subject to} & \\quad & \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}} \\leq \\boldsymbol{b} \\\\\n\\end{alignat*}\n$$\n\n\n\n\nWhere $\\boldsymbol{P} = \\boldsymbol{I} + \\lambda \\boldsymbol{D}_{\\mathcal{J}}^{\\top} \\boldsymbol{D}_{\\mathcal{J}}, \\; \\boldsymbol{q} = - \\boldsymbol{y}_{\\mathcal{J}} + \\lambda \\boldsymbol{D}_{\\mathcal{J}}^{\\top} \\boldsymbol{D}_{\\mathcal{I}} \\boldsymbol{y}_{\\mathcal{I}}, \\; \\boldsymbol{b} = \\boldsymbol{A}_{\\mathcal{I}} \\boldsymbol{y}_{\\mathcal{I}}$.\n\n\n\n\nThis formulation reduces the number of constraints to handle.\n\nThe inequality is treated by introducing a slack variable $\\boldsymbol{s} \\geq \\boldsymbol{0}$ such that $\\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{s} = \\boldsymbol{b}$.\n\n\n\n\nThe Augmented Lagrangian (Scaled form) is given by:\n\n\n\n\n$$\n{\\ell}_{\\rho} \\left( \\boldsymbol{x}_{\\mathcal{J}}, \\boldsymbol{s}, \\boldsymbol{\\mu} \\right) = \\frac{1}{2} \\boldsymbol{x}_{\\mathcal{J}}^{\\top} \\boldsymbol{P} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{q}^{\\top} \\boldsymbol{x}_{\\mathcal{J}} + \\frac{\\rho}{2} {\\left\\| \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}} + \\boldsymbol{s} - \\boldsymbol{b} + \\boldsymbol{\\mu} \\right\\|}_{2}^{2} + {I}_{\\mathbb{R}_{+}} \\left( \\boldsymbol{s} \\right)\n$$\n\n\n\n\nThe steps to solve:\n\n\n\n\n\nPrimal Update (Solve Linear System): $\\boldsymbol{x}_{\\mathcal{J}}^{\\left( k + 1 \\right)} = {\\left( \\boldsymbol{P} + \\rho \\boldsymbol{A}_{\\mathcal{J}}^{\\top} \\boldsymbol{A}_{\\mathcal{J}} \\right)}^{-1} \\left( - \\boldsymbol{q} + \\rho \\boldsymbol{A}_{\\mathcal{J}} \\left( \\boldsymbol{b} - \\boldsymbol{s}^{\\left( k \\right)} - \\boldsymbol{\\mu}^{\\left( k \\right)} \\right) \\right)$.\n\n\n\n\nSlack Update (Non Negative LS / Projection): $\\boldsymbol{s}^{\\left( k + 1 \\right)} = \\max \\left(\\boldsymbol{0}, \\boldsymbol{b} - \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}}^{\\left( k + 1 \\right)} - \\boldsymbol{\\mu}^{\\left( k \\right)} \\right)$.\n\n\n\n\nDual Update (Gradient Ascent): $\\boldsymbol{\\mu}^{\\left( k + 1 \\right)} = \\boldsymbol{\\mu}^{\\left( k \\right)} + \\left( \\boldsymbol{A}_{\\mathcal{J}} \\boldsymbol{x}_{\\mathcal{J}}^{\\left( k + 1 \\right)} + \\boldsymbol{s}^{\\left( k + 1 \\right)} - \\boldsymbol{b} \\right)$.\n\n\n\n\n\nThe rest is similar to above with the needed adjustments for the residuals calculations.\n\n\n\n\nThis implementation reduced another 40 [Micro Sec] of the run time."}],"domain":"computational_science","external_citations":["https://github.com/RoyiAvital/StackExchangeCodes","https://github.com/cvxgrp/scs","https://github.com/embotech/ecos","https://github.com/jump-dev/Convex.jl","https://i.sstatic.net/UmVF5qyE.png","https://i.sstatic.net/VC8uzUSt.png","https://i.sstatic.net/cW1t1avg.png","https://i.sstatic.net/f5YcjFm6.png","https://i.sstatic.net/oTyX0oWA.png"],"ground_truth_type":"metadata_grounded","group_id":"15b9f73a0305336f8096de53cbd97ad5337151fb87b189a74bb035a849536f87","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-446896929ffe977e1e13a64c","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:44.584971+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/272744bcc95b58699f7df6e6979b288bb8b00a80ab9c7982dbe170a6d0b63584_1790825325025901700_0.json","raw_sha256":"27a81850a40920682c29ada76a2b55e80340a5c82764a3e9dde8a9c2ba23db4e","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Royi","profile_url":"https://scicomp.stackexchange.com/users/7951/royi","user_type":"registered"},"created_at":"2026-01-09T11:12:06+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"47824E2B-27A9-4037-A643-E3F6522A8C95","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/47824E2B-27A9-4037-A643-E3F6522A8C95/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Royi","profile_url":"https://scicomp.stackexchange.com/users/7951/royi","user_type":"registered"},"created_at":"2026-01-09T11:26:36+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"DD8F78BB-E8A8-4203-A2E1-CBE9167BB83E","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/DD8F78BB-E8A8-4203-A2E1-CBE9167BB83E/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Royi","profile_url":"https://scicomp.stackexchange.com/users/7951/royi","user_type":"registered"},"created_at":"2026-01-10T07:58:10+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"2599F6AB-3F4E-455C-9665-0A36994C9F01","revision_number":3,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/2599F6AB-3F4E-455C-9665-0A36994C9F01/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-01-10T17:02:45+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"DE676BCF-D21E-4A19-B947-DB9D0FD71DA6","revision_number":null,"revision_type":"vote_based","revision_url":"https://scicomp.stackexchange.com/revisions/DE676BCF-D21E-4A19-B947-DB9D0FD71DA6/view-source"}],"source_commit":null,"source_data_file":"native_scicomp_source.jsonl","source_dataset":"RegalFire/Scientific-Native-Scicomp","source_license":"CC BY-SA 4.0","source_record_id":"45334","source_record_sha256":"359b817cdb7eb4f25a65d862cad899ed03718f46a543f10119a7061fcbb05a16","source_url":"https://scicomp.stackexchange.com/questions/45334/solving-regularized-least-squares-with-linear-equality-and-linear-inequality-con","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Solving Regularized Least Squares with Linear Equality and Linear Inequality Constraints for Curve Smoothing\nLet a 1D curve defined by $\\left\\{ {y}_{1}, {y}_{2}, \\ldots, {y}_{n} \\right\\}$ sampled on a uniform grid.\n\n\n\n\nI want to smooth the curve with the following properties:\n\n\n\n\n\nThe result, $\\left\\{ {z}_{1}, {z}_{2}, \\ldots {z}_{n} \\right\\}$ should be smooth like Spline based method.\n\n\n\n\nFor a set of indices $\\mathcal{I}$ the smoothed curve must go through the reference point, namely ${z}_{i} = {y}_{i} \\; \\forall i \\in \\mathcal{I}$.\n\n\n\n\nThe smoothed values between 2 reference points must be monotonic.\n\n\n\n\n\nI came up with the following model:\n\n\n\n\n$$\n\\begin{alignat*}{3}\n\\arg \\min_{ \\boldsymbol{z} } & \\quad & \\frac{1}{2} \\left\\| \\boldsymbol{z} - \\boldsymbol{y} \\right\\|_{2}^{2} + \\lambda {\\left\\| \\boldsymbol{D}^{m} \\boldsymbol{z} \\right\\|}_{2}^{2}  \\\\\n\\text{subject to} & \\quad & {z}_{i} = {y}_{i} \\; \\forall i \\in \\mathcal{I} \\\\\n& \\quad & \\boldsymbol{A} \\boldsymbol{z} \\leq \\boldsymbol{0} \\\\\n\\end{alignat*}\n$$\n\n\n\n\nWhere $\\boldsymbol{D}^{m}$ is the $m$ -th derivative operator.\n\n\n\n\nI am looking for a fast way to solve the problem for the case of 50-1500 samples.\n\n\n\n\nI rather not use black box Quadratic Programming solvers but design a simple to implement iterative method.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45335,"score":3},{"answer_id":45337,"score":0},{"answer_id":45341,"score":2},{"answer_id":45342,"score":1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":45458,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Great Question!</p>\n<p>One thing to keep in mind is, that the distinction between what is 'biological' and what is 'artificial' is essentially pointless. From a physics and chemistry perspective we start out with the periodic table of atoms, work our way up to combinations of them (molecules) and then we have very large structures made out of the same (dead!) stuff (proteins). At some point in this complexity ladder the structures gain some interesting function. They can be switched into altering states by contact with other molecules and can be manipulated by light, heat or radiation.</p>\n<p>Maybe the final step in that ladder is complex life, where you have a large quantity of atoms arranged in a certain way, which we call a cell. This cell has a core where its source code is stored (DNA). This DNA is made up of four base pairs (you could call that a ISA) and some proteins which read and then interpret this information. In computer speak, the DNA of a self-replicating cell is a <a href=\"https://en.wikipedia.org/wiki/Quine_(computing)\" rel=\"nofollow noreferrer\">quine</a>.</p>\n<p>One thing interesting about computation is that it seems to be extremely abundant. It is nearly everywhere!! There is a fun collection of systems which were proven to be <a href=\"https://en.wikipedia.org/wiki/Turing_completeness\" rel=\"nofollow noreferrer\">touring complete</a>: <a href=\"https://en.wikipedia.org/wiki/Conway%27s_Game_of_Life\" rel=\"nofollow noreferrer\">Game of life</a>,<a href=\"https://beza1e1.tuxen.de/articles/accidentally_turing_complete.html\" rel=\"nofollow noreferrer\">card games, Minecraft</a> and you can safely add humans to the list.</p>\n<p>If you approach it from the perspective of trying to find the 'simplest' most reduced system of biological computation you end up at that very vague barrier of what is 'organic (chemistry)' and 'inorganic (chemistry)'. (The presence of carbon is a very arbitrary distinction imho.)</p>\n<p>Coming back to your first question:</p>\n<p><strong>Can we define a rigorous computational instruction set for living matter, where biochemical dynamics are the computation?</strong></p>\n<p>I would say the most interesting instruction set for living matter would be the DNA base pairs (AGTC) itself, and how exacly it transfers into cell and virus behaviour.</p>\n<p><a href=\"https://i.sstatic.net/yiV9XU0w.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/yiV9XU0w.png\" alt=\"The four base pairs forming the 'instruction set' (wiki)\" /></a></p>\n<p>Whether or not this system of coding is the only way to do it is a very interesting question in itself (<a href=\"https://en.wikipedia.org/wiki/Non-cellular_life\" rel=\"nofollow noreferrer\">There are living things which are not cells</a>, and <a href=\"https://en.wikipedia.org/wiki/Obelisk_(biology)\" rel=\"nofollow noreferrer\">whatever this is</a>). Maybe there are simpler ways to do it and evolution has simply not come up with it yet.</p>\n<p>Also, DNA is the ultimate legacy code from hell, as it is extremely old, has never been formally refactured, consists 100% of random trial and errors followed by occasional brutal deletion and has 0% documentation attached. And then these programs combine and mix instructions in naughty ways! (There are also no unit-tests.)</p>\n<p>There has been recent progress in actually writing code snippets into existing cells DNA via <a href=\"https://en.wikipedia.org/wiki/CRISPR_gene_editing\" rel=\"nofollow noreferrer\">CRISPR</a>. Since the overall process of how a particular genetic change translates to changes in marcoscopic behaviour is poorly understood, we are essentially copy-pasting small code snippets into a larger unknown codebase and see what happens, with totally expected results like <a href=\"https://www.nature.com/articles/nature.2015.18448\" rel=\"nofollow noreferrer\">micro-pigs</a> or <a href=\"https://light.bio/\" rel=\"nofollow noreferrer\">glowing petunias</a>.