{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I have never heard it being called a &quot;GC clamp&quot; but designing primers with GC near the 3' end is a standard way to make the 3' end duplex more stable, allowing for greater efficiency but possibly lower specificity. It is NOT a rule, just something to keep in mind. It seems some people interpret &quot;near the 3' end&quot; as 5 nt and others as 6 nt. I does not matter. What matters is Tm, possible secondary structures, primer dimers, too high AT content near the 3' end lowering the efficiency, too high CG content near the 3' end resulting in non–specific annealing, etc.</p>\n","answer_id":114131,"answer_text":"I have never heard it being called a \"GC clamp\" but designing primers with GC near the 3' end is a standard way to make the 3' end duplex more stable, allowing for greater efficiency but possibly lower specificity. It is NOT a rule, just something to keep in mind. It seems some people interpret \"near the 3' end\" as 5 nt and others as 6 nt. I does not matter. What matters is Tm, possible secondary structures, primer dimers, too high AT content near the 3' end lowering the efficiency, too high CG content near the 3' end resulting in non–specific annealing, etc.","answer_url":"https://biology.stackexchange.com/a/114131","author":"mmhryc","author_url":"https://biology.stackexchange.com/users/78965/mmhryc","content_license":"CC BY-SA 4.0","created_at":"2024-02-20T03:44:41+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:41.651282+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/49b81e7da29b3c5ecc961908934a60a3e3d33576f623d7db6647c4f4b3b18dba_0.json","raw_sha256":"0cb9219330a5c9d57f3e474dcdd137ab3c3ae83667c4b84bf434435a38149889","source_api":"Stack Exchange API 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BY-SA 4.0","context_id":"114131","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"mmhryc","profile_url":"https://biology.stackexchange.com/users/78965/mmhryc","user_type":"registered"},"created_at":"2024-02-20T03:44:41+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"5BF19B11-6418-4A61-9C2F-3378C722E067","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5BF19B11-6418-4A61-9C2F-3378C722E067/view-source"}],"url":"https://biology.stackexchange.com/a/114131"}],"contexts":[{"context_id":"question","html":"<p><strong>Hello there!</strong></p>\n<p>After reading different sources regarding designing of qPCR primers, I'm a little confused regarding the concept of GC clamp.</p>\n<p><strong>Can you help me by telling which of these cases below is considered a GC clamp:</strong></p>\n<p><strong>A)</strong> Any single G or C found at the last 5 nucleotides of the 3' end of a primer.</p>\n<p>or</p>\n<p><strong>B)</strong> Any single G or C found at the very last nucleotide of the 3' end of a primer.</p>\n<p>or</p>\n<p><strong>C)</strong> A couple of G or C (GG, GC, CG, or CC) found at the last 5 nucleotides of the 3' end of a primer.</p>\n<p>Thank you!</p>\n<blockquote>\n<p>Edit 1 in response to (Maximilian Press)</p>\n</blockquote>\n<ol>\n<li>Here in this book titled &quot;Real Time PCR&quot; Page 131 , based on table\n7.1 <strong>one would say that option C (couple of G or C) is the correct one</strong>\n<a href=\"https://www.google.com.eg/books/edition/Real_time_PCR/-v-U-mXWg-gC?hl=en&amp;gbpv=1&amp;dq=gc+clamp+qpcr+primer+design&amp;pg=PA131&amp;printsec=frontcover\" rel=\"nofollow noreferrer\">https://www.google.com.eg/books/edition/Real_time_PCR/-v-U-mXWg-gC?hl=en&amp;gbpv=1&amp;dq=gc+clamp+qpcr+primer+design&amp;pg=PA131&amp;printsec=frontcover</a></li>\n</ol>\n<p><a href=\"https://i.sstatic.net/Lmf4N.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/Lmf4N.jpg\" alt=\"Table 7.1 Design criteria for real-time PCR primers, SYBR® Green detection\" /></a></p>\n<ol start=\"2\">\n<li>And in the source by Steven Bradburn, PhD. which (Maximilian Press) has kindly provided\nthe author explains that any single G or C base is considered a GC\nclamp regardless of its position as long as it is in the last 5\nnucleotides of the 3' end\n<strong>which makes option A the correct one</strong></li>\n</ol>\n<p><a href=\"https://toptipbio.com/gc-clamp-pcr/\" rel=\"nofollow noreferrer\">https://toptipbio.com/gc-clamp-pcr/</a></p>\n<p><a href=\"https://i.sstatic.net/XpliR.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/XpliR.png\" alt=\"enter image description here\" /></a></p>\n<ol start=\"3\">\n<li>Yet again in this conversation the contributor (Somanna Ajjamada) said: &quot;GC clamping at 3', that is having a single G or C at the 3' end or  a couple of G/C within the last 6 bp at 3' end of primer&quot;</li>\n</ol>\n<p>Making a (couple of G or C) is considered a clamp and also a single G or C base is a clamp but only if the said single base is at the end of the 3' end and he also states that you should look at the last 6 nucleotides not 5 nucleotides as suggested by Steven Bradburn, PhD\n<strong>This makes option B correct</strong></p>\n<p><a href=\"https://biology.stackexchange.com/a/80622/76328\">https://biology.stackexchange.com/a/80622/76328</a></p>\n","text":"Hello there!\n\n\n\n\nAfter reading different sources regarding designing of qPCR primers, I'm a little confused regarding the concept of GC clamp.\n\n\n\n\nCan you help me by telling which of these cases below is considered a GC clamp:\n\n\n\n\nA) Any single G or C found at the last 5 nucleotides of the 3' end of a primer.\n\n\n\n\nor\n\n\n\n\nB) Any single G or C found at the very last nucleotide of the 3' end of a primer.\n\n\n\n\nor\n\n\n\n\nC) A couple of G or C (GG, GC, CG, or CC) found at the last 5 nucleotides of the 3' end of a primer.\n\n\n\n\nThank you!\n\n\n\n\n\n\n\nEdit 1 in response to (Maximilian Press)\n\n\n\n\n\n\n\n\nHere in this book titled \"Real Time PCR\" Page 131 , based on table\n7.1 one would say that option C (couple of G or C) is the correct one\nhttps://www.google.com.eg/books/edition/Real_time_PCR/-v-U-mXWg-gC?hl=en&gbpv=1&dq=gc+clamp+qpcr+primer+design&pg=PA131&printsec=frontcover (https://www.google.com.eg/books/edition/Real_time_PCR/-v-U-mXWg-gC?hl=en&gbpv=1&dq=gc+clamp+qpcr+primer+design&pg=PA131&printsec=frontcover)\n\n\n\n\n\n[image: Table 7.1 Design criteria for real-time PCR primers, SYBR® Green detection; source: https://i.sstatic.net/Lmf4N.jpg] (https://i.sstatic.net/Lmf4N.jpg)\n\n\n\n\n\nAnd in the source by Steven Bradburn, PhD. which (Maximilian Press) has kindly provided\nthe author explains that any single G or C base is considered a GC\nclamp regardless of its position as long as it is in the last 5\nnucleotides of the 3' end\nwhich makes option A the correct one\n\n\n\n\n\nhttps://toptipbio.com/gc-clamp-pcr/ (https://toptipbio.com/gc-clamp-pcr/)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/XpliR.png] (https://i.sstatic.net/XpliR.png)\n\n\n\n\n\nYet again in this conversation the contributor (Somanna Ajjamada) said: \"GC clamping at 3', that is having a single G or C at the 3' end or  a couple of G/C within the last 6 bp at 3' end of primer\"\n\n\n\n\n\nMaking a (couple of G or C) is considered a clamp and also a single G or C base is a clamp but only if the said single base is at the end of the 3' end and he also states that you should look at the last 6 nucleotides not 5 nucleotides as suggested by Steven Bradburn, PhD\nThis makes option B correct\n\n\n\n\nhttps://biology.stackexchange.com/a/80622/76328 (https://biology.stackexchange.com/a/80622/76328)"},{"context_id":"114131","html":"<p>I have never heard it being called a &quot;GC clamp&quot; but designing primers with GC near the 3' end is a standard way to make the 3' end duplex more stable, allowing for greater efficiency but possibly lower specificity. It is NOT a rule, just something to keep in mind. It seems some people interpret &quot;near the 3' end&quot; as 5 nt and others as 6 nt. I does not matter. What matters is Tm, possible secondary structures, primer dimers, too high AT content near the 3' end lowering the efficiency, too high CG content near the 3' end resulting in non–specific annealing, etc.</p>\n","text":"I have never heard it being called a \"GC clamp\" but designing primers with GC near the 3' end is a standard way to make the 3' end duplex more stable, allowing for greater efficiency but possibly lower specificity. It is NOT a rule, just something to keep in mind. It seems some people interpret \"near the 3' end\" as 5 nt and others as 6 nt. I does not matter. What matters is Tm, possible secondary structures, primer dimers, too high AT content near the 3' end lowering the efficiency, too high CG content near the 3' end resulting in non–specific annealing, etc."}],"domain":"biology","external_citations":["https://biology.stackexchange.com/a/80622/76328","https://i.sstatic.net/Lmf4N.jpg","https://i.sstatic.net/XpliR.png","https://toptipbio.com/gc-clamp-pcr/","https://www.google.com.eg/books/edition/Real_time_PCR/-v-U-mXWg-gC?hl=en&gbpv=1&dq=gc+clamp+qpcr+primer+design&pg=PA131&printsec=frontcover"],"ground_truth_type":"metadata_grounded","group_id":"aa7eceb5eddc20956a7fa7b58d80913c9aa7e744a08f90dcff57c5461d095ac2","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-bededdc527d8bba891a8beae","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 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4.0","contributor":{"display_name":"H001O","profile_url":"https://biology.stackexchange.com/users/76328/h001o","user_type":"registered"},"created_at":"2023-07-22T17:50:24+00:00","raw_file":"raw/codex_api_v1/fb7126698e65b75ed03bf96280ca339b40e6c365d087fc910992cbae55d5d7cc_1790824008103740000_0.json","raw_sha256":"08885036fa8ad49012e514ce869ff200275514fbc30b6de44e83baf44b0c4470","revision_guid":"AFDBEB3B-8440-4A35-A598-8FEE81D0504B","revision_number":7,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AFDBEB3B-8440-4A35-A598-8FEE81D0504B/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2024-03-21T04:03:40+00:00","raw_file":"raw/codex_api_v1/a04a0f8b9b816f605414240c86ef0796529040fa885a4b1183bd818d12b64e65_0.json","raw_sha256":"630e8bf25473aeb8900409dec408d29d2bdc2011bc3b72f26995c17452a2c689","revision_guid":"9D2F291A-C3A0-497B-8AD4-E178DB03D280","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/9D2F291A-C3A0-497B-8AD4-E178DB03D280/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":"112647","source_record_sha256":"92c372b28adb296e65e25d995322124085c5c737af1a4b38a9214788073168cd","source_url":"https://biology.stackexchange.com/questions/112647/what-should-be-considered-a-gc-clamp-in-a-qpcr-primer","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What should be considered a GC clamp in a qPCR primer?\nHello there!\n\n\n\n\nAfter reading different sources regarding designing of qPCR primers, I'm a little confused regarding the concept of GC clamp.\n\n\n\n\nCan you help me by telling which of these cases below is considered a GC clamp:\n\n\n\n\nA) Any single G or C found at the last 5 nucleotides of the 3' end of a primer.\n\n\n\n\nor\n\n\n\n\nB) Any single G or C found at the very last nucleotide of the 3' end of a primer.\n\n\n\n\nor\n\n\n\n\nC) A couple of G or C (GG, GC, CG, or CC) found at the last 5 nucleotides of the 3' end of a primer.\n\n\n\n\nThank you!\n\n\n\n\n\n\n\nEdit 1 in response to (Maximilian Press)\n\n\n\n\n\n\n\n\nHere in this book titled \"Real Time PCR\" Page 131 , based on table\n7.1 one would say that option C (couple of G or C) is the correct one\nhttps://www.google.com.eg/books/edition/Real_time_PCR/-v-U-mXWg-gC?hl=en&gbpv=1&dq=gc+clamp+qpcr+primer+design&pg=PA131&printsec=frontcover (https://www.google.com.eg/books/edition/Real_time_PCR/-v-U-mXWg-gC?hl=en&gbpv=1&dq=gc+clamp+qpcr+primer+design&pg=PA131&printsec=frontcover)\n\n\n\n\n\n[image: Table 7.1 Design criteria for real-time PCR primers, SYBR® Green detection; source: https://i.sstatic.net/Lmf4N.jpg] (https://i.sstatic.net/Lmf4N.jpg)\n\n\n\n\n\nAnd in the source by Steven Bradburn, PhD. which (Maximilian Press) has kindly provided\nthe author explains that any single G or C base is considered a GC\nclamp regardless of its position as long as it is in the last 5\nnucleotides of the 3' end\nwhich makes option A the correct one\n\n\n\n\n\nhttps://toptipbio.com/gc-clamp-pcr/ (https://toptipbio.com/gc-clamp-pcr/)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/XpliR.png] (https://i.sstatic.net/XpliR.png)\n\n\n\n\n\nYet again in this conversation the contributor (Somanna Ajjamada) said: \"GC clamping at 3', that is having a single G or C at the 3' end or  a couple of G/C within the last 6 bp at 3' end of primer\"\n\n\n\n\n\nMaking a (couple of G or C) is considered a clamp and also a single G or C base is a clamp but only if the said single base is at the end of the 3' end and he also states that you should look at the last 6 nucleotides not 5 nucleotides as suggested by Steven Bradburn, PhD\nThis makes option B correct\n\n\n\n\nhttps://biology.stackexchange.com/a/80622/76328 (https://biology.stackexchange.com/a/80622/76328)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114131,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>When you study archaeology, you dig and find everything becomes buried very fast through burrowing and overgrowth subsidence. You can find <em>a lot</em> of bones when you walk a minute away from the beaten track, and very rarely on paths, often gray and beige. Humans very often move nice skulls as trophies.</p>\n<p>Skulls provide a microclimate for moss, ants, beetles, plants, low-wind zones and snags to collect leaves. Humans like to pick them up and move them, rodents gnaw them, the jaw tumbles away, bug and bird droppings, acids and humidity dissolve them, frost cracks the pores.</p>\n<p>Plants compete for space and grow around bones and hide them. Bugs dig networks of burrows and make the soil cave in a bit, worms place middens on the sides, A hoof or a femur will be covered by wild grass in 3-5 years, a horse skull in 10-20 years.</p>\n<p>In the arctic there aren't horses, cows, deer, only seashore megafauna. Bones get snowed over. Else they are subject to freeze-thaw weathering, water stays in the pores of the bones, freezes and expands every day, and erodes them.</p>\n<p>In the forest, leaf fall and sticks accumulate 1-5cm every year, trees fall over, the soil is alive with fungus mycelia and bugs, It's also quite an acid environment. Bones would be expected to stay uncovered for less than 15-20 years.</p>\n<p>In the desert, there aren't lots of big animals, and the bones can last a very long time there, we can find awesome cadavers in regions of low biological, geological and glacial activity.</p>\n<p>Human transportation near paths\nScavenging\nAnimals hide away when they are ill\nGnawing\nMoss\nFreeze thaw\nGeological activity\nSubsidence\nGlacial activity\nSand dunes\nTrampling by other animals</p>\n","answer_id":112669,"answer_text":"When you study archaeology, you dig and find everything becomes buried very fast through burrowing and overgrowth subsidence. You can find a lot of bones when you walk a minute away from the beaten track, and very rarely on paths, often gray and beige. Humans very often move nice skulls as trophies.\n\n\n\n\nSkulls provide a microclimate for moss, ants, beetles, plants, low-wind zones and snags to collect leaves. Humans like to pick them up and move them, rodents gnaw them, the jaw tumbles away, bug and bird droppings, acids and humidity dissolve them, frost cracks the pores.\n\n\n\n\nPlants compete for space and grow around bones and hide them. Bugs dig networks of burrows and make the soil cave in a bit, worms place middens on the sides, A hoof or a femur will be covered by wild grass in 3-5 years, a horse skull in 10-20 years.\n\n\n\n\nIn the arctic there aren't horses, cows, deer, only seashore megafauna. Bones get snowed over. Else they are subject to freeze-thaw weathering, water stays in the pores of the bones, freezes and expands every day, and erodes them.\n\n\n\n\nIn the forest, leaf fall and sticks accumulate 1-5cm every year, trees fall over, the soil is alive with fungus mycelia and bugs, It's also quite an acid environment. Bones would be expected to stay uncovered for less than 15-20 years.\n\n\n\n\nIn the desert, there aren't lots of big animals, and the bones can last a very long time there, we can find awesome cadavers in regions of low biological, geological and glacial activity.\n\n\n\n\nHuman transportation near paths\nScavenging\nAnimals hide away when they are ill\nGnawing\nMoss\nFreeze thaw\nGeological activity\nSubsidence\nGlacial activity\nSand dunes\nTrampling by other animals","answer_url":"https://biology.stackexchange.com/a/112669","author":"bandybabboon","author_url":"https://biology.stackexchange.com/users/8952/bandybabboon","content_license":"CC BY-SA 4.0","created_at":"2023-07-26T10:53:22+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":112667,"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":"2023-07-26T10:53:22+00:00","raw_file":"raw/codex_api_v1/fb7126698e65b75ed03bf96280ca339b40e6c365d087fc910992cbae55d5d7cc_1790824008103740000_0.json","raw_sha256":"08885036fa8ad49012e514ce869ff200275514fbc30b6de44e83baf44b0c4470","revision_guid":"D0384004-1493-4F1A-AACF-C4A1BB8A4C96","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D0384004-1493-4F1A-AACF-C4A1BB8A4C96/view-source"},{"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":"2023-07-26T11:04:05+00:00","raw_file":"raw/codex_api_v1/fb7126698e65b75ed03bf96280ca339b40e6c365d087fc910992cbae55d5d7cc_1790824008103740000_0.json","raw_sha256":"08885036fa8ad49012e514ce869ff200275514fbc30b6de44e83baf44b0c4470","revision_guid":"7DD8D77F-5504-4199-80E3-BCF9FB83D2F3","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7DD8D77F-5504-4199-80E3-BCF9FB83D2F3/view-source"},{"content_license":null,"contributor":{"display_name":"Chris","profile_url":"https://biology.stackexchange.com/users/5144/chris","user_type":"moderator"},"created_at":"2023-07-27T08:16:51+00:00","raw_file":"raw/codex_api_v1/fb7126698e65b75ed03bf96280ca339b40e6c365d087fc910992cbae55d5d7cc_1790824008103740000_0.json","raw_sha256":"08885036fa8ad49012e514ce869ff200275514fbc30b6de44e83baf44b0c4470","revision_guid":"D0A38672-C119-4668-A6E0-5534E836F6E6","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/D0A38672-C119-4668-A6E0-5534E836F6E6/view-source"}],"score":-1},{"answer_html":"<p>Even a superficial Google search will tell you by the title of the hits you get that bones are eaten, e.g. <a href=\"https://en.wikipedia.org/wiki/Osteophagy\" rel=\"nofollow noreferrer\">my top hit</a>.