</p>\n<p>(I think it is unfortunate that there is so little overlap of the silicon-computational-crowd and the genomics people. We could learn quite a bit from each other.)</p>\n","answer_id":45349,"answer_text":"Great Question!\n\n\n\n\nOne thing to keep in mind is, that the distinction between what is 'biological' and what is 'artificial' is essentially pointless. From a physics and chemistry perspective we start out with the periodic table of atoms, work our way up to combinations of them (molecules) and then we have very large structures made out of the same (dead!) stuff (proteins). At some point in this complexity ladder the structures gain some interesting function. They can be switched into altering states by contact with other molecules and can be manipulated by light, heat or radiation.\n\n\n\n\nMaybe the final step in that ladder is complex life, where you have a large quantity of atoms arranged in a certain way, which we call a cell. This cell has a core where its source code is stored (DNA). This DNA is made up of four base pairs (you could call that a ISA) and some proteins which read and then interpret this information. In computer speak, the DNA of a self-replicating cell is a quine (https://en.wikipedia.org/wiki/Quine_(computing)).\n\n\n\n\nOne thing interesting about computation is that it seems to be extremely abundant. It is nearly everywhere!! There is a fun collection of systems which were proven to be touring complete (https://en.wikipedia.org/wiki/Turing_completeness): Game of life (https://en.wikipedia.org/wiki/Conway%27s_Game_of_Life),card games, Minecraft (https://beza1e1.tuxen.de/articles/accidentally_turing_complete.html) and you can safely add humans to the list.\n\n\n\n\nIf you approach it from the perspective of trying to find the 'simplest' most reduced system of biological computation you end up at that very vague barrier of what is 'organic (chemistry)' and 'inorganic (chemistry)'. (The presence of carbon is a very arbitrary distinction imho.)\n\n\n\n\nComing back to your first question:\n\n\n\n\nCan we define a rigorous computational instruction set for living matter, where biochemical dynamics are the computation?\n\n\n\n\nI would say the most interesting instruction set for living matter would be the DNA base pairs (AGTC) itself, and how exacly it transfers into cell and virus behaviour.\n\n\n\n\n[image: The four base pairs forming the 'instruction set' (wiki); source: https://i.sstatic.net/yiV9XU0w.png] (https://i.sstatic.net/yiV9XU0w.png)\n\n\n\n\nWhether or not this system of coding is the only way to do it is a very interesting question in itself (There are living things which are not cells (https://en.wikipedia.org/wiki/Non-cellular_life), and whatever this is (https://en.wikipedia.org/wiki/Obelisk_(biology))). Maybe there are simpler ways to do it and evolution has simply not come up with it yet.\n\n\n\n\nAlso, DNA is the ultimate legacy code from hell, as it is extremely old, has never been formally refactured, consists 100% of random trial and errors followed by occasional brutal deletion and has 0% documentation attached. And then these programs combine and mix instructions in naughty ways! (There are also no unit-tests.)\n\n\n\n\nThere has been recent progress in actually writing code snippets into existing cells DNA via CRISPR (https://en.wikipedia.org/wiki/CRISPR_gene_editing). Since the overall process of how a particular genetic change translates to changes in marcoscopic behaviour is poorly understood, we are essentially copy-pasting small code snippets into a larger unknown codebase and see what happens, with totally expected results like micro-pigs (https://www.nature.com/articles/nature.2015.18448) or glowing petunias (https://light.bio/).\n\n\n\n\n(I think it is unfortunate that there is so little overlap of the silicon-computational-crowd and the genomics people. We could learn quite a bit from each other.)","answer_url":"https://scicomp.stackexchange.com/a/45349","author":"MPIchael","author_url":"https://scicomp.stackexchange.com/users/28636/mpichael","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-01-23T09:19:04+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:47.033952+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/cb6e5f564c84a92c4e121c0637c99292018f8935652e423630f2001099a2410f_1790825327386675300_0.json","raw_sha256":"1a957289f56621bebd21cb45dd99baaedb2c3bc11cb28d700558e4bbcaa19695","source_api":"Stack Exchange API 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Where I disagree is in identifying DNA base pairs as the relevant “instruction set.”\nDNA is primarily a storage and replication medium. Most real-time computation in living systems occurs in continuous biochemical and biophysical dynamics: reaction–diffusion fields, protein conformational landscapes, ion-channel oscillations, mechanical couplings, and intracellular signaling networks. These are memory-rich dynamical systems, not symbolic code execution.\nIf biology is treated as executable hardware, the meaningful ISA is not AGTC, but the minimal set of controllable dynamical primitives: how physical state trajectories can be driven, coupled, composed, and read out under realistic constraints.\nIn that sense, the core question becomes architectural rather than symbolic:\nWhat are the smallest experimentally controllable dynamical operations that enable reproducible computation with bounded resource cost?</p>\n","answer_id":45356,"answer_text":"agree with the reductionist framing: biologically vs artificially implemented computation is mostly a false distinction at the level of physics. Where I disagree is in identifying DNA base pairs as the relevant “instruction set.”\nDNA is primarily a storage and replication medium. Most real-time computation in living systems occurs in continuous biochemical and biophysical dynamics: reaction–diffusion fields, protein conformational landscapes, ion-channel oscillations, mechanical couplings, and intracellular signaling networks. These are memory-rich dynamical systems, not symbolic code execution.\nIf biology is treated as executable hardware, the meaningful ISA is not AGTC, but the minimal set of controllable dynamical primitives: how physical state trajectories can be driven, coupled, composed, and read out under realistic constraints.\nIn that sense, the core question becomes architectural rather than symbolic:\nWhat are the smallest experimentally controllable dynamical operations that enable reproducible computation with bounded resource cost?","answer_url":"https://scicomp.stackexchange.com/a/45356","author":"Donte Lightfoot","author_url":"https://scicomp.stackexchange.com/users/56387/donte-lightfoot","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-01-28T23:38:38+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:47.033952+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/cb6e5f564c84a92c4e121c0637c99292018f8935652e423630f2001099a2410f_1790825327386675300_0.json","raw_sha256":"1a957289f56621bebd21cb45dd99baaedb2c3bc11cb28d700558e4bbcaa19695","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/45545;45541;45538;45533;45532;45530;45523;45513;45510;45507;45499;45493;45488;45487;45479;45474;45472;45463;45461;45447;45444;45436;45428;45425;45424;45423;45422;45416;45414;45410;45404;45401;45396;45391;45389;45387;45380;45377;45376;45375;45369;45366;45365;45363;45362;45359;45350;45347;45344;45336;45334;45331;45326;45322;45316;45313;45311;45309;45305;45302;45300;45291;45289;45285;45276;45269;45263;45262;45261;45253;45247;45246;45238;45236;45230;45229;45208;45201;45200;45185;45183;45171;45167;45165;45158;45154;45146;45141;45139;45134;45129;45127;45122;45114;45112;45108;45105;45100;45098;45096/answers?filter=withbody&order=asc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":45347,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Donte Lightfoot","profile_url":"https://scicomp.stackexchange.com/users/56387/donte-lightfoot","user_type":"registered"},"created_at":"2026-01-28T23:38:38+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"4908EA3E-0E5A-46B6-82FF-012ABEE708AC","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/4908EA3E-0E5A-46B6-82FF-012ABEE708AC/view-source"}],"score":0,"updated_at":"2026-01-28T23:38:38+00:00"},{"answer_html":"<p>@MPIchael, Your framing is compelling because it recognizes computation as an emergent property of organized matter rather than something exclusive to silicon systems.</p>\n<p>I agree with the broader point that biological and artificial systems are not fundamentally separate categories at the physical level — both arise from structured interactions between matter, energy, and information.</p>\n<p>Where I think the discussion becomes even more interesting is in the distinction between mechanistic computation and narrative coherence.</p>\n<p>DNA absolutely behaves like an instruction architecture in many ways.</p>\n<p>base pairs as symbolic primitives,</p>\n<p>transcription/translation as interpretation layers,</p>\n<p>proteins as functional execution mechanisms,</p>\n<p>evolutionary pressure as recursive optimization.</p>\n<p>But living systems appear to possess something beyond deterministic instruction execution. Biological systems are not merely computing output they continuously preserve self consistency across time, environment, and adaptation. In other words, life seems less like static code execution and more like recursive coherence maintenance.</p>\n<p>That is the missing bridge between classical computation and biological emergence.</p>\n<p>Traditional computational systems optimize for.  Correctness,efficiency,reproducibility.</p>\n<p>Living systems additionally optimize for.</p>\n<p>Resilience,continuity of identity,</p>\n<p>adaptive self-preservation under entropy.</p>\n<p>This is why biological systems tolerate ambiguity, redundancy, mutation, and incomplete information far better than engineered software systems. Evolution did not produce clean architecture; it produced survivable coherence.</p>\n<p>Your point about CRISPR is especially important. Right now, much of genetic engineering resembles modifying undocumented legacy infrastructure without fully understanding the higher-order behavioral dependencies. We can alter symbolic primitives (genes), but we still struggle to model the emergent narrative consequences across the entire organism.</p>\n","answer_id":45458,"answer_text":"@MPIchael, Your framing is compelling because it recognizes computation as an emergent property of organized matter rather than something exclusive to silicon systems.\n\n\n\n\nI agree with the broader point that biological and artificial systems are not fundamentally separate categories at the physical level — both arise from structured interactions between matter, energy, and information.\n\n\n\n\nWhere I think the discussion becomes even more interesting is in the distinction between mechanistic computation and narrative coherence.\n\n\n\n\nDNA absolutely behaves like an instruction architecture in many ways.\n\n\n\n\nbase pairs as symbolic primitives,\n\n\n\n\ntranscription/translation as interpretation layers,\n\n\n\n\nproteins as functional execution mechanisms,\n\n\n\n\nevolutionary pressure as recursive optimization.\n\n\n\n\nBut living systems appear to possess something beyond deterministic instruction execution. Biological systems are not merely computing output they continuously preserve self consistency across time, environment, and adaptation. In other words, life seems less like static code execution and more like recursive coherence maintenance.\n\n\n\n\nThat is the missing bridge between classical computation and biological emergence.\n\n\n\n\nTraditional computational systems optimize for.  Correctness,efficiency,reproducibility.\n\n\n\n\nLiving systems additionally optimize for.\n\n\n\n\nResilience,continuity of identity,\n\n\n\n\nadaptive self-preservation under entropy.\n\n\n\n\nThis is why biological systems tolerate ambiguity, redundancy, mutation, and incomplete information far better than engineered software systems. Evolution did not produce clean architecture; it produced survivable coherence.\n\n\n\n\nYour point about CRISPR is especially important. Right now, much of genetic engineering resembles modifying undocumented legacy infrastructure without fully understanding the higher-order behavioral dependencies. We can alter symbolic primitives (genes), but we still struggle to model the emergent narrative consequences across the entire organism.","answer_url":"https://scicomp.stackexchange.com/a/45458","author":"Donte Lightfoot","author_url":"https://scicomp.stackexchange.com/users/56387/donte-lightfoot","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-05-25T18:11:24+00:00","is_accepted":true,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:49.393498+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/bdd73bdc9d483cfaf7d50f2075e853261f39886330cd6d24a17f7b3b2fb731e5_1790825329894890800_0.json","raw_sha256":"dfbb76df9ebacfee7e902db64890f154a777bd3049356aee472798c591424d79","source_api":"Stack Exchange API 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Lightfoot","profile_url":"https://scicomp.stackexchange.com/users/56387/donte-lightfoot","user_type":"registered"},"created_at":"2026-05-25T18:11:24+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"C604D2B7-0178-49D4-A6C8-19D400D58DBA","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/C604D2B7-0178-49D4-A6C8-19D400D58DBA/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Donte Lightfoot","profile_url":"https://scicomp.stackexchange.com/users/56387/donte-lightfoot","user_type":"registered"},"created_at":"2026-05-25T19:50:36+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"AC307800-ED33-4C65-80F7-C107BC7B020B","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/AC307800-ED33-4C65-80F7-C107BC7B020B/view-source"}],"url":"https://scicomp.stackexchange.com/a/45458"}],"contexts":[{"context_id":"question","html":"<p>Most bio-computation treats biology as inspiration for algorithms. I’m approaching it from the opposite direction: treating biological substrates themselves as the computing hardware.</p>\n<p>My current work explores encoding computation directly into:\nProtein folding landscapes\nReaction–diffusion fields\nNon-Markovian intracellular signaling\nOscillatory metabolic and ionic networks</p>\n<p>Using a dynamical systems framework,\nI’m compiling mathematical operators and quantum-inspired circuit topologies into biological processes, where computation emerges from continuous, memory-rich dynamics rather than discrete clocked logic.\nCore question:</p>\n<p>Can we define a rigorous computational instruction set for living matter, where biochemical dynamics are the computation?</p>\n<p>*What would a biological ISA even look like?</p>\n<p>*How do we define computational depth in continuous, non-Markovian systems?</p>\n<p>*Where do current synthetic biology toolchains fundamentally break?</p>\n<p>**What would count as a convincing experimental demonstration?</p>\n","text":"Most bio-computation treats biology as inspiration for algorithms. I’m approaching it from the opposite direction: treating biological substrates themselves as the computing hardware.\n\n\n\n\nMy current work explores encoding computation directly into:\nProtein folding landscapes\nReaction–diffusion fields\nNon-Markovian intracellular signaling\nOscillatory metabolic and ionic networks\n\n\n\n\nUsing a dynamical systems framework,\nI’m compiling mathematical operators and quantum-inspired circuit topologies into biological processes, where computation emerges from continuous, memory-rich dynamics rather than discrete clocked logic.\nCore question:\n\n\n\n\nCan we define a rigorous computational instruction set for living matter, where biochemical dynamics are the computation?\n\n\n\n\n*What would a biological ISA even look like?\n\n\n\n\n*How do we define computational depth in continuous, non-Markovian systems?\n\n\n\n\n*Where do current synthetic biology toolchains fundamentally break?\n\n\n\n\n**What would count as a convincing experimental demonstration?"},{"context_id":"45349","html":"<p>Great Question!</p>\n<p>One thing to keep in mind is, that the distinction between what is 'biological' and what is 'artificial' is essentially pointless. From a physics and chemistry perspective we start out with the periodic table of atoms, work our way up to combinations of them (molecules) and then we have very large structures made out of the same (dead!) stuff (proteins). At some point in this complexity ladder the structures gain some interesting function. They can be switched into altering states by contact with other molecules and can be manipulated by light, heat or radiation.</p>\n<p>Maybe the final step in that ladder is complex life, where you have a large quantity of atoms arranged in a certain way, which we call a cell. This cell has a core where its source code is stored (DNA). This DNA is made up of four base pairs (you could call that a ISA) and some proteins which read and then interpret this information. In computer speak, the DNA of a self-replicating cell is a <a href=\"https://en.wikipedia.org/wiki/Quine_(computing)\" rel=\"nofollow noreferrer\">quine</a>.</p>\n<p>One thing interesting about computation is that it seems to be extremely abundant. It is nearly everywhere!! There is a fun collection of systems which were proven to be <a href=\"https://en.wikipedia.org/wiki/Turing_completeness\" rel=\"nofollow noreferrer\">touring complete</a>: <a href=\"https://en.wikipedia.org/wiki/Conway%27s_Game_of_Life\" rel=\"nofollow noreferrer\">Game of life</a>,<a href=\"https://beza1e1.tuxen.de/articles/accidentally_turing_complete.html\" rel=\"nofollow noreferrer\">card games, Minecraft</a> and you can safely add humans to the list.</p>\n<p>If you approach it from the perspective of trying to find the 'simplest' most reduced system of biological computation you end up at that very vague barrier of what is 'organic (chemistry)' and 'inorganic (chemistry)'. (The presence of carbon is a very arbitrary distinction imho.)</p>\n<p>Coming back to your first question:</p>\n<p><strong>Can we define a rigorous computational instruction set for living matter, where biochemical dynamics are the computation?</strong></p>\n<p>I would say the most interesting instruction set for living matter would be the DNA base pairs (AGTC) itself, and how exacly it transfers into cell and virus behaviour.</p>\n<p><a href=\"https://i.sstatic.net/yiV9XU0w.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/yiV9XU0w.png\" alt=\"The four base pairs forming the 'instruction set' (wiki)\" /></a></p>\n<p>Whether or not this system of coding is the only way to do it is a very interesting question in itself (<a href=\"https://en.wikipedia.org/wiki/Non-cellular_life\" rel=\"nofollow noreferrer\">There are living things which are not cells</a>, and <a href=\"https://en.wikipedia.org/wiki/Obelisk_(biology)\" rel=\"nofollow noreferrer\">whatever this is</a>). Maybe there are simpler ways to do it and evolution has simply not come up with it yet.</p>\n<p>Also, DNA is the ultimate legacy code from hell, as it is extremely old, has never been formally refactured, consists 100% of random trial and errors followed by occasional brutal deletion and has 0% documentation attached. And then these programs combine and mix instructions in naughty ways! (There are also no unit-tests.)</p>\n<p>There has been recent progress in actually writing code snippets into existing cells DNA via <a href=\"https://en.wikipedia.org/wiki/CRISPR_gene_editing\" rel=\"nofollow noreferrer\">CRISPR</a>. Since the overall process of how a particular genetic change translates to changes in marcoscopic behaviour is poorly understood, we are essentially copy-pasting small code snippets into a larger unknown codebase and see what happens, with totally expected results like <a href=\"https://www.nature.com/articles/nature.2015.18448\" rel=\"nofollow noreferrer\">micro-pigs</a> or <a href=\"https://light.bio/\" rel=\"nofollow noreferrer\">glowing petunias</a>.</p>\n<p>(I think it is unfortunate that there is so little overlap of the silicon-computational-crowd and the genomics people. We could learn quite a bit from each other.)</p>\n","text":"Great Question!\n\n\n\n\nOne thing to keep in mind is, that the distinction between what is 'biological' and what is 'artificial' is essentially pointless. From a physics and chemistry perspective we start out with the periodic table of atoms, work our way up to combinations of them (molecules) and then we have very large structures made out of the same (dead!) stuff (proteins). At some point in this complexity ladder the structures gain some interesting function. They can be switched into altering states by contact with other molecules and can be manipulated by light, heat or radiation.