</p>\n<p>Osteophagy simply means <em>bone eating</em>. I'm not sure why it applies to herbivores in particular; maybe because it seems to be strange behavior in an herbivore, whereas it's expected in a carnivore.</p>\n<p>Phosphate is crucial to life, but isn't abundant in 'edible nature' (plants, etc.). It is abundant in bone, however, and because it is crucial to growth and energy production, animals eat bones however they can. Some animals, e.g. those without teeth, will swallow small bones whole. Carnivores and capable omnivores will crush susceptible bones by chewing on them; herbivores will just grind away at them and consume the bits they can generate.</p>\n<p>From Wikipedia, a cow chewing on a bone.</p>\n<p><a href=\"https://i.sstatic.net/BXt39m.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/BXt39m.jpg\" alt=\"enter image description here\" /></a></p>\n<p>How about <a href=\"https://www.bu.edu/articles/2016/squirrel-bone-gnawing/\" rel=\"nofollow noreferrer\">a squirrel</a>?</p>\n<p><a href=\"https://i.sstatic.net/pYrJtm.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/pYrJtm.jpg\" alt=\"enter image description here\" /></a></p>\n<p>Or a <a href=\"https://www.nationalgeographic.com/animals/article/deer-eating-human-forensics-decomposition\" rel=\"nofollow noreferrer\">deer eating human bones</a>:</p>\n<p><a href=\"https://i.sstatic.net/nKTY8m.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/nKTY8m.jpg\" alt=\"enter image description here\" /></a></p>\n<p>This answer could be longer, but why go on? The answer is obvious.</p>\n<p><sub><a href=\"https://www.wildlifeact.com/blog/osteophagia-how-wild-animals-use-supplements/\" rel=\"nofollow noreferrer\">Osteophagia: How Wild Animals Use Supplements</a></sub></p>\n","answer_id":112673,"answer_text":"Even a superficial Google search will tell you by the title of the hits you get that bones are eaten, e.g. my top hit (https://en.wikipedia.org/wiki/Osteophagy).\n\n\n\n\nOsteophagy simply means bone eating. I'm not sure why it applies to herbivores in particular; maybe because it seems to be strange behavior in an herbivore, whereas it's expected in a carnivore.\n\n\n\n\nPhosphate is crucial to life, but isn't abundant in 'edible nature' (plants, etc.). It is abundant in bone, however, and because it is crucial to growth and energy production, animals eat bones however they can. Some animals, e.g. those without teeth, will swallow small bones whole. Carnivores and capable omnivores will crush susceptible bones by chewing on them; herbivores will just grind away at them and consume the bits they can generate.\n\n\n\n\nFrom Wikipedia, a cow chewing on a bone.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/BXt39m.jpg] (https://i.sstatic.net/BXt39m.jpg)\n\n\n\n\nHow about a squirrel (https://www.bu.edu/articles/2016/squirrel-bone-gnawing/)?\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/pYrJtm.jpg] (https://i.sstatic.net/pYrJtm.jpg)\n\n\n\n\nOr a deer eating human bones (https://www.nationalgeographic.com/animals/article/deer-eating-human-forensics-decomposition):\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/nKTY8m.jpg] (https://i.sstatic.net/nKTY8m.jpg)\n\n\n\n\nThis answer could be longer, but why go on? The answer is obvious.\n\n\n\n\nOsteophagia: How Wild Animals Use Supplements (https://www.wildlifeact.com/blog/osteophagia-how-wild-animals-use-supplements/)","answer_url":"https://biology.stackexchange.com/a/112673","author":"anongoodnurse","author_url":"https://biology.stackexchange.com/users/5198/anongoodnurse","content_license":"CC BY-SA 4.0","created_at":"2023-07-26T21:49:54+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":112667,"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":"2023-07-26T21:49:54+00:00","raw_file":"raw/codex_api_v1/fb7126698e65b75ed03bf96280ca339b40e6c365d087fc910992cbae55d5d7cc_1790824008103740000_0.json","raw_sha256":"08885036fa8ad49012e514ce869ff200275514fbc30b6de44e83baf44b0c4470","revision_guid":"BBD8206C-DE72-4836-A118-D1A12B4AE9F8","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/BBD8206C-DE72-4836-A118-D1A12B4AE9F8/view-source"}],"score":3},{"answer_html":"<h2>they rot, get eaten, or get weathered away. Under extremely rare circumstances they fossilize.</h2>\n<p>What you are talking about is called bone <a href=\"https://en.wikipedia.org/wiki/Taphonomy\" rel=\"nofollow noreferrer\">taphonomy</a>.</p>\n<p><a href=\"https://i.sstatic.net/sG4Sr.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/sG4Sr.png\" alt=\"enter image description here\" /></a></p>\n<p>You can do a simple experiment yourself, put hooves or bones partially buried in dirt in your yard and check on them from time to time, depending on where oyu live what happens will vary quite a lot. Paleontologist and forensic scientists have studied this a lot to understand fossil and human remains respectively.</p>\n<p>What happens to them</p>\n<ol>\n<li><p>Normal erosion processes and soft tissue decomposition break the bone in to smaller pieces. The same thing that breaks down rocks breakdown bone just faster. Physical and chemical weather all work on bone. Bone is soft and permeable as rock goes so it weathers very quickly.</p>\n</li>\n<li><p>Bacteria, insects, fungi, plant roots, or other organisms break them down and eat them. You can prevent this by drying the bone out and keeping it away from soil, (soils keeps the bone moist and makes it easy for those things to reach the bone) Bone like any organic material rots, oxygen and water make it happen faster and bigger organisms can eat them faster.</p>\n</li>\n</ol>\n<p>You can see the same thing with any organic material which is why we dry meat and fruit to preserve them. Also why we cover organic materials like leather or wood in oils to keep them dry. or cover them in poisonous chemicals just like you can do with bone, it slows down their decomposition. in really dry places or conditions with no oxygen bone can take very long to decay. A cow skull defleshed and nailed to a barn in the desert will take a very long time to decay centuries or longer, a bone left on the jungle floor wet and covered in dirt and leaf litter will be gone in months, assuming you can keep things from eating it, (bone is a high demand resource in forests where phosphorous is in high demand).</p>\n<p>Different materials decompose at different rates. Under absolutely perfect conditions the bone does not decay completely, creating a fossil. I personally have pulled unfossilized mammoth bones out of clay rich desert soil in Wyoming, the bone had all the structural strength of dry rotted wood, any handling caused bone to flake off, but it was still a complete mammoth leg bone, its decay had been severely slowed by dry, cold, anoxic conditions. We do find lots of buried bone in the right environments.</p>\n<h2>Soils is not static</h2>\n<p>If you put bone on top of soil it will not stay on top of the soil. soils turns over due to thermal, erosional, and biological forces. things get buried, see frost heaving and soil creep as examples. Soil is not static it is always on the move. Deserts in particular tend to be highly erosional, which is why we look for fossil in deserts,  new rock is constantly being exposed and destroyed.</p>\n<p>Now deserts and cold regions do have much slower rates of decay which is why you can find remains that are decades or even centuries old in such places. Bones are found in bogs and <a href=\"https://www.smithsonianmag.com/science-nature/five-fascinating-ice-age-finds-discovered-in-yukon-permafrost-180979521/\" rel=\"nofollow noreferrer\">permafrost for instance</a>.  things like sunlight, temperature, abrasion, weather and such can all breakdown bone. Also you vastly overestimate how many animals there are in such places, even if all their bones did not decay they still would not make up a noticeable portion of the topsoil. in places where the animal remains are that common they do make up a significant portion of the soil we call those coral sand beaches, where mechanically broken up animal shells make up the majority of the soil.</p>\n<p><strong>Sources about bone decomposition and diagenesis</strong></p>\n<p><a href=\"https://pubmed.ncbi.nlm.nih.gov/20646883/#:%7E:text=Abstract,or%20as%20long%20as%2030.\" rel=\"nofollow noreferrer\">https://pubmed.ncbi.nlm.nih.gov/20646883/#:~:text=Abstract,or%20as%20long%20as%2030.</a></p>\n<p><a href=\"https://www.scientificamerican.com/article/dust-to-dust/\" rel=\"nofollow noreferrer\">https://www.scientificamerican.com/article/dust-to-dust/</a></p>\n<p><a href=\"https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1061&amp;context=nebanthro\" rel=\"nofollow noreferrer\">https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1061&amp;context=nebanthro</a></p>\n<p><a href=\"https://www.jstor.org/stable/2400259\" rel=\"nofollow noreferrer\">https://www.jstor.org/stable/2400259</a></p>\n<p><a href=\"https://www.sciencedirect.com/science/article/abs/pii/S003101821630164X\" rel=\"nofollow noreferrer\">https://www.sciencedirect.com/science/article/abs/pii/S003101821630164X</a></p>\n<p><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8224596/\" rel=\"nofollow noreferrer\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8224596/</a></p>\n<p><strong>Sources about soil and erosion turnover</strong></p>\n<p><a href=\"https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/soil-movement\" rel=\"nofollow noreferrer\">https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/soil-movement</a></p>\n<p><a href=\"https://www.sciencedirect.com/science/article/abs/pii/B9780123864734000014\" rel=\"nofollow noreferrer\">https://www.sciencedirect.com/science/article/abs/pii/B9780123864734000014</a></p>\n<p><strong>Bonus</strong></p>\n<p><a href=\"https://www.scienceabc.com/humans/skeleton-mystery-dont-bones-decay-decompose.html\" rel=\"nofollow noreferrer\">Great simplified of review of decomposition.</a></p>\n","answer_id":112694,"answer_text":"they rot, get eaten, or get weathered away. Under extremely rare circumstances they fossilize.\n\n\n\n\nWhat you are talking about is called bone taphonomy (https://en.wikipedia.org/wiki/Taphonomy).\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/sG4Sr.png] (https://i.sstatic.net/sG4Sr.png)\n\n\n\n\nYou can do a simple experiment yourself, put hooves or bones partially buried in dirt in your yard and check on them from time to time, depending on where oyu live what happens will vary quite a lot. Paleontologist and forensic scientists have studied this a lot to understand fossil and human remains respectively.\n\n\n\n\nWhat happens to them\n\n\n\n\n\n\n\nNormal erosion processes and soft tissue decomposition break the bone in to smaller pieces. The same thing that breaks down rocks breakdown bone just faster. Physical and chemical weather all work on bone. Bone is soft and permeable as rock goes so it weathers very quickly.\n\n\n\n\n\n\n\n\n\nBacteria, insects, fungi, plant roots, or other organisms break them down and eat them. You can prevent this by drying the bone out and keeping it away from soil, (soils keeps the bone moist and makes it easy for those things to reach the bone) Bone like any organic material rots, oxygen and water make it happen faster and bigger organisms can eat them faster.\n\n\n\n\n\n\n\n\nYou can see the same thing with any organic material which is why we dry meat and fruit to preserve them. Also why we cover organic materials like leather or wood in oils to keep them dry. or cover them in poisonous chemicals just like you can do with bone, it slows down their decomposition. in really dry places or conditions with no oxygen bone can take very long to decay. A cow skull defleshed and nailed to a barn in the desert will take a very long time to decay centuries or longer, a bone left on the jungle floor wet and covered in dirt and leaf litter will be gone in months, assuming you can keep things from eating it, (bone is a high demand resource in forests where phosphorous is in high demand).\n\n\n\n\nDifferent materials decompose at different rates. Under absolutely perfect conditions the bone does not decay completely, creating a fossil. I personally have pulled unfossilized mammoth bones out of clay rich desert soil in Wyoming, the bone had all the structural strength of dry rotted wood, any handling caused bone to flake off, but it was still a complete mammoth leg bone, its decay had been severely slowed by dry, cold, anoxic conditions. We do find lots of buried bone in the right environments.\n\n\n\n\nSoils is not static\n\n\n\n\nIf you put bone on top of soil it will not stay on top of the soil. soils turns over due to thermal, erosional, and biological forces. things get buried, see frost heaving and soil creep as examples. Soil is not static it is always on the move. Deserts in particular tend to be highly erosional, which is why we look for fossil in deserts,  new rock is constantly being exposed and destroyed.\n\n\n\n\nNow deserts and cold regions do have much slower rates of decay which is why you can find remains that are decades or even centuries old in such places. Bones are found in bogs and permafrost for instance (https://www.smithsonianmag.com/science-nature/five-fascinating-ice-age-finds-discovered-in-yukon-permafrost-180979521/).  things like sunlight, temperature, abrasion, weather and such can all breakdown bone. Also you vastly overestimate how many animals there are in such places, even if all their bones did not decay they still would not make up a noticeable portion of the topsoil. in places where the animal remains are that common they do make up a significant portion of the soil we call those coral sand beaches, where mechanically broken up animal shells make up the majority of the soil.\n\n\n\n\nSources about bone decomposition and diagenesis\n\n\n\n\nhttps://pubmed.ncbi.nlm.nih.gov/20646883/#:~:text=Abstract,or%20as%20long%20as%2030. (https://pubmed.ncbi.nlm.nih.gov/20646883/#:%7E:text=Abstract,or%20as%20long%20as%2030.)\n\n\n\n\nhttps://www.scientificamerican.com/article/dust-to-dust/ (https://www.scientificamerican.com/article/dust-to-dust/)\n\n\n\n\nhttps://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1061&context=nebanthro (https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1061&context=nebanthro)\n\n\n\n\nhttps://www.jstor.org/stable/2400259 (https://www.jstor.org/stable/2400259)\n\n\n\n\nhttps://www.sciencedirect.com/science/article/abs/pii/S003101821630164X (https://www.sciencedirect.com/science/article/abs/pii/S003101821630164X)\n\n\n\n\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8224596/ (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8224596/)\n\n\n\n\nSources about soil and erosion turnover\n\n\n\n\nhttps://www.sciencedirect.com/topics/agricultural-and-biological-sciences/soil-movement (https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/soil-movement)\n\n\n\n\nhttps://www.sciencedirect.com/science/article/abs/pii/B9780123864734000014 (https://www.sciencedirect.com/science/article/abs/pii/B9780123864734000014)\n\n\n\n\nBonus\n\n\n\n\nGreat simplified of review of decomposition. (https://www.scienceabc.com/humans/skeleton-mystery-dont-bones-decay-decompose.html)","answer_url":"https://biology.stackexchange.com/a/112694","author":"John","author_url":"https://biology.stackexchange.com/users/28022/john","content_license":"CC BY-SA 4.0","created_at":"2023-07-29T14:09:48+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 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4.0","contributor":{"display_name":"John","profile_url":"https://biology.stackexchange.com/users/28022/john","user_type":"registered"},"created_at":"2023-07-29T22:24:13+00:00","raw_file":"raw/codex_api_v1/fb7126698e65b75ed03bf96280ca339b40e6c365d087fc910992cbae55d5d7cc_1790824008103740000_0.json","raw_sha256":"08885036fa8ad49012e514ce869ff200275514fbc30b6de44e83baf44b0c4470","revision_guid":"EEAB895F-D6F2-4C2D-83BE-FCFCA1AB1AB8","revision_number":12,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/EEAB895F-D6F2-4C2D-83BE-FCFCA1AB1AB8/view-source"}],"score":1},{"answer_html":"<p>Let's look at the <a href=\"https://en.m.wikipedia.org/wiki/Corpse_decomposition\" rel=\"nofollow noreferrer\">decomposition of a corpse</a> as a whole.</p>\n<ol>\n<li>Fresh</li>\n<li>Bloat</li>\n<li>Active decay</li>\n<li>Advanced decay</li>\n<li>Dry state</li>\n</ol>\n<p>You can skip to the dry state, which answers your question specifically.</p>\n<hr />\n<p>A prerequisite to studying decomposition is knowing that decomposers break down organic material by secreting enzymes turning it into dark liquid form that's possible for them to absorb. Foul gases are produced in the process.