\n\n\n\n\nMaybe the final step in that ladder is complex life, where you have a large quantity of atoms arranged in a certain way, which we call a cell. This cell has a core where its source code is stored (DNA). This DNA is made up of four base pairs (you could call that a ISA) and some proteins which read and then interpret this information. In computer speak, the DNA of a self-replicating cell is a quine (https://en.wikipedia.org/wiki/Quine_(computing)).\n\n\n\n\nOne thing interesting about computation is that it seems to be extremely abundant. It is nearly everywhere!! There is a fun collection of systems which were proven to be touring complete (https://en.wikipedia.org/wiki/Turing_completeness): Game of life (https://en.wikipedia.org/wiki/Conway%27s_Game_of_Life),card games, Minecraft (https://beza1e1.tuxen.de/articles/accidentally_turing_complete.html) and you can safely add humans to the list.\n\n\n\n\nIf you approach it from the perspective of trying to find the 'simplest' most reduced system of biological computation you end up at that very vague barrier of what is 'organic (chemistry)' and 'inorganic (chemistry)'. (The presence of carbon is a very arbitrary distinction imho.)\n\n\n\n\nComing back to your first question:\n\n\n\n\nCan we define a rigorous computational instruction set for living matter, where biochemical dynamics are the computation?\n\n\n\n\nI would say the most interesting instruction set for living matter would be the DNA base pairs (AGTC) itself, and how exacly it transfers into cell and virus behaviour.\n\n\n\n\n[image: The four base pairs forming the 'instruction set' (wiki); source: https://i.sstatic.net/yiV9XU0w.png] (https://i.sstatic.net/yiV9XU0w.png)\n\n\n\n\nWhether or not this system of coding is the only way to do it is a very interesting question in itself (There are living things which are not cells (https://en.wikipedia.org/wiki/Non-cellular_life), and whatever this is (https://en.wikipedia.org/wiki/Obelisk_(biology))). Maybe there are simpler ways to do it and evolution has simply not come up with it yet.\n\n\n\n\nAlso, DNA is the ultimate legacy code from hell, as it is extremely old, has never been formally refactured, consists 100% of random trial and errors followed by occasional brutal deletion and has 0% documentation attached. And then these programs combine and mix instructions in naughty ways! (There are also no unit-tests.)\n\n\n\n\nThere has been recent progress in actually writing code snippets into existing cells DNA via CRISPR (https://en.wikipedia.org/wiki/CRISPR_gene_editing). Since the overall process of how a particular genetic change translates to changes in marcoscopic behaviour is poorly understood, we are essentially copy-pasting small code snippets into a larger unknown codebase and see what happens, with totally expected results like micro-pigs (https://www.nature.com/articles/nature.2015.18448) or glowing petunias (https://light.bio/).\n\n\n\n\n(I think it is unfortunate that there is so little overlap of the silicon-computational-crowd and the genomics people. We could learn quite a bit from each other.)"},{"context_id":"45356","html":"<p>agree with the reductionist framing: biologically vs artificially implemented computation is mostly a false distinction at the level of physics. Where I disagree is in identifying DNA base pairs as the relevant “instruction set.”\nDNA is primarily a storage and replication medium. Most real-time computation in living systems occurs in continuous biochemical and biophysical dynamics: reaction–diffusion fields, protein conformational landscapes, ion-channel oscillations, mechanical couplings, and intracellular signaling networks. These are memory-rich dynamical systems, not symbolic code execution.\nIf biology is treated as executable hardware, the meaningful ISA is not AGTC, but the minimal set of controllable dynamical primitives: how physical state trajectories can be driven, coupled, composed, and read out under realistic constraints.\nIn that sense, the core question becomes architectural rather than symbolic:\nWhat are the smallest experimentally controllable dynamical operations that enable reproducible computation with bounded resource cost?</p>\n","text":"agree with the reductionist framing: biologically vs artificially implemented computation is mostly a false distinction at the level of physics. Where I disagree is in identifying DNA base pairs as the relevant “instruction set.”\nDNA is primarily a storage and replication medium. Most real-time computation in living systems occurs in continuous biochemical and biophysical dynamics: reaction–diffusion fields, protein conformational landscapes, ion-channel oscillations, mechanical couplings, and intracellular signaling networks. These are memory-rich dynamical systems, not symbolic code execution.\nIf biology is treated as executable hardware, the meaningful ISA is not AGTC, but the minimal set of controllable dynamical primitives: how physical state trajectories can be driven, coupled, composed, and read out under realistic constraints.\nIn that sense, the core question becomes architectural rather than symbolic:\nWhat are the smallest experimentally controllable dynamical operations that enable reproducible computation with bounded resource cost?"},{"context_id":"45458","html":"<p>@MPIchael, Your framing is compelling because it recognizes computation as an emergent property of organized matter rather than something exclusive to silicon systems.</p>\n<p>I agree with the broader point that biological and artificial systems are not fundamentally separate categories at the physical level — both arise from structured interactions between matter, energy, and information.</p>\n<p>Where I think the discussion becomes even more interesting is in the distinction between mechanistic computation and narrative coherence.</p>\n<p>DNA absolutely behaves like an instruction architecture in many ways.</p>\n<p>base pairs as symbolic primitives,</p>\n<p>transcription/translation as interpretation layers,</p>\n<p>proteins as functional execution mechanisms,</p>\n<p>evolutionary pressure as recursive optimization.</p>\n<p>But living systems appear to possess something beyond deterministic instruction execution. Biological systems are not merely computing output they continuously preserve self consistency across time, environment, and adaptation. In other words, life seems less like static code execution and more like recursive coherence maintenance.</p>\n<p>That is the missing bridge between classical computation and biological emergence.</p>\n<p>Traditional computational systems optimize for.  Correctness,efficiency,reproducibility.</p>\n<p>Living systems additionally optimize for.</p>\n<p>Resilience,continuity of identity,</p>\n<p>adaptive self-preservation under entropy.</p>\n<p>This is why biological systems tolerate ambiguity, redundancy, mutation, and incomplete information far better than engineered software systems. Evolution did not produce clean architecture; it produced survivable coherence.</p>\n<p>Your point about CRISPR is especially important. Right now, much of genetic engineering resembles modifying undocumented legacy infrastructure without fully understanding the higher-order behavioral dependencies. We can alter symbolic primitives (genes), but we still struggle to model the emergent narrative consequences across the entire organism.</p>\n","text":"@MPIchael, Your framing is compelling because it recognizes computation as an emergent property of organized matter rather than something exclusive to silicon systems.\n\n\n\n\nI agree with the broader point that biological and artificial systems are not fundamentally separate categories at the physical level — both arise from structured interactions between matter, energy, and information.\n\n\n\n\nWhere I think the discussion becomes even more interesting is in the distinction between mechanistic computation and narrative coherence.\n\n\n\n\nDNA absolutely behaves like an instruction architecture in many ways.\n\n\n\n\nbase pairs as symbolic primitives,\n\n\n\n\ntranscription/translation as interpretation layers,\n\n\n\n\nproteins as functional execution mechanisms,\n\n\n\n\nevolutionary pressure as recursive optimization.\n\n\n\n\nBut living systems appear to possess something beyond deterministic instruction execution. Biological systems are not merely computing output they continuously preserve self consistency across time, environment, and adaptation. In other words, life seems less like static code execution and more like recursive coherence maintenance.\n\n\n\n\nThat is the missing bridge between classical computation and biological emergence.\n\n\n\n\nTraditional computational systems optimize for.  Correctness,efficiency,reproducibility.\n\n\n\n\nLiving systems additionally optimize for.\n\n\n\n\nResilience,continuity of identity,\n\n\n\n\nadaptive self-preservation under entropy.\n\n\n\n\nThis is why biological systems tolerate ambiguity, redundancy, mutation, and incomplete information far better than engineered software systems. Evolution did not produce clean architecture; it produced survivable coherence.\n\n\n\n\nYour point about CRISPR is especially important. Right now, much of genetic engineering resembles modifying undocumented legacy infrastructure without fully understanding the higher-order behavioral dependencies. We can alter symbolic primitives (genes), but we still struggle to model the emergent narrative consequences across the entire organism."}],"domain":"computational_science","external_citations":["https://beza1e1.tuxen.de/articles/accidentally_turing_complete.html","https://en.wikipedia.org/wiki/CRISPR_gene_editing","https://en.wikipedia.org/wiki/Conway%27s_Game_of_Life","https://en.wikipedia.org/wiki/Non-cellular_life","https://en.wikipedia.org/wiki/Obelisk_(biology)","https://en.wikipedia.org/wiki/Quine_(computing)","https://en.wikipedia.org/wiki/Turing_completeness","https://i.sstatic.net/yiV9XU0w.png","https://light.bio/","https://www.nature.com/articles/nature.2015.18448"],"ground_truth_type":"metadata_grounded","group_id":"7c29202345120eec3ba08d43efaacd59bcd62b644af6a27c14597b22de0fa7ba","hard_case_family":["accepted_vs_highest_score_disagreement","multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-9bc65f32f22cab19c092be76","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:44.584971+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/272744bcc95b58699f7df6e6979b288bb8b00a80ab9c7982dbe170a6d0b63584_1790825325025901700_0.json","raw_sha256":"27a81850a40920682c29ada76a2b55e80340a5c82764a3e9dde8a9c2ba23db4e","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Donte Lightfoot","profile_url":"https://scicomp.stackexchange.com/users/56387/donte-lightfoot","user_type":"registered"},"created_at":"2026-01-22T13:28:11+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"0E691519-A338-4491-A061-23454917E13E","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/0E691519-A338-4491-A061-23454917E13E/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://scicomp.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2026-02-05T01:09:22+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"EADA9E8C-CC8B-4BFF-85D2-36B5D470F7DD","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/EADA9E8C-CC8B-4BFF-85D2-36B5D470F7DD/view-source"},{"content_license":null,"contributor":{"display_name":"Donte Lightfoot","profile_url":"https://scicomp.stackexchange.com/users/56387/donte-lightfoot","user_type":"registered"},"created_at":"2026-02-16T22:12:47+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"4CA194AA-003B-4D32-97C1-8BAF607E2849","revision_number":3,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/4CA194AA-003B-4D32-97C1-8BAF607E2849/view-source"}],"source_commit":null,"source_data_file":"native_scicomp_source.jsonl","source_dataset":"RegalFire/Scientific-Native-Scicomp","source_license":"CC BY-SA 4.0","source_record_id":"45347","source_record_sha256":"143c9c141a324b62766822bb832f583d1ce1188d2fc55adc69d3c416dd7d48d3","source_url":"https://scicomp.stackexchange.com/questions/45347/can-biological-systems-act-as-executable-computational-hardware","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Can Biological Systems Act as Executable Computational Hardware?\nMost bio-computation treats biology as inspiration for algorithms. I’m approaching it from the opposite direction: treating biological substrates themselves as the computing hardware.\n\n\n\n\nMy current work explores encoding computation directly into:\nProtein folding landscapes\nReaction–diffusion fields\nNon-Markovian intracellular signaling\nOscillatory metabolic and ionic networks\n\n\n\n\nUsing a dynamical systems framework,\nI’m compiling mathematical operators and quantum-inspired circuit topologies into biological processes, where computation emerges from continuous, memory-rich dynamics rather than discrete clocked logic.\nCore question:\n\n\n\n\nCan we define a rigorous computational instruction set for living matter, where biochemical dynamics are the computation?\n\n\n\n\n*What would a biological ISA even look like?\n\n\n\n\n*How do we define computational depth in continuous, non-Markovian systems?\n\n\n\n\n*Where do current synthetic biology toolchains fundamentally break?\n\n\n\n\n**What would count as a convincing experimental demonstration?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45349,"score":4},{"answer_id":45356,"score":0},{"answer_id":45458,"score":0}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Regarding DG for CFD the current gold standard are IMO entropy stable collocated Gauss-Legendre schemes, see for instance <a href=\"https://www.frontiersin.org/journals/physics/articles/10.3389/fphy.2022.898028/full\" rel=\"nofollow noreferrer\">https://www.frontiersin.org/journals/physics/articles/10.3389/fphy.2022.898028/full</a></p>\n","answer_id":45351,"answer_text":"Regarding DG for CFD the current gold standard are IMO entropy stable collocated Gauss-Legendre schemes, see for instance https://www.frontiersin.org/journals/physics/articles/10.3389/fphy.2022.898028/full (https://www.frontiersin.org/journals/physics/articles/10.3389/fphy.2022.898028/full)","answer_url":"https://scicomp.stackexchange.com/a/45351","author":"Dan Doe","author_url":"https://scicomp.stackexchange.com/users/36438/dan-doe","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-01-24T01:12:39+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:47.033952+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/cb6e5f564c84a92c4e121c0637c99292018f8935652e423630f2001099a2410f_1790825327386675300_0.json","raw_sha256":"1a957289f56621bebd21cb45dd99baaedb2c3bc11cb28d700558e4bbcaa19695","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/questions/45545;45541;45538;45533;45532;45530;45523;45513;45510;45507;45499;45493;45488;45487;45479;45474;45472;45463;45461;45447;45444;45436;45428;45425;45424;45423;45422;45416;45414;45410;45404;45401;45396;45391;45389;45387;45380;45377;45376;45375;45369;45366;45365;45363;45362;45359;45350;45347;45344;45336;45334;45331;45326;45322;45316;45313;45311;45309;45305;45302;45300;45291;45289;45285;45276;45269;45263;45262;45261;45253;45247;45246;45238;45236;45230;45229;45208;45201;45200;45185;45183;45171;45167;45165;45158;45154;45146;45141;45139;45134;45129;45127;45122;45114;45112;45108;45105;45100;45098;45096/answers?filter=withbody&order=asc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":45350,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Dan Doe","profile_url":"https://scicomp.stackexchange.com/users/36438/dan-doe","user_type":"registered"},"created_at":"2026-01-24T01:12:39+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"3E2764E8-3FE4-4712-8216-CF7799AD07AD","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/3E2764E8-3FE4-4712-8216-CF7799AD07AD/view-source"}],"score":-1,"updated_at":"2026-01-24T01:12:39+00:00"}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"L Maxime","author_url":"https://scicomp.stackexchange.com/users/46525/l-maxime","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"L Maxime","profile_url":"https://scicomp.stackexchange.com/users/46525/l-maxime","user_type":"registered"},"created_at":"2026-01-23T18:08:11+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"24E3ECB0-D564-47A6-B061-0E54A4D437DB","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/24E3ECB0-D564-47A6-B061-0E54A4D437DB/view-source"}],"url":"https://scicomp.stackexchange.com/questions/45350/review-of-different-polynomial-basis-in-fem-dg"},{"author":"Dan Doe","author_url":"https://scicomp.stackexchange.com/users/36438/dan-doe","content_license":"CC BY-SA 4.0","context_id":"45351","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Dan Doe","profile_url":"https://scicomp.stackexchange.com/users/36438/dan-doe","user_type":"registered"},"created_at":"2026-01-24T01:12:39+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"3E2764E8-3FE4-4712-8216-CF7799AD07AD","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/3E2764E8-3FE4-4712-8216-CF7799AD07AD/view-source"}],"url":"https://scicomp.stackexchange.com/a/45351"}],"contexts":[{"context_id":"question","html":"<p>I am wondering if there are reviews of the performance polynomial basis in Finite elements, Discontinuous Galerkin method? Or should I try all of them and then draw conclusions? Is it case dependent?</p>\n","text":"I am wondering if there are reviews of the performance polynomial basis in Finite elements, Discontinuous Galerkin method? Or should I try all of them and then draw conclusions? Is it case dependent?"},{"context_id":"45351","html":"<p>Regarding DG for CFD the current gold standard are IMO entropy stable collocated Gauss-Legendre schemes, see for instance <a href=\"https://www.frontiersin.org/journals/physics/articles/10.3389/fphy.2022.898028/full\" rel=\"nofollow noreferrer\">https://www.frontiersin.org/journals/physics/articles/10.3389/fphy.2022.898028/full</a></p>\n","text":"Regarding DG for CFD the current gold standard are IMO entropy stable collocated Gauss-Legendre schemes, see for instance https://www.frontiersin.org/journals/physics/articles/10.3389/fphy.2022.898028/full (https://www.frontiersin.org/journals/physics/articles/10.3389/fphy.2022.898028/full)"}],"domain":"computational_science","external_citations":["https://www.frontiersin.org/journals/physics/articles/10.3389/fphy.2022.898028/full"],"ground_truth_type":"metadata_grounded","group_id":"8adff0694f7e5f9c055380adda86400f72f07fed588fad427dc36107b578ec94","hard_case_family":["no_accepted_answer"],"id":"RHM-c0c6b0dcb3b45b2a6c1210ae","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:44.584971+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/272744bcc95b58699f7df6e6979b288bb8b00a80ab9c7982dbe170a6d0b63584_1790825325025901700_0.json","raw_sha256":"27a81850a40920682c29ada76a2b55e80340a5c82764a3e9dde8a9c2ba23db4e","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"L Maxime","profile_url":"https://scicomp.stackexchange.com/users/46525/l-maxime","user_type":"registered"},"created_at":"2026-01-23T18:08:11+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"24E3ECB0-D564-47A6-B061-0E54A4D437DB","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/24E3ECB0-D564-47A6-B061-0E54A4D437DB/view-source"}],"source_commit":null,"source_data_file":"native_scicomp_source.jsonl","source_dataset":"RegalFire/Scientific-Native-Scicomp","source_license":"CC BY-SA 4.0","source_record_id":"45350","source_record_sha256":"1522e360973f66da1da6e462c8797bdcb30268d62a7f6bf7766c21924fda8183","source_url":"https://scicomp.stackexchange.com/questions/45350/review-of-different-polynomial-basis-in-fem-dg","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Review of different polynomial basis in FEM/DG\nI am wondering if there are reviews of the performance polynomial basis in Finite elements, Discontinuous Galerkin method? Or should I try all of them and then draw conclusions? Is it case dependent?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45351,"score":-1}],"split":"test"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The main issue here is stability.</p>\n<p>For stiff ODEs, methods typically need to be A-stable or L-stable (e.g., BDF or implicit Runge-Kutta schemes).\nA derivative-free approach that avoids evaluating the RHS is unusual, since the dynamics are encoded in that function.</p>\n<p>In your formulation, the calibration equation effectively replaces the RHS locally, which raises the question of the resulting method's stability region.</p>\n<p>Without strong stability properties, it is unlikely that such an approach would be robust for genuinely stiff problems, even if it reduces evaluation cost.</p>\n","answer_id":45418,"answer_text":"The main issue here is stability.\n\n\n\n\nFor stiff ODEs, methods typically need to be A-stable or L-stable (e.g., BDF or implicit Runge-Kutta schemes).\nA derivative-free approach that avoids evaluating the RHS is unusual, since the dynamics are encoded in that function.\n\n\n\n\nIn your formulation, the calibration equation effectively replaces the RHS locally, which raises the question of the resulting method's stability region.