</p>\n<p>Also, it's best to think about decomposition as a bunch of processes caused by several agents happening and progressing at the same time.</p>\n<hr />\n<p>When you hear fresh state, think of anything that ends with mortis:</p>\n<ul>\n<li>Algor mortis (decrease of body temperature to ambient temperature)</li>\n<li>Rigor mortis (temporary stiffness of muscles due to decreased ATP which is required to relax muscles until decay starts)</li>\n<li>Livor mortis (pooling of blood at the site closest to the ground)</li>\n</ul>\n<hr />\n<p>Bloat happens because gut flora starts breaking through the wall of the gut. The wall is normally protected by the epithelial cell layer which has a high rate of shedding and regeneration. Since regeneration stops, flora can now bypass into the underlying tissue and start feeding on the body from the inside which results in the formation of</p>\n<ul>\n<li>Gas (has foul smell)</li>\n<li>Liquid (dark purge fluid that leaks through orifices because of increased pressure from gases in the intestine)</li>\n</ul>\n<p><a href=\"https://en.m.wikipedia.org/wiki/Autolysis_(biology)\" rel=\"nofollow noreferrer\">Autolysis</a> also starts where lysosomes containing lysozymes break up and release the hydrolytic enzymes which break down tissue so skin slippage may occur.</p>\n<hr />\n<p>Liquifaction by decomposers continues causing darkening and loosening of the exterior.</p>\n<p>Blowflies are attracted to the foul smells (even the smell of excrement) and thus, approach the corpse early and lay their eggs which hatch releasing maggots that feed on the corpse.</p>\n<p>Several species of insects also start feeding on the corpse but that starts later.</p>\n<p>Adipocere (corpse wax) may also form from decomposition of fat preventing further decomposition.</p>\n<hr />\n<p>In advanced decay, most tissue has <a href=\"https://en.m.wikipedia.org/wiki/Putrefaction\" rel=\"nofollow noreferrer\">liquified and loosened</a>.</p>\n<hr />\n<p>What remains from the corpse is the dry or skeletonised state. Dry here indicates that all the liquid produced from the action of decomposers has been taken up and what remains is the hard tissue, bone or the skeleton.</p>\n<hr />\n<p>If the skeleton becomes covered in soil, scavengers (animals) do not <a href=\"https://en.m.wikipedia.org/wiki/Osteophagy#:%7E:text=It%20has%20been%20seen%20in,to%20chew%20softer%20fresh%20bones.\" rel=\"nofollow noreferrer\">eat</a> it and it breaks down in acidic soil over a long time period.</p>\n<p>If the soil is neutral, it takes much longer time for this to take place.</p>\n<p>If the soil is</p>\n<ul>\n<li>dry, anoxic or slightly alkaline (unsuitable for decomposer activity)</li>\n<li>salty (has <a href=\"https://simple.m.wikipedia.org/wiki/Mohs_scale_of_mineral_hardness#:%7E:text=Gypsum%20is%20harder%3A%20it%20can,scale%20is%20for%20natural%20minerals.\" rel=\"nofollow noreferrer\">minerals</a> which can form long-lasting hard structures)</li>\n</ul>\n<p>the bones may <a href=\"https://en.m.wikipedia.org/wiki/Fossil\" rel=\"nofollow noreferrer\">fossilize</a>.</p>\n","answer_id":112695,"answer_text":"Let's look at the decomposition of a corpse (https://en.m.wikipedia.org/wiki/Corpse_decomposition) as a whole.\n\n\n\n\n\nFresh\n\n\n\n\nBloat\n\n\n\n\nActive decay\n\n\n\n\nAdvanced decay\n\n\n\n\nDry state\n\n\n\n\n\nYou can skip to the dry state, which answers your question specifically.\n\n\n\n\n\n\n\nA prerequisite to studying decomposition is knowing that decomposers break down organic material by secreting enzymes turning it into dark liquid form that's possible for them to absorb. Foul gases are produced in the process.\n\n\n\n\nAlso, it's best to think about decomposition as a bunch of processes caused by several agents happening and progressing at the same time.\n\n\n\n\n\n\n\nWhen you hear fresh state, think of anything that ends with mortis:\n\n\n\n\n\nAlgor mortis (decrease of body temperature to ambient temperature)\n\n\n\n\nRigor mortis (temporary stiffness of muscles due to decreased ATP which is required to relax muscles until decay starts)\n\n\n\n\nLivor mortis (pooling of blood at the site closest to the ground)\n\n\n\n\n\n\n\n\nBloat happens because gut flora starts breaking through the wall of the gut. The wall is normally protected by the epithelial cell layer which has a high rate of shedding and regeneration. Since regeneration stops, flora can now bypass into the underlying tissue and start feeding on the body from the inside which results in the formation of\n\n\n\n\n\nGas (has foul smell)\n\n\n\n\nLiquid (dark purge fluid that leaks through orifices because of increased pressure from gases in the intestine)\n\n\n\n\n\nAutolysis (https://en.m.wikipedia.org/wiki/Autolysis_(biology)) also starts where lysosomes containing lysozymes break up and release the hydrolytic enzymes which break down tissue so skin slippage may occur.\n\n\n\n\n\n\n\nLiquifaction by decomposers continues causing darkening and loosening of the exterior.\n\n\n\n\nBlowflies are attracted to the foul smells (even the smell of excrement) and thus, approach the corpse early and lay their eggs which hatch releasing maggots that feed on the corpse.\n\n\n\n\nSeveral species of insects also start feeding on the corpse but that starts later.\n\n\n\n\nAdipocere (corpse wax) may also form from decomposition of fat preventing further decomposition.\n\n\n\n\n\n\n\nIn advanced decay, most tissue has liquified and loosened (https://en.m.wikipedia.org/wiki/Putrefaction).\n\n\n\n\n\n\n\nWhat remains from the corpse is the dry or skeletonised state. Dry here indicates that all the liquid produced from the action of decomposers has been taken up and what remains is the hard tissue, bone or the skeleton.\n\n\n\n\n\n\n\nIf the skeleton becomes covered in soil, scavengers (animals) do not eat (https://en.m.wikipedia.org/wiki/Osteophagy#:%7E:text=It%20has%20been%20seen%20in,to%20chew%20softer%20fresh%20bones.) it and it breaks down in acidic soil over a long time period.\n\n\n\n\nIf the soil is neutral, it takes much longer time for this to take place.\n\n\n\n\nIf the soil is\n\n\n\n\n\ndry, anoxic or slightly alkaline (unsuitable for decomposer activity)\n\n\n\n\nsalty (has minerals (https://simple.m.wikipedia.org/wiki/Mohs_scale_of_mineral_hardness#:%7E:text=Gypsum%20is%20harder%3A%20it%20can,scale%20is%20for%20natural%20minerals.) which can form long-lasting hard structures)\n\n\n\n\n\nthe bones may fossilize 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Especially in hot and dry climates, steppe and desert regions, as well as in the arctic.\nTherefore, it should be expected that a large number of bones will be found on the surface of the soil, also underground in the topsoil.\nBut nothing like this actually happens.\nWhere do the bones of dead animals go?</p>\n","text":"I've spent quite a bit of time in the wild, but I've seen little to no bones lying on the ground.\nLarge bones such as skulls, spines, horns, hooves are not eaten by any other animals, and even microorganisms. thanks to which they can persist for decades on the ground surface. Especially in hot and dry climates, steppe and desert regions, as well as in the arctic.\nTherefore, it should be expected that a large number of bones will be found on the surface of the soil, also underground in the topsoil.\nBut nothing like this actually happens.\nWhere do the bones of dead animals go?"},{"context_id":"112669","html":"<p>When you study archaeology, you dig and find everything becomes buried very fast through burrowing and overgrowth subsidence. You can find <em>a lot</em> of bones when you walk a minute away from the beaten track, and very rarely on paths, often gray and beige. Humans very often move nice skulls as trophies.</p>\n<p>Skulls provide a microclimate for moss, ants, beetles, plants, low-wind zones and snags to collect leaves. Humans like to pick them up and move them, rodents gnaw them, the jaw tumbles away, bug and bird droppings, acids and humidity dissolve them, frost cracks the pores.</p>\n<p>Plants compete for space and grow around bones and hide them. Bugs dig networks of burrows and make the soil cave in a bit, worms place middens on the sides, A hoof or a femur will be covered by wild grass in 3-5 years, a horse skull in 10-20 years.</p>\n<p>In the arctic there aren't horses, cows, deer, only seashore megafauna. Bones get snowed over. Else they are subject to freeze-thaw weathering, water stays in the pores of the bones, freezes and expands every day, and erodes them.</p>\n<p>In the forest, leaf fall and sticks accumulate 1-5cm every year, trees fall over, the soil is alive with fungus mycelia and bugs, It's also quite an acid environment. Bones would be expected to stay uncovered for less than 15-20 years.</p>\n<p>In the desert, there aren't lots of big animals, and the bones can last a very long time there, we can find awesome cadavers in regions of low biological, geological and glacial activity.</p>\n<p>Human transportation near paths\nScavenging\nAnimals hide away when they are ill\nGnawing\nMoss\nFreeze thaw\nGeological activity\nSubsidence\nGlacial activity\nSand dunes\nTrampling by other animals</p>\n","text":"When you study archaeology, you dig and find everything becomes buried very fast through burrowing and overgrowth subsidence. You can find a lot of bones when you walk a minute away from the beaten track, and very rarely on paths, often gray and beige. Humans very often move nice skulls as trophies.\n\n\n\n\nSkulls provide a microclimate for moss, ants, beetles, plants, low-wind zones and snags to collect leaves. Humans like to pick them up and move them, rodents gnaw them, the jaw tumbles away, bug and bird droppings, acids and humidity dissolve them, frost cracks the pores.\n\n\n\n\nPlants compete for space and grow around bones and hide them. Bugs dig networks of burrows and make the soil cave in a bit, worms place middens on the sides, A hoof or a femur will be covered by wild grass in 3-5 years, a horse skull in 10-20 years.\n\n\n\n\nIn the arctic there aren't horses, cows, deer, only seashore megafauna. Bones get snowed over. Else they are subject to freeze-thaw weathering, water stays in the pores of the bones, freezes and expands every day, and erodes them.\n\n\n\n\nIn the forest, leaf fall and sticks accumulate 1-5cm every year, trees fall over, the soil is alive with fungus mycelia and bugs, It's also quite an acid environment. Bones would be expected to stay uncovered for less than 15-20 years.\n\n\n\n\nIn the desert, there aren't lots of big animals, and the bones can last a very long time there, we can find awesome cadavers in regions of low biological, geological and glacial activity.\n\n\n\n\nHuman transportation near paths\nScavenging\nAnimals hide away when they are ill\nGnawing\nMoss\nFreeze thaw\nGeological activity\nSubsidence\nGlacial activity\nSand dunes\nTrampling by other animals"},{"context_id":"112673","html":"<p>Even a superficial Google search will tell you by the title of the hits you get that bones are eaten, e.g. <a href=\"https://en.wikipedia.org/wiki/Osteophagy\" rel=\"nofollow noreferrer\">my top hit</a>.</p>\n<p>Osteophagy simply means <em>bone eating</em>. I'm not sure why it applies to herbivores in particular; maybe because it seems to be strange behavior in an herbivore, whereas it's expected in a carnivore.</p>\n<p>Phosphate is crucial to life, but isn't abundant in 'edible nature' (plants, etc.). It is abundant in bone, however, and because it is crucial to growth and energy production, animals eat bones however they can. Some animals, e.g. those without teeth, will swallow small bones whole. Carnivores and capable omnivores will crush susceptible bones by chewing on them; herbivores will just grind away at them and consume the bits they can generate.</p>\n<p>From Wikipedia, a cow chewing on a bone.</p>\n<p><a href=\"https://i.sstatic.net/BXt39m.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/BXt39m.jpg\" alt=\"enter image description here\" /></a></p>\n<p>How about <a href=\"https://www.bu.edu/articles/2016/squirrel-bone-gnawing/\" rel=\"nofollow noreferrer\">a squirrel</a>?</p>\n<p><a href=\"https://i.sstatic.net/pYrJtm.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/pYrJtm.jpg\" alt=\"enter image description here\" /></a></p>\n<p>Or a <a href=\"https://www.nationalgeographic.com/animals/article/deer-eating-human-forensics-decomposition\" rel=\"nofollow noreferrer\">deer eating human bones</a>:</p>\n<p><a href=\"https://i.sstatic.net/nKTY8m.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/nKTY8m.jpg\" alt=\"enter image description here\" /></a></p>\n<p>This answer could be longer, but why go on? The answer is obvious.</p>\n<p><sub><a href=\"https://www.wildlifeact.com/blog/osteophagia-how-wild-animals-use-supplements/\" rel=\"nofollow noreferrer\">Osteophagia: How Wild Animals Use Supplements</a></sub></p>\n","text":"Even a superficial Google search will tell you by the title of the hits you get that bones are eaten, e.g. my top hit (https://en.wikipedia.org/wiki/Osteophagy).\n\n\n\n\nOsteophagy simply means bone eating. I'm not sure why it applies to herbivores in particular; maybe because it seems to be strange behavior in an herbivore, whereas it's expected in a carnivore.\n\n\n\n\nPhosphate is crucial to life, but isn't abundant in 'edible nature' (plants, etc.). It is abundant in bone, however, and because it is crucial to growth and energy production, animals eat bones however they can. Some animals, e.g. those without teeth, will swallow small bones whole. Carnivores and capable omnivores will crush susceptible bones by chewing on them; herbivores will just grind away at them and consume the bits they can generate.\n\n\n\n\nFrom Wikipedia, a cow chewing on a bone.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/BXt39m.jpg] (https://i.sstatic.net/BXt39m.jpg)\n\n\n\n\nHow about a squirrel (https://www.bu.edu/articles/2016/squirrel-bone-gnawing/)?\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/pYrJtm.jpg] (https://i.sstatic.net/pYrJtm.jpg)\n\n\n\n\nOr a deer eating human bones (https://www.nationalgeographic.com/animals/article/deer-eating-human-forensics-decomposition):\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/nKTY8m.jpg] (https://i.sstatic.net/nKTY8m.jpg)\n\n\n\n\nThis answer could be longer, but why go on? The answer is obvious.\n\n\n\n\nOsteophagia: How Wild Animals Use Supplements (https://www.wildlifeact.com/blog/osteophagia-how-wild-animals-use-supplements/)"},{"context_id":"112694","html":"<h2>they rot, get eaten, or get weathered away. Under extremely rare circumstances they fossilize.</h2>\n<p>What you are talking about is called bone <a href=\"https://en.wikipedia.org/wiki/Taphonomy\" rel=\"nofollow noreferrer\">taphonomy</a>.</p>\n<p><a href=\"https://i.sstatic.net/sG4Sr.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/sG4Sr.png\" alt=\"enter image description here\" /></a></p>\n<p>You can do a simple experiment yourself, put hooves or bones partially buried in dirt in your yard and check on them from time to time, depending on where oyu live what happens will vary quite a lot. Paleontologist and forensic scientists have studied this a lot to understand fossil and human remains respectively.</p>\n<p>What happens to them</p>\n<ol>\n<li><p>Normal erosion processes and soft tissue decomposition break the bone in to smaller pieces. The same thing that breaks down rocks breakdown bone just faster. Physical and chemical weather all work on bone. Bone is soft and permeable as rock goes so it weathers very quickly.</p>\n</li>\n<li><p>Bacteria, insects, fungi, plant roots, or other organisms break them down and eat them. You can prevent this by drying the bone out and keeping it away from soil, (soils keeps the bone moist and makes it easy for those things to reach the bone) Bone like any organic material rots, oxygen and water make it happen faster and bigger organisms can eat them faster.</p>\n</li>\n</ol>\n<p>You can see the same thing with any organic material which is why we dry meat and fruit to preserve them. Also why we cover organic materials like leather or wood in oils to keep them dry. or cover them in poisonous chemicals just like you can do with bone, it slows down their decomposition. in really dry places or conditions with no oxygen bone can take very long to decay. A cow skull defleshed and nailed to a barn in the desert will take a very long time to decay centuries or longer, a bone left on the jungle floor wet and covered in dirt and leaf litter will be gone in months, assuming you can keep things from eating it, (bone is a high demand resource in forests where phosphorous is in high demand).</p>\n<p>Different materials decompose at different rates. Under absolutely perfect conditions the bone does not decay completely, creating a fossil. I personally have pulled unfossilized mammoth bones out of clay rich desert soil in Wyoming, the bone had all the structural strength of dry rotted wood, any handling caused bone to flake off, but it was still a complete mammoth leg bone, its decay had been severely slowed by dry, cold, anoxic conditions. We do find lots of buried bone in the right environments.</p>\n<h2>Soils is not static</h2>\n<p>If you put bone on top of soil it will not stay on top of the soil. soils turns over due to thermal, erosional, and biological forces. things get buried, see frost heaving and soil creep as examples. Soil is not static it is always on the move. Deserts in particular tend to be highly erosional, which is why we look for fossil in deserts,  new rock is constantly being exposed and destroyed.