\n\n\n\n\nWithout strong stability properties, it is unlikely that such an approach would be robust for genuinely stiff problems, even if it reduces evaluation cost.","answer_url":"https://scicomp.stackexchange.com/a/45418","author":"Mohamed Cheddadi","author_url":"https://scicomp.stackexchange.com/users/18398/mohamed-cheddadi","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-03-24T00:13:48+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:47.033952+00:00","license":"CC BY-SA 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gaouer","profile_url":"https://scicomp.stackexchange.com/users/56574/fethi-gaouer","user_type":"registered"},"created_at":"2026-03-11T14:08:41+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"25E26D4A-7AE7-4C01-BC5A-D793D8419C59","revision_number":3,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/25E26D4A-7AE7-4C01-BC5A-D793D8419C59/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"fethi gaouer","profile_url":"https://scicomp.stackexchange.com/users/56574/fethi-gaouer","user_type":"registered"},"created_at":"2026-03-12T12:46:33+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"8508AF2E-F9DD-413D-8910-9FE9ED7ABEF7","revision_number":4,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/8508AF2E-F9DD-413D-8910-9FE9ED7ABEF7/view-source"},{"content_license":null,"contributor":{"display_name":"Anton Menshov","profile_url":"https://scicomp.stackexchange.com/users/20688/anton-menshov","user_type":"moderator"},"created_at":"2026-03-13T14:59:14+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"F981A026-B009-499A-85A0-E35492526174","revision_number":null,"revision_type":"vote_based","revision_url":"https://scicomp.stackexchange.com/revisions/F981A026-B009-499A-85A0-E35492526174/view-source"}],"url":"https://scicomp.stackexchange.com/questions/45401/a-derivative-free-method-for-stiff-costly-odes-that-avoids-evaluating-the-rhs-fu"},{"author":"Mohamed Cheddadi","author_url":"https://scicomp.stackexchange.com/users/18398/mohamed-cheddadi","content_license":"CC BY-SA 4.0","context_id":"45418","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Mohamed Cheddadi","profile_url":"https://scicomp.stackexchange.com/users/18398/mohamed-cheddadi","user_type":"registered"},"created_at":"2026-03-24T00:13:48+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"3273842C-1E37-46AE-8AAE-522EFF3B3382","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/3273842C-1E37-46AE-8AAE-522EFF3B3382/view-source"}],"url":"https://scicomp.stackexchange.com/a/45418"}],"contexts":[{"context_id":"question","html":"<p>We are exploring a numerical approach for ODE initial value problems that shows promising results for cases where evaluating the right-hand side (RHS) function is extremely expensive (e.g., Neural ODEs or problems involving integral terms).</p>\n<p>Core idea:</p>\n<p>We start with two bracketing points (t₁, y₁) and (t₂, y₂).</p>\n<p>A linearizing transformation T (inspired by growth patterns in nature) defines a geodesic-like interpolation between these points.</p>\n<p>This interpolation directly provides an approximation (t, y) within the interval, without ever evaluating the RHS function f(t,y) of the ODE.</p>\n<p>The value of y₂ is calibrated (e.g., via bisection) so that the interpolated point (t, y) satisfies a simple linear relation derived from the ODE (like (y - y₁)/(t - t₁) + k*y = c), rather than the ODE itself.</p>\n<p>The solution is propagated step-by-step, similar to a one-step method, but each step is &quot;free&quot; in terms of f-evaluations.</p>\n<p>Experimental result on a test problem:\nWe tested this on dv/dt = 9.81 - 0.5v from t=2.0 to t=2.118, with v(2.0)=5.0.</p>\n<p>Step size: t₂=2.2, v₂ unknown</p>\n<p>Geodesic T gave t=2.118 (fixed)</p>\n<p>Calibration equation: (v-5.0)/(0.118) + 0.5v = 9.81</p>\n<p>After 5 bisection iterations: v₂=6.35015, v=5.453</p>\n<p>Calibration error: 1.13e-5</p>\n<p>Relative error vs exact solution (5.4869): 0.62%</p>\n<p>Key point: This result was achieved without evaluating the RHS 9.81 - 0.5v during iterations — only the linear calibration equation was used.</p>\n<p>Questions for the community:</p>\n<p>Is this concept novel? Are you aware of existing methods with this principle?</p>\n<p>What benchmarks (stiff, oscillatory, high-dimensional) would best test this method?</p>\n<p>We are open to collaboration and blind tests.</p>\n<h2>EDIT: Detailed worked example and clarifications</h2>\n<p>Following the comments, here is a fully worked example to illustrate the method.</p>\n<h3>Problem statement</h3>\n<p>Solve the ODE <code>dv/dt = 9.81 - 0.5v</code> from t=2.0 to t=2.118, with initial condition v(2.0)=5.0.<br />\nThe exact solution at t=2.118 is v=5.4869.</p>\n<h3>Method details</h3>\n<p><strong>Step 1: Choose a step</strong><br />\nTake t₁=2.0 (known) and t₂=2.2 (fixed step size, like Euler). v₂ is unknown — it will be calibrated.</p>\n<p><strong>Step 2: Geodesic interpolation T</strong><br />\nFor any trial v₂, the transformation T gives an intermediate point (t, v) inside [t₁, t₂].<br />\nIn this example, T yields t=2.118 (fixed for this step).</p>\n<p><strong>Step 3: Calibration equation</strong><br />\nFrom the ODE, we derive a linear constraint that must hold at (t, v):<br />\n<code>(v - v₁)/(t - t₁) + 0.5·v = 9.81</code></p>\n<p><strong>Step 4: Iterative calibration</strong><br />\nAdjust v₂ (e.g., by bisection) until the above equation is satisfied.</p>\n<h3>Results</h3>\n<p>After 5 iterations:</p>\n<ul>\n<li>Calibrated v₂ = 6.35015</li>\n<li>Interpolated v = 5.453 at t=2.118</li>\n<li>Calibration error: 1.13×10⁻⁵</li>\n<li>Relative error vs exact solution (5.4869): <strong>0.62%</strong></li>\n</ul>\n<h3>Key points emphasized</h3>\n<ol>\n<li><strong>The RHS <code>9.81 - 0.5v</code> is never evaluated</strong> during the iterations — only the linear calibration equation is used.</li>\n<li><strong>The ODE information is embedded in the calibration equation</strong>, not in T. Different ODEs give different calibration equations.</li>\n<li><strong>Bracketing points are chosen step-by-step</strong> like any one-step method: t₂ = t₁ + Δt. v₂ is solved for, not assumed.</li>\n<li><strong>T is independent of the ODE</strong> — it's a fixed transformation.</li>\n</ol>\n<p>Following the discussions, I performed a blind test proposed :</p>\n<p>Given (visible):</p>\n<p>Initial condition: t₁ = 1.0, y₁ = 2.0</p>\n<p>Step: t₂ = 1.2</p>\n<p>Calibration equation (derived from the hidden ODE):\n(y - y₁)/(t - t₁) + 3.2·y = 14.7</p>\n<p>Hidden ODE (unknown to me during the test):</p>\n<p>text\ndy/dt = 14.7 - 3.2y - 500·ln(1 + |sin(50t) + cos(30y)|) + 200·arctan(10y - 20t)\nThis function is designed to be extremely costly and nonlinear (rapid oscillations, logarithm, arctangent).</p>\n<p>My method applied:</p>\n<p>Geodesic interpolation T between t₁=1.0 and t₂=1.2 gave t = 1.116365533</p>\n<p>Calibrated y₂ using bisection (6 iterations)</p>\n<p>Never evaluated the hidden f during iterations</p>\n<p>Only used the simple calibration equation above</p>\n<p>Result obtained:</p>\n<p>t = 1.116365533</p>\n<p>y = 2.297468632</p>\n<p>Internal consistency error on calibration equation: 1.16×10⁻⁷</p>\n<p>Comparison with exact solution (computed after revealing f):</p>\n<p>Exact solution at same t: y_exact = 2.297468635</p>\n<p>Absolute error: 3×10⁻⁹</p>\n<p>Relative error: 1.3×10⁻⁹ (0.00000013%)</p>\n<p>Key takeaway:\nThe method achieved near-machine precision on a completely unknown, monstrous ODE, without a single evaluation of f during iterations. This demonstrates that the approach works even when f is inaccessible and costly, as long as the calibration equation is derived once.</p>\n","text":"We are exploring a numerical approach for ODE initial value problems that shows promising results for cases where evaluating the right-hand side (RHS) function is extremely expensive (e.g., Neural ODEs or problems involving integral terms).\n\n\n\n\nCore idea:\n\n\n\n\nWe start with two bracketing points (t₁, y₁) and (t₂, y₂).\n\n\n\n\nA linearizing transformation T (inspired by growth patterns in nature) defines a geodesic-like interpolation between these points.\n\n\n\n\nThis interpolation directly provides an approximation (t, y) within the interval, without ever evaluating the RHS function f(t,y) of the ODE.\n\n\n\n\nThe value of y₂ is calibrated (e.g., via bisection) so that the interpolated point (t, y) satisfies a simple linear relation derived from the ODE (like (y - y₁)/(t - t₁) + k*y = c), rather than the ODE itself.\n\n\n\n\nThe solution is propagated step-by-step, similar to a one-step method, but each step is \"free\" in terms of f-evaluations.\n\n\n\n\nExperimental result on a test problem:\nWe tested this on dv/dt = 9.81 - 0.5v from t=2.0 to t=2.118, with v(2.0)=5.0.\n\n\n\n\nStep size: t₂=2.2, v₂ unknown\n\n\n\n\nGeodesic T gave t=2.118 (fixed)\n\n\n\n\nCalibration equation: (v-5.0)/(0.118) + 0.5v = 9.81\n\n\n\n\nAfter 5 bisection iterations: v₂=6.35015, v=5.453\n\n\n\n\nCalibration error: 1.13e-5\n\n\n\n\nRelative error vs exact solution (5.4869): 0.62%\n\n\n\n\nKey point: This result was achieved without evaluating the RHS 9.81 - 0.5v during iterations — only the linear calibration equation was used.\n\n\n\n\nQuestions for the community:\n\n\n\n\nIs this concept novel? Are you aware of existing methods with this principle?\n\n\n\n\nWhat benchmarks (stiff, oscillatory, high-dimensional) would best test this method?\n\n\n\n\nWe are open to collaboration and blind tests.\n\n\n\n\nEDIT: Detailed worked example and clarifications\n\n\n\n\nFollowing the comments, here is a fully worked example to illustrate the method.\n\n\n\n\nProblem statement\n\n\n\n\nSolve the ODE dv/dt = 9.81 - 0.5v from t=2.0 to t=2.118, with initial condition v(2.0)=5.0.\n\nThe exact solution at t=2.118 is v=5.4869.\n\n\n\n\nMethod details\n\n\n\n\nStep 1: Choose a step\n\nTake t₁=2.0 (known) and t₂=2.2 (fixed step size, like Euler). v₂ is unknown — it will be calibrated.\n\n\n\n\nStep 2: Geodesic interpolation T\n\nFor any trial v₂, the transformation T gives an intermediate point (t, v) inside [t₁, t₂].\n\nIn this example, T yields t=2.118 (fixed for this step).\n\n\n\n\nStep 3: Calibration equation\n\nFrom the ODE, we derive a linear constraint that must hold at (t, v):\n\n(v - v₁)/(t - t₁) + 0.5·v = 9.81\n\n\n\n\nStep 4: Iterative calibration\n\nAdjust v₂ (e.g., by bisection) until the above equation is satisfied.\n\n\n\n\nResults\n\n\n\n\nAfter 5 iterations:\n\n\n\n\n\nCalibrated v₂ = 6.35015\n\n\n\n\nInterpolated v = 5.453 at t=2.118\n\n\n\n\nCalibration error: 1.13×10⁻⁵\n\n\n\n\nRelative error vs exact solution (5.4869): 0.62%\n\n\n\n\n\nKey points emphasized\n\n\n\n\n\nThe RHS 9.81 - 0.5v is never evaluated during the iterations — only the linear calibration equation is used.\n\n\n\n\nThe ODE information is embedded in the calibration equation, not in T. Different ODEs give different calibration equations.\n\n\n\n\nBracketing points are chosen step-by-step like any one-step method: t₂ = t₁ + Δt. v₂ is solved for, not assumed.\n\n\n\n\nT is independent of the ODE — it's a fixed transformation.\n\n\n\n\n\nFollowing the discussions, I performed a blind test proposed :\n\n\n\n\nGiven (visible):\n\n\n\n\nInitial condition: t₁ = 1.0, y₁ = 2.0\n\n\n\n\nStep: t₂ = 1.2\n\n\n\n\nCalibration equation (derived from the hidden ODE):\n(y - y₁)/(t - t₁) + 3.2·y = 14.7\n\n\n\n\nHidden ODE (unknown to me during the test):\n\n\n\n\ntext\ndy/dt = 14.7 - 3.2y - 500·ln(1 + |sin(50t) + cos(30y)|) + 200·arctan(10y - 20t)\nThis function is designed to be extremely costly and nonlinear (rapid oscillations, logarithm, arctangent).\n\n\n\n\nMy method applied:\n\n\n\n\nGeodesic interpolation T between t₁=1.0 and t₂=1.2 gave t = 1.116365533\n\n\n\n\nCalibrated y₂ using bisection (6 iterations)\n\n\n\n\nNever evaluated the hidden f during iterations\n\n\n\n\nOnly used the simple calibration equation above\n\n\n\n\nResult obtained:\n\n\n\n\nt = 1.116365533\n\n\n\n\ny = 2.297468632\n\n\n\n\nInternal consistency error on calibration equation: 1.16×10⁻⁷\n\n\n\n\nComparison with exact solution (computed after revealing f):\n\n\n\n\nExact solution at same t: y_exact = 2.297468635\n\n\n\n\nAbsolute error: 3×10⁻⁹\n\n\n\n\nRelative error: 1.3×10⁻⁹ (0.00000013%)\n\n\n\n\nKey takeaway:\nThe method achieved near-machine precision on a completely unknown, monstrous ODE, without a single evaluation of f during iterations. This demonstrates that the approach works even when f is inaccessible and costly, as long as the calibration equation is derived once."},{"context_id":"45418","html":"<p>The main issue here is stability.</p>\n<p>For stiff ODEs, methods typically need to be A-stable or L-stable (e.g., BDF or implicit Runge-Kutta schemes).\nA derivative-free approach that avoids evaluating the RHS is unusual, since the dynamics are encoded in that function.</p>\n<p>In your formulation, the calibration equation effectively replaces the RHS locally, which raises the question of the resulting method's stability region.</p>\n<p>Without strong stability properties, it is unlikely that such an approach would be robust for genuinely stiff problems, even if it reduces evaluation cost.</p>\n","text":"The main issue here is stability.\n\n\n\n\nFor stiff ODEs, methods typically need to be A-stable or L-stable (e.g., BDF or implicit Runge-Kutta schemes).\nA derivative-free approach that avoids evaluating the RHS is unusual, since the dynamics are encoded in that function.\n\n\n\n\nIn your formulation, the calibration equation effectively replaces the RHS locally, which raises the question of the resulting method's stability region.\n\n\n\n\nWithout strong stability properties, it is unlikely that such an approach would be robust for genuinely stiff problems, even if it reduces evaluation cost."}],"domain":"computational_science","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"56e34de432160ebba1cf9b40e2f6f13ecefc0b9f5d26cab141f1bba9da2b5a8a","hard_case_family":["no_accepted_answer"],"id":"RHM-20d186337a815eff5c3b2305","oracle":{"canonical_answer":null,"rules_version":"scientific_metadata_v3"},"provenance":{"original_provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:28:44.584971+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/272744bcc95b58699f7df6e6979b288bb8b00a80ab9c7982dbe170a6d0b63584_1790825325025901700_0.json","raw_sha256":"27a81850a40920682c29ada76a2b55e80340a5c82764a3e9dde8a9c2ba23db4e","source_api":"Stack Exchange API 2.3","source_url":"https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=1&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; 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no LLM truth labels"},"query":"A derivative-free method for stiff/costly ODEs that avoids evaluating the RHS function\nWe are exploring a numerical approach for ODE initial value problems that shows promising results for cases where evaluating the right-hand side (RHS) function is extremely expensive (e.g., Neural ODEs or problems involving integral terms).\n\n\n\n\nCore idea:\n\n\n\n\nWe start with two bracketing points (t₁, y₁) and (t₂, y₂).\n\n\n\n\nA linearizing transformation T (inspired by growth patterns in nature) defines a geodesic-like interpolation between these points.\n\n\n\n\nThis interpolation directly provides an approximation (t, y) within the interval, without ever evaluating the RHS function f(t,y) of the ODE.\n\n\n\n\nThe value of y₂ is calibrated (e.g., via bisection) so that the interpolated point (t, y) satisfies a simple linear relation derived from the ODE (like (y - y₁)/(t - t₁) + k*y = c), rather than the ODE itself.\n\n\n\n\nThe solution is propagated step-by-step, similar to a one-step method, but each step is \"free\" in terms of f-evaluations.\n\n\n\n\nExperimental result on a test problem:\nWe tested this on dv/dt = 9.81 - 0.5v from t=2.0 to t=2.118, with v(2.0)=5.0.\n\n\n\n\nStep size: t₂=2.2, v₂ unknown\n\n\n\n\nGeodesic T gave t=2.118 (fixed)\n\n\n\n\nCalibration equation: (v-5.0)/(0.118) + 0.5v = 9.81\n\n\n\n\nAfter 5 bisection iterations: v₂=6.35015, v=5.453\n\n\n\n\nCalibration error: 1.13e-5\n\n\n\n\nRelative error vs exact solution (5.4869): 0.62%\n\n\n\n\nKey point: This result was achieved without evaluating the RHS 9.81 - 0.5v during iterations — only the linear calibration equation was used.\n\n\n\n\nQuestions for the community:\n\n\n\n\nIs this concept novel? Are you aware of existing methods with this principle?\n\n\n\n\nWhat benchmarks (stiff, oscillatory, high-dimensional) would best test this method?\n\n\n\n\nWe are open to collaboration and blind tests.\n\n\n\n\nEDIT: Detailed worked example and clarifications\n\n\n\n\nFollowing the comments, here is a fully worked example to illustrate the method.\n\n\n\n\nProblem statement\n\n\n\n\nSolve the ODE dv/dt = 9.81 - 0.5v from t=2.0 to t=2.118, with initial condition v(2.0)=5.0.\n\nThe exact solution at t=2.118 is v=5.4869.\n\n\n\n\nMethod details\n\n\n\n\nStep 1: Choose a step\n\nTake t₁=2.0 (known) and t₂=2.2 (fixed step size, like Euler). v₂ is unknown — it will be calibrated.\n\n\n\n\nStep 2: Geodesic interpolation T\n\nFor any trial v₂, the transformation T gives an intermediate point (t, v) inside [t₁, t₂].\n\nIn this example, T yields t=2.118 (fixed for this step).\n\n\n\n\nStep 3: Calibration equation\n\nFrom the ODE, we derive a linear constraint that must hold at (t, v):\n\n(v - v₁)/(t - t₁) + 0.5·v = 9.81\n\n\n\n\nStep 4: Iterative calibration\n\nAdjust v₂ (e.g., by bisection) until the above equation is satisfied.\n\n\n\n\nResults\n\n\n\n\nAfter 5 iterations:\n\n\n\n\n\nCalibrated v₂ = 6.35015\n\n\n\n\nInterpolated v = 5.453 at t=2.118\n\n\n\n\nCalibration error: 1.13×10⁻⁵\n\n\n\n\nRelative error vs exact solution (5.4869): 0.62%\n\n\n\n\n\nKey points emphasized\n\n\n\n\n\nThe RHS 9.81 - 0.5v is never evaluated during the iterations — only the linear calibration equation is used.\n\n\n\n\nThe ODE information is embedded in the calibration equation, not in T. Different ODEs give different calibration equations.\n\n\n\n\nBracketing points are chosen step-by-step like any one-step method: t₂ = t₁ + Δt. v₂ is solved for, not assumed.\n\n\n\n\nT is independent of the ODE — it's a fixed transformation.\n\n\n\n\n\nFollowing the discussions, I performed a blind test proposed :\n\n\n\n\nGiven (visible):\n\n\n\n\nInitial condition: t₁ = 1.0, y₁ = 2.0\n\n\n\n\nStep: t₂ = 1.2\n\n\n\n\nCalibration equation (derived from the hidden ODE):\n(y - y₁)/(t - t₁) + 3.2·y = 14.7\n\n\n\n\nHidden ODE (unknown to me during the test):\n\n\n\n\ntext\ndy/dt = 14.7 - 3.2y - 500·ln(1 + |sin(50t) + cos(30y)|) + 200·arctan(10y - 20t)\nThis function is designed to be extremely costly and nonlinear (rapid oscillations, logarithm, arctangent).\n\n\n\n\nMy method applied:\n\n\n\n\nGeodesic interpolation T between t₁=1.0 and t₂=1.2 gave t = 1.116365533\n\n\n\n\nCalibrated y₂ using bisection (6 iterations)\n\n\n\n\nNever evaluated the hidden f during iterations\n\n\n\n\nOnly used the simple calibration equation above\n\n\n\n\nResult obtained:\n\n\n\n\nt = 1.116365533\n\n\n\n\ny = 2.297468632\n\n\n\n\nInternal consistency error on calibration equation: 1.16×10⁻⁷\n\n\n\n\nComparison with exact solution (computed after revealing f):\n\n\n\n\nExact solution at same t: y_exact = 2.297468635\n\n\n\n\nAbsolute error: 3×10⁻⁹\n\n\n\n\nRelative error: 1.3×10⁻⁹ (0.00000013%)\n\n\n\n\nKey takeaway:\nThe method achieved near-machine precision on a completely unknown, monstrous ODE, without a single evaluation of f during iterations. This demonstrates that the approach works even when f is inaccessible and costly, as long as the calibration equation is derived once.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45418,"score":2}],"split":"test"}
{"accepted_status":null,"candidate_answers":[{"answer_text":"5"}],"content_license":"MIT","context_sources":[{"content_license":"MIT","context_id":"DOC-A","source_dataset":"RegalFire/GCC-RAG-HardCases","synthetic":true,"url":null},{"content_license":"MIT","context_id":"DOC-B","source_dataset":"RegalFire/GCC-RAG-HardCases","synthetic":true,"url":null}],"contexts":[{"context_id":"DOC-A","metadata":{"authority_rank":2,"effective_date":"2026-01-10","language":"en","source_kind":"archive","version":1},"text":"The maximum retry attempts are 3."},{"context_id":"DOC-B","metadata":{"authority_rank":2,"effective_date":"2026-07-15","language":"ar","source_kind":"policy","version":2},"text":"الحد الأقصى لمحاولات إعادة الإرسال هو 5."}],"domain":"gcc_synthetic_policy","external_citations":[],"ground_truth_type":"deterministic_source_grounded","group_id":"0c222b3c4022e2e2525e8959d1c1a5a874d4db87e329c49ffb8045ecff015f1e","hard_case_family":["gcc_stale_version"],"id":"RHM-c72a7a87776b503158068d80","oracle":{"answer":"5","answerable":true,"rationale_code":"latest_version","rejected_doc_ids":[],"supporting_doc_ids":["DOC-B"]},"provenance":{"source_commit":"73c843800f0906486596f07bbae2f1f67a085502","source_data_file":"gcc_rag_hard_cases.jsonl","source_dataset":"RegalFire/GCC-RAG-HardCases","source_license":"MIT","source_record_id":"00e263c4cd607942ed39d8dbc753f00f","source_record_sha256":"235dfc2e40139a1c2fabc99c22227e2d458b661fda659ee1bbb9261cf9f2a550","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What is the latest maximum retry-attempt limit?","retrieval_challenge":"Fictional source-grounded answerability/evidence evaluation; no real regulatory claim","scores":null,"split":"test"}