</p>\n<p>Now deserts and cold regions do have much slower rates of decay which is why you can find remains that are decades or even centuries old in such places. Bones are found in bogs and <a href=\"https://www.smithsonianmag.com/science-nature/five-fascinating-ice-age-finds-discovered-in-yukon-permafrost-180979521/\" rel=\"nofollow noreferrer\">permafrost for instance</a>.  things like sunlight, temperature, abrasion, weather and such can all breakdown bone. Also you vastly overestimate how many animals there are in such places, even if all their bones did not decay they still would not make up a noticeable portion of the topsoil. in places where the animal remains are that common they do make up a significant portion of the soil we call those coral sand beaches, where mechanically broken up animal shells make up the majority of the soil.</p>\n<p><strong>Sources about bone decomposition and diagenesis</strong></p>\n<p><a href=\"https://pubmed.ncbi.nlm.nih.gov/20646883/#:%7E:text=Abstract,or%20as%20long%20as%2030.\" rel=\"nofollow noreferrer\">https://pubmed.ncbi.nlm.nih.gov/20646883/#:~:text=Abstract,or%20as%20long%20as%2030.</a></p>\n<p><a href=\"https://www.scientificamerican.com/article/dust-to-dust/\" rel=\"nofollow noreferrer\">https://www.scientificamerican.com/article/dust-to-dust/</a></p>\n<p><a href=\"https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1061&amp;context=nebanthro\" rel=\"nofollow noreferrer\">https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1061&amp;context=nebanthro</a></p>\n<p><a href=\"https://www.jstor.org/stable/2400259\" rel=\"nofollow noreferrer\">https://www.jstor.org/stable/2400259</a></p>\n<p><a href=\"https://www.sciencedirect.com/science/article/abs/pii/S003101821630164X\" rel=\"nofollow noreferrer\">https://www.sciencedirect.com/science/article/abs/pii/S003101821630164X</a></p>\n<p><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8224596/\" rel=\"nofollow noreferrer\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8224596/</a></p>\n<p><strong>Sources about soil and erosion turnover</strong></p>\n<p><a href=\"https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/soil-movement\" rel=\"nofollow noreferrer\">https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/soil-movement</a></p>\n<p><a href=\"https://www.sciencedirect.com/science/article/abs/pii/B9780123864734000014\" rel=\"nofollow noreferrer\">https://www.sciencedirect.com/science/article/abs/pii/B9780123864734000014</a></p>\n<p><strong>Bonus</strong></p>\n<p><a href=\"https://www.scienceabc.com/humans/skeleton-mystery-dont-bones-decay-decompose.html\" rel=\"nofollow noreferrer\">Great simplified of review of decomposition.</a></p>\n","text":"they rot, get eaten, or get weathered away. Under extremely rare circumstances they fossilize.\n\n\n\n\nWhat you are talking about is called bone taphonomy (https://en.wikipedia.org/wiki/Taphonomy).\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/sG4Sr.png] (https://i.sstatic.net/sG4Sr.png)\n\n\n\n\nYou can do a simple experiment yourself, put hooves or bones partially buried in dirt in your yard and check on them from time to time, depending on where oyu live what happens will vary quite a lot. Paleontologist and forensic scientists have studied this a lot to understand fossil and human remains respectively.\n\n\n\n\nWhat happens to them\n\n\n\n\n\n\n\nNormal erosion processes and soft tissue decomposition break the bone in to smaller pieces. The same thing that breaks down rocks breakdown bone just faster. Physical and chemical weather all work on bone. Bone is soft and permeable as rock goes so it weathers very quickly.\n\n\n\n\n\n\n\n\n\nBacteria, insects, fungi, plant roots, or other organisms break them down and eat them. You can prevent this by drying the bone out and keeping it away from soil, (soils keeps the bone moist and makes it easy for those things to reach the bone) Bone like any organic material rots, oxygen and water make it happen faster and bigger organisms can eat them faster.\n\n\n\n\n\n\n\n\nYou can see the same thing with any organic material which is why we dry meat and fruit to preserve them. Also why we cover organic materials like leather or wood in oils to keep them dry. or cover them in poisonous chemicals just like you can do with bone, it slows down their decomposition. in really dry places or conditions with no oxygen bone can take very long to decay. A cow skull defleshed and nailed to a barn in the desert will take a very long time to decay centuries or longer, a bone left on the jungle floor wet and covered in dirt and leaf litter will be gone in months, assuming you can keep things from eating it, (bone is a high demand resource in forests where phosphorous is in high demand).\n\n\n\n\nDifferent materials decompose at different rates. Under absolutely perfect conditions the bone does not decay completely, creating a fossil. I personally have pulled unfossilized mammoth bones out of clay rich desert soil in Wyoming, the bone had all the structural strength of dry rotted wood, any handling caused bone to flake off, but it was still a complete mammoth leg bone, its decay had been severely slowed by dry, cold, anoxic conditions. We do find lots of buried bone in the right environments.\n\n\n\n\nSoils is not static\n\n\n\n\nIf you put bone on top of soil it will not stay on top of the soil. soils turns over due to thermal, erosional, and biological forces. things get buried, see frost heaving and soil creep as examples. Soil is not static it is always on the move. Deserts in particular tend to be highly erosional, which is why we look for fossil in deserts,  new rock is constantly being exposed and destroyed.\n\n\n\n\nNow deserts and cold regions do have much slower rates of decay which is why you can find remains that are decades or even centuries old in such places. Bones are found in bogs and permafrost for instance (https://www.smithsonianmag.com/science-nature/five-fascinating-ice-age-finds-discovered-in-yukon-permafrost-180979521/).  things like sunlight, temperature, abrasion, weather and such can all breakdown bone. Also you vastly overestimate how many animals there are in such places, even if all their bones did not decay they still would not make up a noticeable portion of the topsoil. in places where the animal remains are that common they do make up a significant portion of the soil we call those coral sand beaches, where mechanically broken up animal shells make up the majority of the soil.\n\n\n\n\nSources about bone decomposition and diagenesis\n\n\n\n\nhttps://pubmed.ncbi.nlm.nih.gov/20646883/#:~:text=Abstract,or%20as%20long%20as%2030. (https://pubmed.ncbi.nlm.nih.gov/20646883/#:%7E:text=Abstract,or%20as%20long%20as%2030.)\n\n\n\n\nhttps://www.scientificamerican.com/article/dust-to-dust/ (https://www.scientificamerican.com/article/dust-to-dust/)\n\n\n\n\nhttps://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1061&context=nebanthro (https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1061&context=nebanthro)\n\n\n\n\nhttps://www.jstor.org/stable/2400259 (https://www.jstor.org/stable/2400259)\n\n\n\n\nhttps://www.sciencedirect.com/science/article/abs/pii/S003101821630164X (https://www.sciencedirect.com/science/article/abs/pii/S003101821630164X)\n\n\n\n\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8224596/ (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8224596/)\n\n\n\n\nSources about soil and erosion turnover\n\n\n\n\nhttps://www.sciencedirect.com/topics/agricultural-and-biological-sciences/soil-movement (https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/soil-movement)\n\n\n\n\nhttps://www.sciencedirect.com/science/article/abs/pii/B9780123864734000014 (https://www.sciencedirect.com/science/article/abs/pii/B9780123864734000014)\n\n\n\n\nBonus\n\n\n\n\nGreat simplified of review of decomposition. (https://www.scienceabc.com/humans/skeleton-mystery-dont-bones-decay-decompose.html)"},{"context_id":"112695","html":"<p>Let's look at the <a href=\"https://en.m.wikipedia.org/wiki/Corpse_decomposition\" rel=\"nofollow noreferrer\">decomposition of a corpse</a> as a whole.</p>\n<ol>\n<li>Fresh</li>\n<li>Bloat</li>\n<li>Active decay</li>\n<li>Advanced decay</li>\n<li>Dry state</li>\n</ol>\n<p>You can skip to the dry state, which answers your question specifically.</p>\n<hr />\n<p>A prerequisite to studying decomposition is knowing that decomposers break down organic material by secreting enzymes turning it into dark liquid form that's possible for them to absorb. Foul gases are produced in the process.</p>\n<p>Also, it's best to think about decomposition as a bunch of processes caused by several agents happening and progressing at the same time.</p>\n<hr />\n<p>When you hear fresh state, think of anything that ends with mortis:</p>\n<ul>\n<li>Algor mortis (decrease of body temperature to ambient temperature)</li>\n<li>Rigor mortis (temporary stiffness of muscles due to decreased ATP which is required to relax muscles until decay starts)</li>\n<li>Livor mortis (pooling of blood at the site closest to the ground)</li>\n</ul>\n<hr />\n<p>Bloat happens because gut flora starts breaking through the wall of the gut. The wall is normally protected by the epithelial cell layer which has a high rate of shedding and regeneration. Since regeneration stops, flora can now bypass into the underlying tissue and start feeding on the body from the inside which results in the formation of</p>\n<ul>\n<li>Gas (has foul smell)</li>\n<li>Liquid (dark purge fluid that leaks through orifices because of increased pressure from gases in the intestine)</li>\n</ul>\n<p><a href=\"https://en.m.wikipedia.org/wiki/Autolysis_(biology)\" rel=\"nofollow noreferrer\">Autolysis</a> also starts where lysosomes containing lysozymes break up and release the hydrolytic enzymes which break down tissue so skin slippage may occur.</p>\n<hr />\n<p>Liquifaction by decomposers continues causing darkening and loosening of the exterior.</p>\n<p>Blowflies are attracted to the foul smells (even the smell of excrement) and thus, approach the corpse early and lay their eggs which hatch releasing maggots that feed on the corpse.</p>\n<p>Several species of insects also start feeding on the corpse but that starts later.</p>\n<p>Adipocere (corpse wax) may also form from decomposition of fat preventing further decomposition.</p>\n<hr />\n<p>In advanced decay, most tissue has <a href=\"https://en.m.wikipedia.org/wiki/Putrefaction\" rel=\"nofollow noreferrer\">liquified and loosened</a>.</p>\n<hr />\n<p>What remains from the corpse is the dry or skeletonised state. Dry here indicates that all the liquid produced from the action of decomposers has been taken up and what remains is the hard tissue, bone or the skeleton.</p>\n<hr />\n<p>If the skeleton becomes covered in soil, scavengers (animals) do not <a href=\"https://en.m.wikipedia.org/wiki/Osteophagy#:%7E:text=It%20has%20been%20seen%20in,to%20chew%20softer%20fresh%20bones.\" rel=\"nofollow noreferrer\">eat</a> it and it breaks down in acidic soil over a long time period.</p>\n<p>If the soil is neutral, it takes much longer time for this to take place.</p>\n<p>If the soil is</p>\n<ul>\n<li>dry, anoxic or slightly alkaline (unsuitable for decomposer activity)</li>\n<li>salty (has <a href=\"https://simple.m.wikipedia.org/wiki/Mohs_scale_of_mineral_hardness#:%7E:text=Gypsum%20is%20harder%3A%20it%20can,scale%20is%20for%20natural%20minerals.\" rel=\"nofollow noreferrer\">minerals</a> which can form long-lasting hard structures)</li>\n</ul>\n<p>the bones may <a href=\"https://en.m.wikipedia.org/wiki/Fossil\" rel=\"nofollow noreferrer\">fossilize</a>.</p>\n","text":"Let's look at the decomposition of a corpse (https://en.m.wikipedia.org/wiki/Corpse_decomposition) as a whole.\n\n\n\n\n\nFresh\n\n\n\n\nBloat\n\n\n\n\nActive decay\n\n\n\n\nAdvanced decay\n\n\n\n\nDry state\n\n\n\n\n\nYou can skip to the dry state, which answers your question specifically.\n\n\n\n\n\n\n\nA prerequisite to studying decomposition is knowing that decomposers break down organic material by secreting enzymes turning it into dark liquid form that's possible for them to absorb. Foul gases are produced in the process.\n\n\n\n\nAlso, it's best to think about decomposition as a bunch of processes caused by several agents happening and progressing at the same time.\n\n\n\n\n\n\n\nWhen you hear fresh state, think of anything that ends with mortis:\n\n\n\n\n\nAlgor mortis (decrease of body temperature to ambient temperature)\n\n\n\n\nRigor mortis (temporary stiffness of muscles due to decreased ATP which is required to relax muscles until decay starts)\n\n\n\n\nLivor mortis (pooling of blood at the site closest to the ground)\n\n\n\n\n\n\n\n\nBloat happens because gut flora starts breaking through the wall of the gut. The wall is normally protected by the epithelial cell layer which has a high rate of shedding and regeneration. Since regeneration stops, flora can now bypass into the underlying tissue and start feeding on the body from the inside which results in the formation of\n\n\n\n\n\nGas (has foul smell)\n\n\n\n\nLiquid (dark purge fluid that leaks through orifices because of increased pressure from gases in the intestine)\n\n\n\n\n\nAutolysis (https://en.m.wikipedia.org/wiki/Autolysis_(biology)) also starts where lysosomes containing lysozymes break up and release the hydrolytic enzymes which break down tissue so skin slippage may occur.\n\n\n\n\n\n\n\nLiquifaction by decomposers continues causing darkening and loosening of the exterior.\n\n\n\n\nBlowflies are attracted to the foul smells (even the smell of excrement) and thus, approach the corpse early and lay their eggs which hatch releasing maggots that feed on the corpse.\n\n\n\n\nSeveral species of insects also start feeding on the corpse but that starts later.\n\n\n\n\nAdipocere (corpse wax) may also form from decomposition of fat preventing further decomposition.\n\n\n\n\n\n\n\nIn advanced decay, most tissue has liquified and loosened (https://en.m.wikipedia.org/wiki/Putrefaction).\n\n\n\n\n\n\n\nWhat remains from the corpse is the dry or skeletonised state. Dry here indicates that all the liquid produced from the action of decomposers has been taken up and what remains is the hard tissue, bone or the skeleton.\n\n\n\n\n\n\n\nIf the skeleton becomes covered in soil, scavengers (animals) do not eat (https://en.m.wikipedia.org/wiki/Osteophagy#:%7E:text=It%20has%20been%20seen%20in,to%20chew%20softer%20fresh%20bones.) it and it breaks down in acidic soil over a long time period.\n\n\n\n\nIf the soil is neutral, it takes much longer time for this to take place.\n\n\n\n\nIf the soil is\n\n\n\n\n\ndry, anoxic or slightly alkaline (unsuitable for decomposer activity)\n\n\n\n\nsalty (has minerals (https://simple.m.wikipedia.org/wiki/Mohs_scale_of_mineral_hardness#:%7E:text=Gypsum%20is%20harder%3A%20it%20can,scale%20is%20for%20natural%20minerals.) which can form long-lasting hard structures)\n\n\n\n\n\nthe bones may fossilize (https://en.m.wikipedia.org/wiki/Fossil)."}],"domain":"biology","external_citations":["https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1061&context=nebanthro","https://en.m.wikipedia.org/wiki/Autolysis_(biology)","https://en.m.wikipedia.org/wiki/Corpse_decomposition","https://en.m.wikipedia.org/wiki/Fossil","https://en.m.wikipedia.org/wiki/Osteophagy#:%7E:text=It%20has%20been%20seen%20in,to%20chew%20softer%20fresh%20bones.","https://en.m.wikipedia.org/wiki/Putrefaction","https://en.wikipedia.org/wiki/Osteophagy","https://en.wikipedia.org/wiki/Taphonomy","https://i.sstatic.net/BXt39m.jpg","https://i.sstatic.net/nKTY8m.jpg","https://i.sstatic.net/pYrJtm.jpg","https://i.sstatic.net/sG4Sr.png","https://pubmed.ncbi.nlm.nih.gov/20646883/#:%7E:text=Abstract,or%20as%20long%20as%2030.","https://simple.m.wikipedia.org/wiki/Mohs_scale_of_mineral_hardness#:%7E:text=Gypsum%20is%20harder%3A%20it%20can,scale%20is%20for%20natural%20minerals.","https://www.bu.edu/articles/2016/squirrel-bone-gnawing/","https://www.jstor.org/stable/2400259","https://www.nationalgeographic.com/animals/article/deer-eating-human-forensics-decomposition","https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8224596/","https://www.scienceabc.com/humans/skeleton-mystery-dont-bones-decay-decompose.html","https://www.sciencedirect.com/science/article/abs/pii/B9780123864734000014","https://www.sciencedirect.com/science/article/abs/pii/S003101821630164X","https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/soil-movement","https://www.scientificamerican.com/article/dust-to-dust/","https://www.smithsonianmag.com/science-nature/five-fascinating-ice-age-finds-discovered-in-yukon-permafrost-180979521/","https://www.wildlifeact.com/blog/osteophagia-how-wild-animals-use-supplements/"],"ground_truth_type":"metadata_grounded","group_id":"4c07dbf7aa388ca5e6b408124af9d45672491565839af90e64dfbc915abc8cd1","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-af71264ca81cfecfe5e5051a","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":"Vladimir Orlov","profile_url":"https://biology.stackexchange.com/users/76360/vladimir-orlov","user_type":"registered"},"created_at":"2023-07-25T19:29:58+00:00","raw_file":"raw/codex_api_v1/fb7126698e65b75ed03bf96280ca339b40e6c365d087fc910992cbae55d5d7cc_1790824008103740000_0.json","raw_sha256":"08885036fa8ad49012e514ce869ff200275514fbc30b6de44e83baf44b0c4470","revision_guid":"2222ED8E-7AF8-4C3E-8A83-346C612B61A9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2222ED8E-7AF8-4C3E-8A83-346C612B61A9/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Vladimir Orlov","profile_url":"https://biology.stackexchange.com/users/76360/vladimir-orlov","user_type":"registered"},"created_at":"2023-07-26T17:42:43+00:00","raw_file":"raw/codex_api_v1/fb7126698e65b75ed03bf96280ca339b40e6c365d087fc910992cbae55d5d7cc_1790824008103740000_0.json","raw_sha256":"08885036fa8ad49012e514ce869ff200275514fbc30b6de44e83baf44b0c4470","revision_guid":"7A7283E1-3CAE-4E70-970C-22B1CDA9B8E2","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7A7283E1-3CAE-4E70-970C-22B1CDA9B8E2/view-source"},{"content_license":null,"contributor":{"display_name":"John","profile_url":"https://biology.stackexchange.com/users/28022/john","user_type":"registered"},"created_at":"2023-07-29T22:25:14+00:00","raw_file":"raw/codex_api_v1/fb7126698e65b75ed03bf96280ca339b40e6c365d087fc910992cbae55d5d7cc_1790824008103740000_0.json","raw_sha256":"08885036fa8ad49012e514ce869ff200275514fbc30b6de44e83baf44b0c4470","revision_guid":"5F85D42B-7A28-4366-9FAD-D667812F0092","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5F85D42B-7A28-4366-9FAD-D667812F0092/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":"112667","source_record_sha256":"efbd5b5d4d9db03c55386e81949297214d72900e1766df50a1ae382a58bc3c66","source_url":"https://biology.stackexchange.com/questions/112667/where-do-the-bones-of-dead-animals-go","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Where do the bones of dead animals go?