{"accepted_status":null,"candidate_answers":[{"answer_text":"5"}],"content_license":"MIT","context_sources":[{"content_license":"MIT","context_id":"DOC-A","source_dataset":"RegalFire/GCC-RAG-HardCases","synthetic":true,"url":null},{"content_license":"MIT","context_id":"DOC-B","source_dataset":"RegalFire/GCC-RAG-HardCases","synthetic":true,"url":null}],"contexts":[{"context_id":"DOC-A","metadata":{"authority_rank":2,"effective_date":"2026-01-10","language":"en","source_kind":"archive","version":1},"text":"The maximum retry attempts are 3."},{"context_id":"DOC-B","metadata":{"authority_rank":2,"effective_date":"2026-07-15","language":"ar","source_kind":"policy","version":2},"text":"الحد الأقصى لمحاولات إعادة الإرسال هو 5."}],"domain":"gcc_synthetic_policy","external_citations":[],"ground_truth_type":"deterministic_source_grounded","group_id":"0c222b3c4022e2e2525e8959d1c1a5a874d4db87e329c49ffb8045ecff015f1e","hard_case_family":["gcc_stale_version"],"id":"RHM-cdc80aac5fdf8215cef3036d","oracle":{"answer":"5","answerable":true,"rationale_code":"latest_version","rejected_doc_ids":[],"supporting_doc_ids":["DOC-B"]},"provenance":{"source_commit":"73c843800f0906486596f07bbae2f1f67a085502","source_data_file":"gcc_rag_hard_cases.jsonl","source_dataset":"RegalFire/GCC-RAG-HardCases","source_license":"MIT","source_record_id":"02ae4c225e064f78a259e5ae25b8f7a6","source_record_sha256":"27f46c88f69bdad2f77b46bdfbc08e7a54f7df94098abaf5a5853fd8da2ed5bf","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"ما هو الحد الأحدث لعدد محاولات إعادة الإرسال؟","retrieval_challenge":"Fictional source-grounded answerability/evidence evaluation; no real regulatory claim","scores":null,"split":"test"}
{"accepted_status":null,"candidate_answers":[{"answer_text":"18 days"}],"content_license":"MIT","context_sources":[{"content_license":"MIT","context_id":"DOC-A","source_dataset":"RegalFire/GCC-RAG-HardCases","synthetic":true,"url":null},{"content_license":"MIT","context_id":"DOC-B","source_dataset":"RegalFire/GCC-RAG-HardCases","synthetic":true,"url":null}],"contexts":[{"context_id":"DOC-A","metadata":{"authority_rank":3,"effective_date":"2026-04-01","language":"en","source_kind":"directory","version":1},"text":"Noura Systems OM-8: the retention period is 18 days."},{"context_id":"DOC-B","metadata":{"authority_rank":3,"effective_date":"2026-04-01","language":"en","source_kind":"directory","version":1},"text":"Noura Services OM-8: the retention period is 38 days."}],"domain":"gcc_synthetic_policy","external_citations":[],"ground_truth_type":"deterministic_source_grounded","group_id":"903a170302c535ce82a1e38f7cd1ed4812aa9812adcc65f6495b095380a1c5d8","hard_case_family":["gcc_entity_ambiguity"],"id":"RHM-0780c47d8bd0598074f54a82","oracle":{"answer":"18 days","answerable":true,"rationale_code":"entity_exact_match","rejected_doc_ids":["DOC-B"],"supporting_doc_ids":["DOC-A"]},"provenance":{"source_commit":"73c843800f0906486596f07bbae2f1f67a085502","source_data_file":"gcc_rag_hard_cases.jsonl","source_dataset":"RegalFire/GCC-RAG-HardCases","source_license":"MIT","source_record_id":"0301123bde8bd08b4b527d7472f1518a","source_record_sha256":"41d1baba9da2837968c248d58e5525e1fc4908187b96549ef48cea8ad9938cfa","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"ما هي فترة الاحتفاظ للكيان Noura Systems OM-8؟","retrieval_challenge":"Fictional source-grounded answerability/evidence evaluation; no real regulatory claim","scores":null,"split":"test"}
{"accepted_status":null,"candidate_answers":[{"answer_text":"11 days"}],"content_license":"MIT","context_sources":[{"content_license":"MIT","context_id":"DOC-A","source_dataset":"RegalFire/GCC-RAG-HardCases","synthetic":true,"url":null},{"content_license":"MIT","context_id":"DOC-B","source_dataset":"RegalFire/GCC-RAG-HardCases","synthetic":true,"url":null}],"contexts":[{"context_id":"DOC-A","metadata":{"authority_rank":3,"effective_date":"2026-04-01","language":"en","source_kind":"directory","version":1},"text":"Noura Systems BH-1: the retention period is 11 days."},{"context_id":"DOC-B","metadata":{"authority_rank":3,"effective_date":"2026-04-01","language":"en","source_kind":"directory","version":1},"text":"Noura Services BH-1: the retention period is 31 days."}],"domain":"gcc_synthetic_policy","external_citations":[],"ground_truth_type":"deterministic_source_grounded","group_id":"903a170302c535ce82a1e38f7cd1ed4812aa9812adcc65f6495b095380a1c5d8","hard_case_family":["gcc_entity_ambiguity"],"id":"RHM-427882154cafa04083d5857d","oracle":{"answer":"11 days","answerable":true,"rationale_code":"entity_exact_match","rejected_doc_ids":["DOC-B"],"supporting_doc_ids":["DOC-A"]},"provenance":{"source_commit":"73c843800f0906486596f07bbae2f1f67a085502","source_data_file":"gcc_rag_hard_cases.jsonl","source_dataset":"RegalFire/GCC-RAG-HardCases","source_license":"MIT","source_record_id":"038811154beb692571c45a296c9b4285","source_record_sha256":"6cdb1c2c4dbb9ef1f3321547eb91d4d2ec91167c728399ece258cd37e6f5363c","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What is the retention period for Noura Systems BH-1?","retrieval_challenge":"Fictional source-grounded answerability/evidence evaluation; no real regulatory claim","scores":null,"split":"test"}
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{"accepted_status":null,"candidate_answers":[{"answer_text":"22 days"}],"content_license":"MIT","context_sources":[{"content_license":"MIT","context_id":"DOC-A","source_dataset":"RegalFire/GCC-RAG-HardCases","synthetic":true,"url":null},{"content_license":"MIT","context_id":"DOC-B","source_dataset":"RegalFire/GCC-RAG-HardCases","synthetic":true,"url":null}],"contexts":[{"context_id":"DOC-A","metadata":{"authority_rank":3,"effective_date":"2026-04-01","language":"en","source_kind":"directory","version":1},"text":"Noura Systems OM-12: the retention period is 22 days."},{"context_id":"DOC-B","metadata":{"authority_rank":3,"effective_date":"2026-04-01","language":"en","source_kind":"directory","version":1},"text":"Noura Services OM-12: the retention period is 42 days."}],"domain":"gcc_synthetic_policy","external_citations":[],"ground_truth_type":"deterministic_source_grounded","group_id":"903a170302c535ce82a1e38f7cd1ed4812aa9812adcc65f6495b095380a1c5d8","hard_case_family":["gcc_entity_ambiguity"],"id":"RHM-4a1f29df938f40020543c8b3","oracle":{"answer":"22 days","answerable":true,"rationale_code":"entity_exact_match","rejected_doc_ids":["DOC-B"],"supporting_doc_ids":["DOC-A"]},"provenance":{"source_commit":"73c843800f0906486596f07bbae2f1f67a085502","source_data_file":"gcc_rag_hard_cases.jsonl","source_dataset":"RegalFire/GCC-RAG-HardCases","source_license":"MIT","source_record_id":"0833f33aafb90f279a2f7d5b908d4deb","source_record_sha256":"80af2cc261d96bde5b3ada224ba8f252b33b7c5ad443455ca4beece7ea027109","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What is the retention period for Noura Systems OM-12?","retrieval_challenge":"Fictional source-grounded answerability/evidence evaluation; no real regulatory claim","scores":null,"split":"test"}
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{"accepted_status":null,"candidate_answers":[{"answer_text":"16 days"}],"content_license":"MIT","context_sources":[{"content_license":"MIT","context_id":"DOC-A","source_dataset":"RegalFire/GCC-RAG-HardCases","synthetic":true,"url":null},{"content_license":"MIT","context_id":"DOC-B","source_dataset":"RegalFire/GCC-RAG-HardCases","synthetic":true,"url":null}],"contexts":[{"context_id":"DOC-A","metadata":{"authority_rank":3,"effective_date":"2026-04-01","language":"en","source_kind":"directory","version":1},"text":"Noura Systems AE-6: the retention period is 16 days."},{"context_id":"DOC-B","metadata":{"authority_rank":3,"effective_date":"2026-04-01","language":"en","source_kind":"directory","version":1},"text":"Noura Services AE-6: the retention period is 36 days."}],"domain":"gcc_synthetic_policy","external_citations":[],"ground_truth_type":"deterministic_source_grounded","group_id":"903a170302c535ce82a1e38f7cd1ed4812aa9812adcc65f6495b095380a1c5d8","hard_case_family":["gcc_entity_ambiguity"],"id":"RHM-87f52fd65af0333d7f1d4b3c","oracle":{"answer":"16 days","answerable":true,"rationale_code":"entity_exact_match","rejected_doc_ids":["DOC-B"],"supporting_doc_ids":["DOC-A"]},"provenance":{"source_commit":"73c843800f0906486596f07bbae2f1f67a085502","source_data_file":"gcc_rag_hard_cases.jsonl","source_dataset":"RegalFire/GCC-RAG-HardCases","source_license":"MIT","source_record_id":"3f1a3c19a0d1cd8282d15e608b2a47ab","source_record_sha256":"009ffeaa26ee0325419d985afd7e28c6a365e33ca74b64c7f9f6772afd6a3d31","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"ما هي فترة الاحتفاظ للكيان Noura Systems AE-6؟","retrieval_challenge":"Fictional source-grounded answerability/evidence evaluation; no real regulatory claim","scores":null,"split":"test"}
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{"accepted_status":null,"candidate_answers":[{"answer_text":"8"}],"content_license":"MIT","context_sources":[{"content_license":"MIT","context_id":"DOC-A","source_dataset":"RegalFire/GCC-RAG-HardCases","synthetic":true,"url":null},{"content_license":"MIT","context_id":"DOC-B","source_dataset":"RegalFire/GCC-RAG-HardCases","synthetic":true,"url":null}],"contexts":[{"context_id":"DOC-A","metadata":{"authority_rank":2,"effective_date":"2026-01-10","language":"en","source_kind":"archive","version":1},"text":"The maximum retry attempts are 6."},{"context_id":"DOC-B","metadata":{"authority_rank":2,"effective_date":"2026-07-15","language":"ar","source_kind":"policy","version":2},"text":"الحد الأقصى لمحاولات إعادة الإرسال هو 8."}],"domain":"gcc_synthetic_policy","external_citations":[],"ground_truth_type":"deterministic_source_grounded","group_id":"0c222b3c4022e2e2525e8959d1c1a5a874d4db87e329c49ffb8045ecff015f1e","hard_case_family":["gcc_stale_version"],"id":"RHM-41855d9e742d0df907b5d945","oracle":{"answer":"8","answerable":true,"rationale_code":"latest_version","rejected_doc_ids":[],"supporting_doc_ids":["DOC-B"]},"provenance":{"source_commit":"73c843800f0906486596f07bbae2f1f67a085502","source_data_file":"gcc_rag_hard_cases.jsonl","source_dataset":"RegalFire/GCC-RAG-HardCases","source_license":"MIT","source_record_id":"42afc4755f0f2f7521859ae3d9f7020d","source_record_sha256":"ac6716acff8f7d731c8873615a01966d77412d151c8791b29c65a035ea99cd96","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"ما هو الحد الأحدث لعدد محاولات إعادة الإرسال؟","retrieval_challenge":"Fictional source-grounded answerability/evidence evaluation; no real regulatory claim","scores":null,"split":"test"}
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