\nI've spent quite a bit of time in the wild, but I've seen little to no bones lying on the ground.\nLarge bones such as skulls, spines, horns, hooves are not eaten by any other animals, and even microorganisms. thanks to which they can persist for decades on the ground surface. Especially in hot and dry climates, steppe and desert regions, as well as in the arctic.\nTherefore, it should be expected that a large number of bones will be found on the surface of the soil, also underground in the topsoil.\nBut nothing like this actually happens.\nWhere do the bones of dead animals go?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":112669,"score":-1},{"answer_id":112673,"score":3},{"answer_id":112694,"score":1},{"answer_id":112695,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<blockquote>\n<p>having more cells mean larger amounts of oxygen are needed</p>\n</blockquote>\n<p>Two things here. First is that that a large muscle usually comes from the <a href=\"https://journals.lww.com/nsca-jscr/fulltext/2010/10000/The_Mechanisms_of_Muscle_Hypertrophy_and_Their.40.aspx\" rel=\"nofollow noreferrer\">individual cells becoming larger</a>, not so much that there are more of them.</p>\n<p>Second, is that exercise means that <a href=\"https://www.jacc.org/doi/abs/10.1016/j.jacc.2005.09.066\" rel=\"nofollow noreferrer\">your body uses the oxygen more efficiently</a> if it's fit (it's unclear whether this refers to it having a higher concentration of oxygen, or whether it is due to changes in metabolic processes).</p>\n<blockquote>\n<p>more DNA-copying errors are made, more free radicals are produced, etc.</p>\n</blockquote>\n<p>Although it's worth pointing that these happen anyway. Exercise doesn't really change much on that front, unless there's an injury.</p>\n<p>Your body has protective mechanisms against these forms of damage, since they happen as part of regular metabolism. They don't just gradually accumulate throughout your lifetime.</p>\n<blockquote>\n<p>I'm obviously missing something, but I'm just having a hard time understanding how something that increases the entropy of your system can be beneficial for your health in the long run.</p>\n</blockquote>\n<p>It helps stave off <a href=\"https://onlinelibrary.wiley.com/doi/abs/10.1111/jne.12533\" rel=\"nofollow noreferrer\">other health conditions</a> that would take you out first.</p>\n<p>System entropy increasing isn't really that big of an issue anyway, since humans aren't a closed system. A warm bath also increases entropy (from heat), but certainly doesn't cause health issues, and hypothermia tends to be quite bad for you, even if it does the opposite.</p>\n","answer_id":112761,"answer_text":"having more cells mean larger amounts of oxygen are needed\n\n\n\n\n\n\n\nTwo things here. First is that that a large muscle usually comes from the individual cells becoming larger (https://journals.lww.com/nsca-jscr/fulltext/2010/10000/The_Mechanisms_of_Muscle_Hypertrophy_and_Their.40.aspx), not so much that there are more of them.\n\n\n\n\nSecond, is that exercise means that your body uses the oxygen more efficiently (https://www.jacc.org/doi/abs/10.1016/j.jacc.2005.09.066) if it's fit (it's unclear whether this refers to it having a higher concentration of oxygen, or whether it is due to changes in metabolic processes).\n\n\n\n\n\n\n\nmore DNA-copying errors are made, more free radicals are produced, etc.\n\n\n\n\n\n\n\nAlthough it's worth pointing that these happen anyway. Exercise doesn't really change much on that front, unless there's an injury.\n\n\n\n\nYour body has protective mechanisms against these forms of damage, since they happen as part of regular metabolism. They don't just gradually accumulate throughout your lifetime.\n\n\n\n\n\n\n\nI'm obviously missing something, but I'm just having a hard time understanding how something that increases the entropy of your system can be beneficial for your health in the long run.\n\n\n\n\n\n\n\nIt helps stave off other health conditions (https://onlinelibrary.wiley.com/doi/abs/10.1111/jne.12533) that would take you out first.\n\n\n\n\nSystem entropy increasing isn't really that big of an issue anyway, since humans aren't a closed system. A warm bath also increases entropy (from heat), but certainly doesn't cause health issues, and hypothermia tends to be quite bad for you, even if it does the opposite.","answer_url":"https://biology.stackexchange.com/a/112761","author":"techno156","author_url":"https://biology.stackexchange.com/users/27285/techno156","content_license":"CC BY-SA 4.0","created_at":"2023-08-09T07:04:10+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":112759,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"techno156","profile_url":"https://biology.stackexchange.com/users/27285/techno156","user_type":"registered"},"created_at":"2023-08-09T07:04:10+00:00","raw_file":"raw/codex_api_v1/a04a0f8b9b816f605414240c86ef0796529040fa885a4b1183bd818d12b64e65_0.json","raw_sha256":"630e8bf25473aeb8900409dec408d29d2bdc2011bc3b72f26995c17452a2c689","revision_guid":"7005B7EF-7D5D-49C2-97AF-87BBC4A0AEE7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7005B7EF-7D5D-49C2-97AF-87BBC4A0AEE7/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Antoine","author_url":"https://biology.stackexchange.com/users/17311/antoine","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Antoine","profile_url":"https://biology.stackexchange.com/users/17311/antoine","user_type":"registered"},"created_at":"2023-08-08T15:09:12+00:00","raw_file":"raw/codex_api_v1/a04a0f8b9b816f605414240c86ef0796529040fa885a4b1183bd818d12b64e65_0.json","raw_sha256":"630e8bf25473aeb8900409dec408d29d2bdc2011bc3b72f26995c17452a2c689","revision_guid":"A03DD1D7-19A1-4C27-93FD-FAF031200080","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A03DD1D7-19A1-4C27-93FD-FAF031200080/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2023-09-08T08:06:40+00:00","raw_file":"raw/codex_api_v1/a04a0f8b9b816f605414240c86ef0796529040fa885a4b1183bd818d12b64e65_0.json","raw_sha256":"630e8bf25473aeb8900409dec408d29d2bdc2011bc3b72f26995c17452a2c689","revision_guid":"26C28284-9757-47FF-ABE6-BA182C0F26D3","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/26C28284-9757-47FF-ABE6-BA182C0F26D3/view-source"}],"url":"https://biology.stackexchange.com/questions/112759/why-is-sport-healthy-if-high-metabolism-decreases-life-expectancy"},{"author":"techno156","author_url":"https://biology.stackexchange.com/users/27285/techno156","content_license":"CC BY-SA 4.0","context_id":"112761","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"techno156","profile_url":"https://biology.stackexchange.com/users/27285/techno156","user_type":"registered"},"created_at":"2023-08-09T07:04:10+00:00","raw_file":"raw/codex_api_v1/a04a0f8b9b816f605414240c86ef0796529040fa885a4b1183bd818d12b64e65_0.json","raw_sha256":"630e8bf25473aeb8900409dec408d29d2bdc2011bc3b72f26995c17452a2c689","revision_guid":"7005B7EF-7D5D-49C2-97AF-87BBC4A0AEE7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7005B7EF-7D5D-49C2-97AF-87BBC4A0AEE7/view-source"}],"url":"https://biology.stackexchange.com/a/112761"}],"contexts":[{"context_id":"question","html":"<p>There is something that appears as a contradiction to a newbie like me.</p>\n<ol>\n<li><p>Sport is widely recognized as healthy and recommended by medical experts.</p>\n</li>\n<li><p>Metabolic rate is inversely correlated with lifespan.</p>\n</li>\n</ol>\n<p>To me, it makes sense that the more energy passes through your system, the more it gets damaged.</p>\n<p>Sport goes against this desirable frugality, as it makes you consume more energy, which requires increasing your energy input to compensate (you eat more food). Also, growing a greater muscular mass increases the amount of energy needed for moving, for maintaining body temperature at rest; having more cells mean larger amounts of oxygen are needed, more DNA-copying errors are made, more free radicals are produced, etc.</p>\n<p>At the same time, I've heard that sport is good because it lowers heartbeat at rest, it makes special immune-system agents enter cells more effectively, and other things...</p>\n<p>I'm obviously missing something, but I'm just having a hard time understanding how something that increases the entropy of your system can be beneficial for your health in the long run.</p>\n","text":"There is something that appears as a contradiction to a newbie like me.\n\n\n\n\n\n\n\nSport is widely recognized as healthy and recommended by medical experts.\n\n\n\n\n\n\n\n\n\nMetabolic rate is inversely correlated with lifespan.\n\n\n\n\n\n\n\n\nTo me, it makes sense that the more energy passes through your system, the more it gets damaged.\n\n\n\n\nSport goes against this desirable frugality, as it makes you consume more energy, which requires increasing your energy input to compensate (you eat more food). Also, growing a greater muscular mass increases the amount of energy needed for moving, for maintaining body temperature at rest; having more cells mean larger amounts of oxygen are needed, more DNA-copying errors are made, more free radicals are produced, etc.\n\n\n\n\nAt the same time, I've heard that sport is good because it lowers heartbeat at rest, it makes special immune-system agents enter cells more effectively, and other things...\n\n\n\n\nI'm obviously missing something, but I'm just having a hard time understanding how something that increases the entropy of your system can be beneficial for your health in the long run."},{"context_id":"112761","html":"<blockquote>\n<p>having more cells mean larger amounts of oxygen are needed</p>\n</blockquote>\n<p>Two things here. First is that that a large muscle usually comes from the <a href=\"https://journals.lww.com/nsca-jscr/fulltext/2010/10000/The_Mechanisms_of_Muscle_Hypertrophy_and_Their.40.aspx\" rel=\"nofollow noreferrer\">individual cells becoming larger</a>, not so much that there are more of them.</p>\n<p>Second, is that exercise means that <a href=\"https://www.jacc.org/doi/abs/10.1016/j.jacc.2005.09.066\" rel=\"nofollow noreferrer\">your body uses the oxygen more efficiently</a> if it's fit (it's unclear whether this refers to it having a higher concentration of oxygen, or whether it is due to changes in metabolic processes).</p>\n<blockquote>\n<p>more DNA-copying errors are made, more free radicals are produced, etc.</p>\n</blockquote>\n<p>Although it's worth pointing that these happen anyway. Exercise doesn't really change much on that front, unless there's an injury.</p>\n<p>Your body has protective mechanisms against these forms of damage, since they happen as part of regular metabolism. They don't just gradually accumulate throughout your lifetime.</p>\n<blockquote>\n<p>I'm obviously missing something, but I'm just having a hard time understanding how something that increases the entropy of your system can be beneficial for your health in the long run.</p>\n</blockquote>\n<p>It helps stave off <a href=\"https://onlinelibrary.wiley.com/doi/abs/10.1111/jne.12533\" rel=\"nofollow noreferrer\">other health conditions</a> that would take you out first.</p>\n<p>System entropy increasing isn't really that big of an issue anyway, since humans aren't a closed system. A warm bath also increases entropy (from heat), but certainly doesn't cause health issues, and hypothermia tends to be quite bad for you, even if it does the opposite.</p>\n","text":"having more cells mean larger amounts of oxygen are needed\n\n\n\n\n\n\n\nTwo things here. First is that that a large muscle usually comes from the individual cells becoming larger (https://journals.lww.com/nsca-jscr/fulltext/2010/10000/The_Mechanisms_of_Muscle_Hypertrophy_and_Their.40.aspx), not so much that there are more of them.\n\n\n\n\nSecond, is that exercise means that your body uses the oxygen more efficiently (https://www.jacc.org/doi/abs/10.1016/j.jacc.2005.09.066) if it's fit (it's unclear whether this refers to it having a higher concentration of oxygen, or whether it is due to changes in metabolic processes).\n\n\n\n\n\n\n\nmore DNA-copying errors are made, more free radicals are produced, etc.\n\n\n\n\n\n\n\nAlthough it's worth pointing that these happen anyway. Exercise doesn't really change much on that front, unless there's an injury.\n\n\n\n\nYour body has protective mechanisms against these forms of damage, since they happen as part of regular metabolism. They don't just gradually accumulate throughout your lifetime.\n\n\n\n\n\n\n\nI'm obviously missing something, but I'm just having a hard time understanding how something that increases the entropy of your system can be beneficial for your health in the long run.\n\n\n\n\n\n\n\nIt helps stave off other health conditions (https://onlinelibrary.wiley.com/doi/abs/10.1111/jne.12533) that would take you out first.\n\n\n\n\nSystem entropy increasing isn't really that big of an issue anyway, since humans aren't a closed system. A warm bath also increases entropy (from heat), but certainly doesn't cause health issues, and hypothermia tends to be quite bad for you, even if it does the opposite."}],"domain":"biology","external_citations":["https://journals.lww.com/nsca-jscr/fulltext/2010/10000/The_Mechanisms_of_Muscle_Hypertrophy_and_Their.40.aspx","https://onlinelibrary.wiley.com/doi/abs/10.1111/jne.12533","https://www.jacc.org/doi/abs/10.1016/j.jacc.2005.09.066"],"ground_truth_type":"metadata_grounded","group_id":"1b831f570845b021e241c6e9825ee5a696783c8aeaeccda39ade32dc688a12d0","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-10a0f5d54685b0858522eb66","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":"Antoine","profile_url":"https://biology.stackexchange.com/users/17311/antoine","user_type":"registered"},"created_at":"2023-08-08T15:09:12+00:00","raw_file":"raw/codex_api_v1/a04a0f8b9b816f605414240c86ef0796529040fa885a4b1183bd818d12b64e65_0.json","raw_sha256":"630e8bf25473aeb8900409dec408d29d2bdc2011bc3b72f26995c17452a2c689","revision_guid":"A03DD1D7-19A1-4C27-93FD-FAF031200080","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A03DD1D7-19A1-4C27-93FD-FAF031200080/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2023-09-08T08:06:40+00:00","raw_file":"raw/codex_api_v1/a04a0f8b9b816f605414240c86ef0796529040fa885a4b1183bd818d12b64e65_0.json","raw_sha256":"630e8bf25473aeb8900409dec408d29d2bdc2011bc3b72f26995c17452a2c689","revision_guid":"26C28284-9757-47FF-ABE6-BA182C0F26D3","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/26C28284-9757-47FF-ABE6-BA182C0F26D3/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":"112759","source_record_sha256":"7276ccfacab6d1b0d0187d3ad0a77b3926006d1bb9fbb8cbfdc07d62a3c6edc0","source_url":"https://biology.stackexchange.com/questions/112759/why-is-sport-healthy-if-high-metabolism-decreases-life-expectancy","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Why is sport healthy if high metabolism decreases life expectancy?\nThere is something that appears as a contradiction to a newbie like me.\n\n\n\n\n\n\n\nSport is widely recognized as healthy and recommended by medical experts.\n\n\n\n\n\n\n\n\n\nMetabolic rate is inversely correlated with lifespan.\n\n\n\n\n\n\n\n\nTo me, it makes sense that the more energy passes through your system, the more it gets damaged.\n\n\n\n\nSport goes against this desirable frugality, as it makes you consume more energy, which requires increasing your energy input to compensate (you eat more food). Also, growing a greater muscular mass increases the amount of energy needed for moving, for maintaining body temperature at rest; having more cells mean larger amounts of oxygen are needed, more DNA-copying errors are made, more free radicals are produced, etc.\n\n\n\n\nAt the same time, I've heard that sport is good because it lowers heartbeat at rest, it makes special immune-system agents enter cells more effectively, and other things...\n\n\n\n\nI'm obviously missing something, but I'm just having a hard time understanding how something that increases the entropy of your system can be beneficial for your health in the long run.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":112761,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>You can't extract the <em>print a heart</em> &quot;code&quot; from DNA, that's not how DNA or development works. Each organ develops according to a pattern influenced by all the other surrounding tissues. It's quite an intricate dance, with folds and migrations occurring at specific times. That's why you can't regrow lost digits or limbs, or replace damaged brain tissue: the connections those pieces make with the rest of the body are only possible during a specific time in development when all the correct cues and relationships are there.</p>\n<p>In other words, to generate an organ the way it is generated in an embryo, you need a whole embryo. To generate one to an adult size that way, you need to grow a whole adult. Science fiction has used this as a plausible approach, but real society finds it problematic to grow people for the sole purpose of organ harvesting.</p>\n<p>Read, for example, the <a href=\"https://en.wikipedia.org/wiki/Heart_development\" rel=\"nofollow noreferrer\">Wikipedia article on heart development</a>:</p>\n<blockquote>\n<p>In the splanchnopleuric mesenchyme on either side of the neural plate, a horseshoe-shaped area develops as the cardiogenic region. This has formed from cardiac myoblasts and blood islands as forerunners of blood cells and vessels.[5] By day 19, an endocardial tube begins to develop in each side of this region. These two tubes grow and by the third week have converged towards each other to merge, using programmed cell death to form a single tube, the tubular heart.[6]</p>\n<p>From splanchnopleuric mesenchyme, the cardiogenic region develops cranially and laterally to the neural plate. In this area, two separate angiogenic cell clusters form on either side and coalesce to form the endocardial tubes. As embryonic folding starts, the two endocardial tubes are pushed into the thoracic cavity, where they begin to fuse together, and this is completed at about 22 days.[7][2]</p>\n</blockquote>\n<p>The only place you get a splanchnopleuric mesenchyme to start with is going to be a developing embryo. The heart is forming from different clusters of cells migrating and differentiating in a particular pattern.</p>\n<p>Scaffolding is more of a trick. It gets you away from the organ-level patterning that shapes the entire structure and lets you deal with just the functional units: individual cell types like myocytes that behave sufficiently robotically that if you create approximately the right conditions they will settle in to do their job.</p>\n","answer_id":112778,"answer_text":"You can't extract the print a heart \"code\" from DNA, that's not how DNA or development works. Each organ develops according to a pattern influenced by all the other surrounding tissues. It's quite an intricate dance, with folds and migrations occurring at specific times. That's why you can't regrow lost digits or limbs, or replace damaged brain tissue: the connections those pieces make with the rest of the body are only possible during a specific time in development when all the correct cues and relationships are there.\n\n\n\n\nIn other words, to generate an organ the way it is generated in an embryo, you need a whole embryo. To generate one to an adult size that way, you need to grow a whole adult. Science fiction has used this as a plausible approach, but real society finds it problematic to grow people for the sole purpose of organ harvesting.\n\n\n\n\nRead, for example, the Wikipedia article on heart development (https://en.wikipedia.org/wiki/Heart_development):\n\n\n\n\n\n\n\nIn the splanchnopleuric mesenchyme on either side of the neural plate, a horseshoe-shaped area develops as the cardiogenic region. This has formed from cardiac myoblasts and blood islands as forerunners of blood cells and vessels.[5] By day 19, an endocardial tube begins to develop in each side of this region. These two tubes grow and by the third week have converged towards each other to merge, using programmed cell death to form a single tube, the tubular heart.[6]\n\n\n\n\nFrom splanchnopleuric mesenchyme, the cardiogenic region develops cranially and laterally to the neural plate. In this area, two separate angiogenic cell clusters form on either side and coalesce to form the endocardial tubes. As embryonic folding starts, the two endocardial tubes are pushed into the thoracic cavity, where they begin to fuse together, and this is completed at about 22 days.[7][2]\n\n\n\n\n\n\n\nThe only place you get a splanchnopleuric mesenchyme to start with is going to be a developing embryo. The heart is forming from different clusters of cells migrating and differentiating in a particular pattern.\n\n\n\n\nScaffolding is more of a trick. It gets you away from the organ-level patterning that shapes the entire structure and lets you deal with just the functional units: individual cell types like myocytes that behave sufficiently robotically that if you create approximately the right conditions they will settle in to do their job.","answer_url":"https://biology.stackexchange.com/a/112778","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2023-08-10T15:24:38+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":112777,"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":"2023-08-10T15:24:38+00:00","raw_file":"raw/codex_api_v1/fe6e1ab1e4f14040deb1423c04616e4dd0e7de39b583b42e88a31f79f9375e98_1790824028764975800_0.json","raw_sha256":"08e023ccc811ec000989abb19f483814e44277588eeabf130aa5dbaf177079bf","revision_guid":"10285487-99B2-47E4-9309-2D5B44A5B61D","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/10285487-99B2-47E4-9309-2D5B44A5B61D/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Gnat","author_url":"https://biology.stackexchange.com/users/73500/gnat","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Gnat","profile_url":"https://biology.stackexchange.com/users/73500/gnat","user_type":"registered"},"created_at":"2023-08-10T15:06:53+00:00","raw_file":"raw/codex_api_v1/fe6e1ab1e4f14040deb1423c04616e4dd0e7de39b583b42e88a31f79f9375e98_1790824028764975800_0.json","raw_sha256":"08e023ccc811ec000989abb19f483814e44277588eeabf130aa5dbaf177079bf","revision_guid":"AE48B198-8ADC-407A-A686-587154186404","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AE48B198-8ADC-407A-A686-587154186404/view-source"}],"url":"https://biology.stackexchange.com/questions/112777/why-is-scaffolding-necessary-in-organ-printing"},{"author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","context_id":"112778","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":"2023-08-10T15:24:38+00:00","raw_file":"raw/codex_api_v1/fe6e1ab1e4f14040deb1423c04616e4dd0e7de39b583b42e88a31f79f9375e98_1790824028764975800_0.json","raw_sha256":"08e023ccc811ec000989abb19f483814e44277588eeabf130aa5dbaf177079bf","revision_guid":"10285487-99B2-47E4-9309-2D5B44A5B61D","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/10285487-99B2-47E4-9309-2D5B44A5B61D/view-source"}],"url":"https://biology.stackexchange.com/a/112778"}],"contexts":[{"context_id":"question","html":"<p>Most organ printing techniques seem to use a structural element for newly created cells to anchor themselves to, be it a biocompatible plastic or some natural material. Naively, I would assume that organs can be generated just the same as they are in an embryo, so why is scaffolding necessary? Here are my guesses:</p>\n<ul>\n<li>The time taken to grow an organ to an adult size this way would take too long to be practical</li>\n<li>Making the necessary germlines to emulate those formed in gastrulation is to difficult</li>\n<li>Organs grown this way collapse into themselves without the exact environment present in an embryo (the pressure in an embryo could be necessary, or the formation of all organs concurrently allows each particular organ to maintain a solid boundary between itself and its neighbors)</li>\n<li>Without scaffolding, organs printed in vitro would not generate the auxiliary structures necessary to be useful (nerve endings, blood vessel, etc.)</li>\n</ul>\n","text":"Most organ printing techniques seem to use a structural element for newly created cells to anchor themselves to, be it a biocompatible plastic or some natural material. Naively, I would assume that organs can be generated just the same as they are in an embryo, so why is scaffolding necessary? Here are my guesses:\n\n\n\n\n\nThe time taken to grow an organ to an adult size this way would take too long to be practical\n\n\n\n\nMaking the necessary germlines to emulate those formed in gastrulation is to difficult\n\n\n\n\nOrgans grown this way collapse into themselves without the exact environment present in an embryo (the pressure in an embryo could be necessary, or the formation of all organs concurrently allows each particular organ to maintain a solid boundary between itself and its neighbors)\n\n\n\n\nWithout scaffolding, organs printed in vitro would not generate the auxiliary structures necessary to be useful (nerve endings, blood vessel, etc.)"},{"context_id":"112778","html":"<p>You can't extract the <em>print a heart</em> &quot;code&quot; from DNA, that's not how DNA or development works. Each organ develops according to a pattern influenced by all the other surrounding tissues. It's quite an intricate dance, with folds and migrations occurring at specific times. That's why you can't regrow lost digits or limbs, or replace damaged brain tissue: the connections those pieces make with the rest of the body are only possible during a specific time in development when all the correct cues and relationships are there.</p>\n<p>In other words, to generate an organ the way it is generated in an embryo, you need a whole embryo. To generate one to an adult size that way, you need to grow a whole adult. Science fiction has used this as a plausible approach, but real society finds it problematic to grow people for the sole purpose of organ harvesting.</p>\n<p>Read, for example, the <a href=\"https://en.wikipedia.org/wiki/Heart_development\" rel=\"nofollow noreferrer\">Wikipedia article on heart development</a>:</p>\n<blockquote>\n<p>In the splanchnopleuric mesenchyme on either side of the neural plate, a horseshoe-shaped area develops as the cardiogenic region. This has formed from cardiac myoblasts and blood islands as forerunners of blood cells and vessels.[5] By day 19, an endocardial tube begins to develop in each side of this region. These two tubes grow and by the third week have converged towards each other to merge, using programmed cell death to form a single tube, the tubular heart.[6]</p>\n<p>From splanchnopleuric mesenchyme, the cardiogenic region develops cranially and laterally to the neural plate. In this area, two separate angiogenic cell clusters form on either side and coalesce to form the endocardial tubes. As embryonic folding starts, the two endocardial tubes are pushed into the thoracic cavity, where they begin to fuse together, and this is completed at about 22 days.[7][2]</p>\n</blockquote>\n<p>The only place you get a splanchnopleuric mesenchyme to start with is going to be a developing embryo. The heart is forming from different clusters of cells migrating and differentiating in a particular pattern.</p>\n<p>Scaffolding is more of a trick. It gets you away from the organ-level patterning that shapes the entire structure and lets you deal with just the functional units: individual cell types like myocytes that behave sufficiently robotically that if you create approximately the right conditions they will settle in to do their job.</p>\n","text":"You can't extract the print a heart \"code\" from DNA, that's not how DNA or development works. Each organ develops according to a pattern influenced by all the other surrounding tissues. It's quite an intricate dance, with folds and migrations occurring at specific times. That's why you can't regrow lost digits or limbs, or replace damaged brain tissue: the connections those pieces make with the rest of the body are only possible during a specific time in development when all the correct cues and relationships are there.\n\n\n\n\nIn other words, to generate an organ the way it is generated in an embryo, you need a whole embryo. To generate one to an adult size that way, you need to grow a whole adult. Science fiction has used this as a plausible approach, but real society finds it problematic to grow people for the sole purpose of organ harvesting.\n\n\n\n\nRead, for example, the Wikipedia article on heart development (https://en.wikipedia.org/wiki/Heart_development):\n\n\n\n\n\n\n\nIn the splanchnopleuric mesenchyme on either side of the neural plate, a horseshoe-shaped area develops as the cardiogenic region. This has formed from cardiac myoblasts and blood islands as forerunners of blood cells and vessels.[5] By day 19, an endocardial tube begins to develop in each side of this region. These two tubes grow and by the third week have converged towards each other to merge, using programmed cell death to form a single tube, the tubular heart.[6]\n\n\n\n\nFrom splanchnopleuric mesenchyme, the cardiogenic region develops cranially and laterally to the neural plate. In this area, two separate angiogenic cell clusters form on either side and coalesce to form the endocardial tubes. As embryonic folding starts, the two endocardial tubes are pushed into the thoracic cavity, where they begin to fuse together, and this is completed at about 22 days.[7][2]\n\n\n\n\n\n\n\nThe only place you get a splanchnopleuric mesenchyme to start with is going to be a developing embryo. The heart is forming from different clusters of cells migrating and differentiating in a particular pattern.\n\n\n\n\nScaffolding is more of a trick. It gets you away from the organ-level patterning that shapes the entire structure and lets you deal with just the functional units: individual cell types like myocytes that behave sufficiently robotically that if you create approximately the right conditions they will settle in to do their job."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Heart_development"],"ground_truth_type":"metadata_grounded","group_id":"ae617dc663cc8c732d31e2ec1790f00cb3cdb5359e177c179194d484b576c1f9","hard_case_family":["no_accepted_answer"],"id":"RHM-73c894f46c6a4612c36f9581","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":"Gnat","profile_url":"https://biology.stackexchange.com/users/73500/gnat","user_type":"registered"},"created_at":"2023-08-10T15:06:53+00:00","raw_file":"raw/codex_api_v1/fe6e1ab1e4f14040deb1423c04616e4dd0e7de39b583b42e88a31f79f9375e98_1790824028764975800_0.json","raw_sha256":"08e023ccc811ec000989abb19f483814e44277588eeabf130aa5dbaf177079bf","revision_guid":"AE48B198-8ADC-407A-A686-587154186404","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AE48B198-8ADC-407A-A686-587154186404/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":"112777","source_record_sha256":"30baac583cd1bae35bc1470f09e963ea9758db1b432ffb4f6de244d8bf9b7f56","source_url":"https://biology.stackexchange.com/questions/112777/why-is-scaffolding-necessary-in-organ-printing","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Why is scaffolding necessary in organ printing?\nMost organ printing techniques seem to use a structural element for newly created cells to anchor themselves to, be it a biocompatible plastic or some natural material. Naively, I would assume that organs can be generated just the same as they are in an embryo, so why is scaffolding necessary? Here are my guesses:\n\n\n\n\n\nThe time taken to grow an organ to an adult size this way would take too long to be practical\n\n\n\n\nMaking the necessary germlines to emulate those formed in gastrulation is to difficult\n\n\n\n\nOrgans grown this way collapse into themselves without the exact environment present in an embryo (the pressure in an embryo could be necessary, or the formation of all organs concurrently allows each particular organ to maintain a solid boundary between itself and its neighbors)\n\n\n\n\nWithout scaffolding, organs printed in vitro would not generate the auxiliary structures necessary to be useful (nerve endings, blood vessel, etc.)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":112778,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I have done this on <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417122/\" rel=\"nofollow noreferrer\">MiSeq</a> and <a href=\"https://genome.cshlp.org/content/28/8/1169\" rel=\"nofollow noreferrer\">NextSeq</a> though it was several years now. It is possible to <a href=\"https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/novaseq/1000000019358_17_novaseq-6000-system-guide.pdf\" rel=\"nofollow noreferrer\">specify cycle numbers in the GUI input</a> (page 54) <em>in theory</em>, unless they changed things (though they only mention up to 151 cycles).</p>\n<p>I previously emailed Illumina technical support about this (the docs for the NextSeq also said &quot;up to 151 cycles&quot;) and they said this:</p>\n<blockquote>\n<p>The reason the MiSeq 300 cycle kit supports for 250x50 is because the MiSeq chemistry has been tested at those long run lengths and the same chemistry is implemented in the 500 cycle kit that allows for 2x250. In the case of the NextSeq, there is no 500 cycle kit and it has not been tested for run lengths beyond 151. That said, there should not be anything in the software that prevents you from running a 250x50 on a NextSeq 300 cycle kit, but the quality for any cycles past 150 may be low.</p>\n</blockquote>\n<p>It might be worth following up with them to make sure that it would still work.</p>\n<p>For our application, the quality was sufficiently good that we were able to use the data (from a capture panel). Admittedly, we were using a somewhat bespoke alignment strategy rather than e.g. traditional variant calling.</p>\n","answer_id":112995,"answer_text":"I have done this on MiSeq (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417122/) and NextSeq (https://genome.cshlp.org/content/28/8/1169) though it was several years now. It is possible to specify cycle numbers in the GUI input (https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/novaseq/1000000019358_17_novaseq-6000-system-guide.pdf) (page 54) in theory, unless they changed things (though they only mention up to 151 cycles).\n\n\n\n\nI previously emailed Illumina technical support about this (the docs for the NextSeq also said \"up to 151 cycles\") and they said this:\n\n\n\n\n\n\n\nThe reason the MiSeq 300 cycle kit supports for 250x50 is because the MiSeq chemistry has been tested at those long run lengths and the same chemistry is implemented in the 500 cycle kit that allows for 2x250. In the case of the NextSeq, there is no 500 cycle kit and it has not been tested for run lengths beyond 151. That said, there should not be anything in the software that prevents you from running a 250x50 on a NextSeq 300 cycle kit, but the quality for any cycles past 150 may be low.\n\n\n\n\n\n\n\nIt might be worth following up with them to make sure that it would still work.\n\n\n\n\nFor our application, the quality was sufficiently good that we were able to use the data (from a capture panel). Admittedly, we were using a somewhat bespoke alignment strategy rather than e.g. traditional variant calling.","answer_url":"https://biology.stackexchange.com/a/112995","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2023-09-13T22:44:57+00:00","is_accepted":false,"provenance":{"attribution_required":true,"collected_at":"2026-10-01T03:03:41.651282+00:00","license":"CC BY-SA 4.0","license_url":"https://creativecommons.org/licenses/by-sa/4.0/","raw_file":"raw/codex_api_v1/49b81e7da29b3c5ecc961908934a60a3e3d33576f623d7db6647c4f4b3b18dba_0.json","raw_sha256":"0cb9219330a5c9d57f3e474dcdd137ab3c3ae83667c4b84bf434435a38149889","source_api":"Stack Exchange API 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4.0","contributor":{"display_name":"user438383","profile_url":"https://biology.stackexchange.com/users/27357/user438383","user_type":"registered"},"created_at":"2023-08-28T15:27:46+00:00","raw_file":"raw/codex_api_v1/9b8fea4e5df4051aa25c1aa90b42eca7481ee703f92ba25aeabed3d0b53e7a04_1790824026598483100_0.json","raw_sha256":"f252fc1b154815b8794116efb3b685202eda8dddb2cd870ae32ee5e82716c300","revision_guid":"3F53B78C-37AA-44D5-9E2E-1F90A933E0A3","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3F53B78C-37AA-44D5-9E2E-1F90A933E0A3/view-source"}],"url":"https://biology.stackexchange.com/questions/112881/asymmetric-sequencing-can-you-sequence-250-bases-on-illumina-novaseq-s4-read"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"112995","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":"2023-09-13T22:44:57+00:00","raw_file":"raw/codex_api_v1/e8748b7df49bb9b59f68b4817681ee53feb08602d6d12031f4363790483c6b15_1790824036177135400_0.json","raw_sha256":"d8e8486d83750bd0525b4548402485b23c19dd77939ab54c8f02885ef95e4871","revision_guid":"7A24E9CC-ACE8-420D-9AD3-F5C499DCBC5B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7A24E9CC-ACE8-420D-9AD3-F5C499DCBC5B/view-source"}],"url":"https://biology.stackexchange.com/a/112995"}],"contexts":[{"context_id":"question","html":"<p>I would like to sequence 250 bases on Illumina Novaseq S4 on read 2.</p>\n<ol>\n<li><p>Kits of illumina come in the following sizes: <a href=\"https://emea.illumina.com/systems/sequencing-platforms/novaseq/specifications.html\" rel=\"nofollow noreferrer\">https://emea.illumina.com/systems/sequencing-platforms/novaseq/specifications.html</a></p>\n</li>\n<li><p>You can setup the sequencer for asymmetric sequencing, so that from a standard paired-end 2*100bp kit reads 150 bases from R1, and only 50 of the R2 (or vice versa).</p>\n</li>\n<li><p>On SP kit they now support 2 x 250 bp, but not on S4.</p>\n</li>\n<li><p>On the largest S4 kit it would be theoretically possible to sequence 250 + 50.</p>\n</li>\n</ol>\n<p>The read quality at 150 bases is excellent, so I expect at least 200 useful bases.\n​</p>\n<ul>\n<li>Did anyone try this, or could point me to relevant information?</li>\n<li>Can you even specify such strong asymmetry in the software?</li>\n<li>Very importantly: Are there any risk of losing the lane?</li>\n<li>Are there any other risks (other than quality issues beyond 150 bases, which i assume I can easily trim away)?</li>\n</ul>\n<p>ps.: Cross posted on <a href=\"https://www.seqanswers.com/forum/sequencing-technologies-companies/illumina-solexa/324964-asymmetric-sequencing-on-illumina-novaseq-s4-beyond-specification-cycle-transferring\" rel=\"nofollow noreferrer\">seqanswers</a> for a possibly more appropriate audience.</p>\n","text":"I would like to sequence 250 bases on Illumina Novaseq S4 on read 2.\n\n\n\n\n\n\n\nKits of illumina come in the following sizes: https://emea.illumina.com/systems/sequencing-platforms/novaseq/specifications.html (https://emea.illumina.com/systems/sequencing-platforms/novaseq/specifications.html)\n\n\n\n\n\n\n\n\n\nYou can setup the sequencer for asymmetric sequencing, so that from a standard paired-end 2*100bp kit reads 150 bases from R1, and only 50 of the R2 (or vice versa).\n\n\n\n\n\n\n\n\n\nOn SP kit they now support 2 x 250 bp, but not on S4.\n\n\n\n\n\n\n\n\n\nOn the largest S4 kit it would be theoretically possible to sequence 250 + 50.\n\n\n\n\n\n\n\n\nThe read quality at 150 bases is excellent, so I expect at least 200 useful bases.\n​\n\n\n\n\n\nDid anyone try this, or could point me to relevant information?\n\n\n\n\nCan you even specify such strong asymmetry in the software?\n\n\n\n\nVery importantly: Are there any risk of losing the lane?\n\n\n\n\nAre there any other risks (other than quality issues beyond 150 bases, which i assume I can easily trim away)?\n\n\n\n\n\nps.: Cross posted on seqanswers (https://www.seqanswers.com/forum/sequencing-technologies-companies/illumina-solexa/324964-asymmetric-sequencing-on-illumina-novaseq-s4-beyond-specification-cycle-transferring) for a possibly more appropriate audience."},{"context_id":"112995","html":"<p>I have done this on <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417122/\" rel=\"nofollow noreferrer\">MiSeq</a> and <a href=\"https://genome.cshlp.org/content/28/8/1169\" rel=\"nofollow noreferrer\">NextSeq</a> though it was several years now. It is possible to <a href=\"https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/novaseq/1000000019358_17_novaseq-6000-system-guide.pdf\" rel=\"nofollow noreferrer\">specify cycle numbers in the GUI input</a> (page 54) <em>in theory</em>, unless they changed things (though they only mention up to 151 cycles).</p>\n<p>I previously emailed Illumina technical support about this (the docs for the NextSeq also said &quot;up to 151 cycles&quot;) and they said this:</p>\n<blockquote>\n<p>The reason the MiSeq 300 cycle kit supports for 250x50 is because the MiSeq chemistry has been tested at those long run lengths and the same chemistry is implemented in the 500 cycle kit that allows for 2x250. In the case of the NextSeq, there is no 500 cycle kit and it has not been tested for run lengths beyond 151. That said, there should not be anything in the software that prevents you from running a 250x50 on a NextSeq 300 cycle kit, but the quality for any cycles past 150 may be low.</p>\n</blockquote>\n<p>It might be worth following up with them to make sure that it would still work.</p>\n<p>For our application, the quality was sufficiently good that we were able to use the data (from a capture panel). Admittedly, we were using a somewhat bespoke alignment strategy rather than e.g. traditional variant calling.</p>\n","text":"I have done this on MiSeq (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417122/) and NextSeq (https://genome.cshlp.org/content/28/8/1169) though it was several years now. It is possible to specify cycle numbers in the GUI input (https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/novaseq/1000000019358_17_novaseq-6000-system-guide.pdf) (page 54) in theory, unless they changed things (though they only mention up to 151 cycles).\n\n\n\n\nI previously emailed Illumina technical support about this (the docs for the NextSeq also said \"up to 151 cycles\") and they said this:\n\n\n\n\n\n\n\nThe reason the MiSeq 300 cycle kit supports for 250x50 is because the MiSeq chemistry has been tested at those long run lengths and the same chemistry is implemented in the 500 cycle kit that allows for 2x250. In the case of the NextSeq, there is no 500 cycle kit and it has not been tested for run lengths beyond 151. That said, there should not be anything in the software that prevents you from running a 250x50 on a NextSeq 300 cycle kit, but the quality for any cycles past 150 may be low.\n\n\n\n\n\n\n\nIt might be worth following up with them to make sure that it would still work.\n\n\n\n\nFor our application, the quality was sufficiently good that we were able to use the data (from a capture panel). Admittedly, we were using a somewhat bespoke alignment strategy rather than e.g. traditional variant calling."}],"domain":"biology","external_citations":["https://emea.illumina.com/systems/sequencing-platforms/novaseq/specifications.html","https://genome.cshlp.org/content/28/8/1169","https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/novaseq/1000000019358_17_novaseq-6000-system-guide.pdf","https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417122/","https://www.seqanswers.com/forum/sequencing-technologies-companies/illumina-solexa/324964-asymmetric-sequencing-on-illumina-novaseq-s4-beyond-specification-cycle-transferring"],"ground_truth_type":"metadata_grounded","group_id":"4893ed39e654c7d3a390bef433dfa2416993eebbc8343212134ab284eeb2e593","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-80873b545c7826ba4309fcc6","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; 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no LLM truth labels"},"query":"Asymmetric sequencing | Can you sequence 250 bases on Illumina Novaseq S4 (read 2)?\nI would like to sequence 250 bases on Illumina Novaseq S4 on read 2.\n\n\n\n\n\n\n\nKits of illumina come in the following sizes: https://emea.illumina.com/systems/sequencing-platforms/novaseq/specifications.html (https://emea.illumina.com/systems/sequencing-platforms/novaseq/specifications.html)\n\n\n\n\n\n\n\n\n\nYou can setup the sequencer for asymmetric sequencing, so that from a standard paired-end 2*100bp kit reads 150 bases from R1, and only 50 of the R2 (or vice versa).\n\n\n\n\n\n\n\n\n\nOn SP kit they now support 2 x 250 bp, but not on S4.\n\n\n\n\n\n\n\n\n\nOn the largest S4 kit it would be theoretically possible to sequence 250 + 50.\n\n\n\n\n\n\n\n\nThe read quality at 150 bases is excellent, so I expect at least 200 useful bases.\n​\n\n\n\n\n\nDid anyone try this, or could point me to relevant information?\n\n\n\n\nCan you even specify such strong asymmetry in the software?\n\n\n\n\nVery importantly: Are there any risk of losing the lane?\n\n\n\n\nAre there any other risks (other than quality issues beyond 150 bases, which i assume I can easily trim away)?\n\n\n\n\n\nps.: Cross posted on seqanswers (https://www.seqanswers.com/forum/sequencing-technologies-companies/illumina-solexa/324964-asymmetric-sequencing-on-illumina-novaseq-s4-beyond-specification-cycle-transferring) for a possibly more appropriate audience.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":112995,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I don't have in depth knowledge about how amphibians are regenerate their limbs but in embryonic development all tissue's cells differentiate and come from stem cells according to tissue they inhibit or enhance the transcription of which genes that defines the attributes of tissue. Connective tissue such as fibroblasts differentiated from mesenchymal stem cells. So, in theory if you want to regnerate or in this case replace the &quot;Feminine&quot; muscle and bone alignment with &quot;masculine&quot; we need Embryonic STEM cells to generate it but also we need to broke down former ones. So just we need to utilize apoptosis and use gene therapy to do that. There is risks involved currently with recent gene theraphy techniques and also concentrations and conditions in vitro are affecting the differentiation process when using ste cells. In short every tissues fate decided by STEM cells. Ah I checked stem cells, I just googled sex change by stem cells and find some articles\nClick <a href=\"https://www.cell.com/stem-cell-reports/fulltext/S2213-6711(22)00513-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2213671122005136%3Fshowall%3Dtrue#secsectitle0010\" rel=\"nofollow noreferrer\">first</a>!  &quot;They produce male and female stem cells from same person that have mosaicism&quot;</p>\n<p>And also <a href=\"https://www.liebertpub.com/doi/10.1089/ten.teb.2022.0067\" rel=\"nofollow noreferrer\">second</a>!&quot;Tissue Engineering Neovagina for Vaginoplasty in Mayer–Rokitansky–Küster–Hauser Syndrome and Gender Dysphoria Patients: A Systematic Review&quot;</p>\n<p>And <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5772725/\" rel=\"nofollow noreferrer\">lastly</a>!&quot;Biotechnologies that empower transgender persons to self-actualize as individuals, partners, spouses, and parents are defining new ways to conceive a child: psychological considerations and ethical issues&quot;</p>\n","answer_id":112903,"answer_text":"I don't have in depth knowledge about how amphibians are regenerate their limbs but in embryonic development all tissue's cells differentiate and come from stem cells according to tissue they inhibit or enhance the transcription of which genes that defines the attributes of tissue. Connective tissue such as fibroblasts differentiated from mesenchymal stem cells. So, in theory if you want to regnerate or in this case replace the \"Feminine\" muscle and bone alignment with \"masculine\" we need Embryonic STEM cells to generate it but also we need to broke down former ones. So just we need to utilize apoptosis and use gene therapy to do that. There is risks involved currently with recent gene theraphy techniques and also concentrations and conditions in vitro are affecting the differentiation process when using ste cells. In short every tissues fate decided by STEM cells. Ah I checked stem cells, I just googled sex change by stem cells and find some articles\nClick first (https://www.cell.com/stem-cell-reports/fulltext/S2213-6711(22)00513-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2213671122005136%3Fshowall%3Dtrue#secsectitle0010)!  \"They produce male and female stem cells from same person that have mosaicism\"\n\n\n\n\nAnd also second (https://www.liebertpub.com/doi/10.1089/ten.teb.2022.0067)!\"Tissue Engineering Neovagina for Vaginoplasty in Mayer–Rokitansky–Küster–Hauser Syndrome and Gender Dysphoria Patients: A Systematic Review\"\n\n\n\n\nAnd lastly (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5772725/)!\"Biotechnologies that empower transgender persons to self-actualize as individuals, partners, spouses, and parents are defining new ways to conceive a child: psychological considerations and ethical issues\"","answer_url":"https://biology.stackexchange.com/a/112903","author":"Nehir Altun","author_url":"https://biology.stackexchange.com/users/76747/nehir-altun","content_license":"CC BY-SA 4.0","created_at":"2023-08-30T00:10:08+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 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Altun","author_url":"https://biology.stackexchange.com/users/76747/nehir-altun","content_license":"CC BY-SA 4.0","context_id":"112903","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Nehir Altun","profile_url":"https://biology.stackexchange.com/users/76747/nehir-altun","user_type":"registered"},"created_at":"2023-08-30T00:10:08+00:00","raw_file":"raw/codex_api_v1/9b8fea4e5df4051aa25c1aa90b42eca7481ee703f92ba25aeabed3d0b53e7a04_1790824026598483100_0.json","raw_sha256":"f252fc1b154815b8794116efb3b685202eda8dddb2cd870ae32ee5e82716c300","revision_guid":"2DBBABFC-9A78-4CFC-9C57-D7726A3FD158","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2DBBABFC-9A78-4CFC-9C57-D7726A3FD158/view-source"}],"url":"https://biology.stackexchange.com/a/112903"}],"contexts":[{"context_id":"question","html":"<p>I have a question regarding how positional memory in fibroblasts work, specifically, where the memory comes from/how its made.</p>\n<p>For example, the Salamander &amp; other amphibians are able to regenerate almost perfect copies of decapitated limbs, but lets say we have a female Salamander who is effectively given hormone therapy to “masculinise” them, if a limb was severed, would it grow back according to the hormone profile? So essentially a bit smaller since males are typically smaller?</p>\n<p>I’m very interested in the possibility of sex change through genetics, especially after bones have fused, effectively a reversal. It seems as though this may be a way forward though I am unsure.</p>\n<p>Thank you for reading!</p>\n","text":"I have a question regarding how positional memory in fibroblasts work, specifically, where the memory comes from/how its made.\n\n\n\n\nFor example, the Salamander & other amphibians are able to regenerate almost perfect copies of decapitated limbs, but lets say we have a female Salamander who is effectively given hormone therapy to “masculinise” them, if a limb was severed, would it grow back according to the hormone profile? So essentially a bit smaller since males are typically smaller?\n\n\n\n\nI’m very interested in the possibility of sex change through genetics, especially after bones have fused, effectively a reversal. It seems as though this may be a way forward though I am unsure.\n\n\n\n\nThank you for reading!"},{"context_id":"112903","html":"<p>I don't have in depth knowledge about how amphibians are regenerate their limbs but in embryonic development all tissue's cells differentiate and come from stem cells according to tissue they inhibit or enhance the transcription of which genes that defines the attributes of tissue. Connective tissue such as fibroblasts differentiated from mesenchymal stem cells. So, in theory if you want to regnerate or in this case replace the &quot;Feminine&quot; muscle and bone alignment with &quot;masculine&quot; we need Embryonic STEM cells to generate it but also we need to broke down former ones. So just we need to utilize apoptosis and use gene therapy to do that. There is risks involved currently with recent gene theraphy techniques and also concentrations and conditions in vitro are affecting the differentiation process when using ste cells. In short every tissues fate decided by STEM cells. Ah I checked stem cells, I just googled sex change by stem cells and find some articles\nClick <a href=\"https://www.cell.com/stem-cell-reports/fulltext/S2213-6711(22)00513-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2213671122005136%3Fshowall%3Dtrue#secsectitle0010\" rel=\"nofollow noreferrer\">first</a>!  &quot;They produce male and female stem cells from same person that have mosaicism&quot;</p>\n<p>And also <a href=\"https://www.liebertpub.com/doi/10.1089/ten.teb.2022.0067\" rel=\"nofollow noreferrer\">second</a>!&quot;Tissue Engineering Neovagina for Vaginoplasty in Mayer–Rokitansky–Küster–Hauser Syndrome and Gender Dysphoria Patients: A Systematic Review&quot;</p>\n<p>And <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5772725/\" rel=\"nofollow noreferrer\">lastly</a>!&quot;Biotechnologies that empower transgender persons to self-actualize as individuals, partners, spouses, and parents are defining new ways to conceive a child: psychological considerations and ethical issues&quot;</p>\n","text":"I don't have in depth knowledge about how amphibians are regenerate their limbs but in embryonic development all tissue's cells differentiate and come from stem cells according to tissue they inhibit or enhance the transcription of which genes that defines the attributes of tissue. Connective tissue such as fibroblasts differentiated from mesenchymal stem cells. So, in theory if you want to regnerate or in this case replace the \"Feminine\" muscle and bone alignment with \"masculine\" we need Embryonic STEM cells to generate it but also we need to broke down former ones. So just we need to utilize apoptosis and use gene therapy to do that. There is risks involved currently with recent gene theraphy techniques and also concentrations and conditions in vitro are affecting the differentiation process when using ste cells. In short every tissues fate decided by STEM cells. Ah I checked stem cells, I just googled sex change by stem cells and find some articles\nClick first (https://www.cell.com/stem-cell-reports/fulltext/S2213-6711(22)00513-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2213671122005136%3Fshowall%3Dtrue#secsectitle0010)!  \"They produce male and female stem cells from same person that have mosaicism\"\n\n\n\n\nAnd also second (https://www.liebertpub.com/doi/10.1089/ten.teb.2022.0067)!\"Tissue Engineering Neovagina for Vaginoplasty in Mayer–Rokitansky–Küster–Hauser Syndrome and Gender Dysphoria Patients: A Systematic Review\"\n\n\n\n\nAnd lastly (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5772725/)!\"Biotechnologies that empower transgender persons to self-actualize as individuals, partners, spouses, and parents are defining new ways to conceive a child: psychological considerations and ethical 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{"accepted_status":{"accepted_answer_id":113908,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>@sir-thinksalot is correct. This is an <em>Ephedra</em> species. You can have a look at <a href=\"https://www.jardindesplantesdeparis.fr/system/files/atoms/files/doc_serre_histoire_des_plantes.pdf\" rel=\"nofollow noreferrer\">this PDF</a> to get some spatial orientation - it should be with the Gnetales. You can look which species of Ephedra are known to be cultivated in French botanical gardens via a <a href=\"https://plantsearch.bgci.org/search?filter%5Bgenus%5D=Ephedra&amp;filter%5Bcountry%5D=FR&amp;filter%5Bcontinent%5D=EU&amp;sort=name\" rel=\"nofollow noreferrer\">search</a> on the BGCI database. I couldn't find a public database for the plants of the Jardin des Plantes, and it isn't mentioned on the <a href=\"https://www.mnhn.fr/fr/les-plantes-de-nos-jardins\" rel=\"nofollow noreferrer\">accompanying MNHN website</a>. If you are really interested, you <a href=\"https://www.jardindesplantesdeparis.fr/fr/contactez-nous\" rel=\"nofollow noreferrer\">can drop them a line</a> and ask which species it is.</p>\n","answer_id":113908,"answer_text":"@sir-thinksalot is correct. This is an Ephedra species. You can have a look at this PDF (https://www.jardindesplantesdeparis.fr/system/files/atoms/files/doc_serre_histoire_des_plantes.pdf) to get some spatial orientation - it should be with the Gnetales. You can look which species of Ephedra are known to be cultivated in French botanical gardens via a search (https://plantsearch.bgci.org/search?filter%5Bgenus%5D=Ephedra&filter%5Bcountry%5D=FR&filter%5Bcontinent%5D=EU&sort=name) on the BGCI database. I couldn't find a public database for the plants of the Jardin des Plantes, and it isn't mentioned on the accompanying MNHN website (https://www.mnhn.fr/fr/les-plantes-de-nos-jardins). If you are really interested, you can drop them a line (https://www.jardindesplantesdeparis.fr/fr/contactez-nous) and ask which species it is.","answer_url":"https://biology.stackexchange.com/a/113908","author":"aae","author_url":"https://biology.stackexchange.com/users/10502/aae","content_license":"CC BY-SA 4.0","created_at":"2024-01-18T10:59:50+00:00","is_accepted":true,"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":113014,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"aae","profile_url":"https://biology.stackexchange.com/users/10502/aae","user_type":"registered"},"created_at":"2024-01-18T10:59:50+00:00","raw_file":"raw/codex_api_v1/fed5002b402abc518f9d443cac70e76046b4c7d61364c4373bcc2f7aa788fb91_1790824061497491200_0.json","raw_sha256":"cab272c600f7d876f66bed0a120539ebe819cda597f762c6492e5203d22b4e07","revision_guid":"94A3B479-3171-4B41-BF10-3C868FD9EC4B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/94A3B479-3171-4B41-BF10-3C868FD9EC4B/view-source"},{"content_license":null,"contributor":{"display_name":"theforestecologist","profile_url":"https://biology.stackexchange.com/users/16866/theforestecologist","user_type":"registered"},"created_at":"2024-05-14T03:36:36+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"43C32364-B139-41E6-B921-3B46362CF511","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/43C32364-B139-41E6-B921-3B46362CF511/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"G. 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Blaickner","profile_url":"https://biology.stackexchange.com/users/76678/g-blaickner","user_type":"registered"},"created_at":"2023-09-16T13:33:34+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"5F377953-C74E-40F7-914A-3B5B215A4BFC","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5F377953-C74E-40F7-914A-3B5B215A4BFC/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2023-11-02T15:00:45+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"CCB50FCB-53AF-4463-A899-7F076A86E8AC","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/CCB50FCB-53AF-4463-A899-7F076A86E8AC/view-source"}],"url":"https://biology.stackexchange.com/questions/113014/identifying-a-plant-in-the-botanical-garden-of-paris"},{"author":"aae","author_url":"https://biology.stackexchange.com/users/10502/aae","content_license":"CC BY-SA 4.0","context_id":"113908","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"aae","profile_url":"https://biology.stackexchange.com/users/10502/aae","user_type":"registered"},"created_at":"2024-01-18T10:59:50+00:00","raw_file":"raw/codex_api_v1/fed5002b402abc518f9d443cac70e76046b4c7d61364c4373bcc2f7aa788fb91_1790824061497491200_0.json","raw_sha256":"cab272c600f7d876f66bed0a120539ebe819cda597f762c6492e5203d22b4e07","revision_guid":"94A3B479-3171-4B41-BF10-3C868FD9EC4B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/94A3B479-3171-4B41-BF10-3C868FD9EC4B/view-source"},{"content_license":null,"contributor":{"display_name":"theforestecologist","profile_url":"https://biology.stackexchange.com/users/16866/theforestecologist","user_type":"registered"},"created_at":"2024-05-14T03:36:36+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"43C32364-B139-41E6-B921-3B46362CF511","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/43C32364-B139-41E6-B921-3B46362CF511/view-source"}],"url":"https://biology.stackexchange.com/a/113908"}],"contexts":[{"context_id":"question","html":"<p>I went to the botanical garden in the &quot;Jardin des Plantes&quot; in Paris. In a glasshouse with the name &quot;Serre de l'histoire des plantes&quot; on the natural history of plants (exhibiting some ancient members of plants like ferns, Cyatheales, etc.), I found the tree-like plant on the picture attached below (the one with grass-like looking &quot;leaves&quot;; unfortunately, I don't have a better picture because it was a bit hidden). There was no sign labelling this particular plant, or at least I was not able to spot any. Does anyone know what type of plant this is? It was rather small, roughly 2 meters in height.</p>\n<p><a href=\"https://i.sstatic.net/3e7wV.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/3e7wV.jpg\" alt=\"enter image description here\" /></a></p>\n<p><a href=\"https://i.sstatic.net/zqc4d.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/zqc4d.jpg\" alt=\"enter image description here\" /></a></p>\n","text":"I went to the botanical garden in the \"Jardin des Plantes\" in Paris. In a glasshouse with the name \"Serre de l'histoire des plantes\" on the natural history of plants (exhibiting some ancient members of plants like ferns, Cyatheales, etc.), I found the tree-like plant on the picture attached below (the one with grass-like looking \"leaves\"; unfortunately, I don't have a better picture because it was a bit hidden). There was no sign labelling this particular plant, or at least I was not able to spot any. Does anyone know what type of plant this is? It was rather small, roughly 2 meters in height.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/3e7wV.jpg] (https://i.sstatic.net/3e7wV.jpg)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/zqc4d.jpg] (https://i.sstatic.net/zqc4d.jpg)"},{"context_id":"113908","html":"<p>@sir-thinksalot is correct. This is an <em>Ephedra</em> species. You can have a look at <a href=\"https://www.jardindesplantesdeparis.fr/system/files/atoms/files/doc_serre_histoire_des_plantes.pdf\" rel=\"nofollow noreferrer\">this PDF</a> to get some spatial orientation - it should be with the Gnetales. You can look which species of Ephedra are known to be cultivated in French botanical gardens via a <a href=\"https://plantsearch.bgci.org/search?filter%5Bgenus%5D=Ephedra&amp;filter%5Bcountry%5D=FR&amp;filter%5Bcontinent%5D=EU&amp;sort=name\" rel=\"nofollow noreferrer\">search</a> on the BGCI database. I couldn't find a public database for the plants of the Jardin des Plantes, and it isn't mentioned on the <a href=\"https://www.mnhn.fr/fr/les-plantes-de-nos-jardins\" rel=\"nofollow noreferrer\">accompanying MNHN website</a>. If you are really interested, you <a href=\"https://www.jardindesplantesdeparis.fr/fr/contactez-nous\" rel=\"nofollow noreferrer\">can drop them a line</a> and ask which species it is.</p>\n","text":"@sir-thinksalot is correct. This is an Ephedra species. You can have a look at this PDF (https://www.jardindesplantesdeparis.fr/system/files/atoms/files/doc_serre_histoire_des_plantes.pdf) to get some spatial orientation - it should be with the Gnetales. You can look which species of Ephedra are known to be cultivated in French botanical gardens via a search (https://plantsearch.bgci.org/search?filter%5Bgenus%5D=Ephedra&filter%5Bcountry%5D=FR&filter%5Bcontinent%5D=EU&sort=name) on the BGCI database. I couldn't find a public database for the plants of the Jardin des Plantes, and it isn't mentioned on the accompanying MNHN website (https://www.mnhn.fr/fr/les-plantes-de-nos-jardins). If you are really interested, you can drop them a line (https://www.jardindesplantesdeparis.fr/fr/contactez-nous) and ask which species it is."}],"domain":"biology","external_citations":["https://i.sstatic.net/3e7wV.jpg","https://i.sstatic.net/zqc4d.jpg","https://plantsearch.bgci.org/search?filter%5Bgenus%5D=Ephedra&filter%5Bcountry%5D=FR&filter%5Bcontinent%5D=EU&sort=name","https://www.jardindesplantesdeparis.fr/fr/contactez-nous","https://www.jardindesplantesdeparis.fr/system/files/atoms/files/doc_serre_histoire_des_plantes.pdf","https://www.mnhn.fr/fr/les-plantes-de-nos-jardins"],"ground_truth_type":"metadata_grounded","group_id":"61f3bcf646a7ea2264f37a0492063f430d6cf361f2844c64228ad72434f87759","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-5aaabcdeaefdb4007f2de37f","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":"G. 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Blaickner","profile_url":"https://biology.stackexchange.com/users/76678/g-blaickner","user_type":"registered"},"created_at":"2023-09-15T12:59:23+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"5737ADC8-3468-40C1-BB83-4520F66B16D0","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5737ADC8-3468-40C1-BB83-4520F66B16D0/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":"2023-09-16T13:33:34+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"5F377953-C74E-40F7-914A-3B5B215A4BFC","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5F377953-C74E-40F7-914A-3B5B215A4BFC/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2023-11-02T15:00:45+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"CCB50FCB-53AF-4463-A899-7F076A86E8AC","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/CCB50FCB-53AF-4463-A899-7F076A86E8AC/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":"113014","source_record_sha256":"2ca701201e3944634aa30f946e3b377c734296701636e8aebbc7fa03e13f6639","source_url":"https://biology.stackexchange.com/questions/113014/identifying-a-plant-in-the-botanical-garden-of-paris","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Identifying a plant in the botanical garden of Paris\nI went to the botanical garden in the \"Jardin des Plantes\" in Paris. In a glasshouse with the name \"Serre de l'histoire des plantes\" on the natural history of plants (exhibiting some ancient members of plants like ferns, Cyatheales, etc.), I found the tree-like plant on the picture attached below (the one with grass-like looking \"leaves\"; unfortunately, I don't have a better picture because it was a bit hidden). There was no sign labelling this particular plant, or at least I was not able to spot any. Does anyone know what type of plant this is? It was rather small, roughly 2 meters in height.\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/3e7wV.jpg] (https://i.sstatic.net/3e7wV.jpg)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/zqc4d.jpg] (https://i.sstatic.net/zqc4d.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113908,"score":3}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Let me give two separate answers.</p>\n<p>First, for your example specifically, you could design a test to see whether body size has any selective effect from your proposed mechanisms.  There are 4 tests, you'd need to do to establish the hypothesis. First you have to test whether the opposite sex finds your proposed trait attractive.  For example, inject half the animals with growth hormone so they become large and see if the opposite sex prefers them or not.  Second, stunt the growth of half the animals so they become small and again test to see whether the opposite sex actually finds them attractive or not. It's possible the opposite sex won't even notice the difference much less make mating choices based on them.  You need two more experiments to establish the cost of the trait in natural selection.  Test whether larger animals have more trouble surviving harsh winter by measuring the amount of food they each eat and seeing if animals that eat less food actually suffer health consequences.  Maybe they just hibernate an extra week and everything is fine.  Similarly with the small animals, test to see if small animals really do get caught and eaten by predators more often.  Only once you have shown that the trait of interest has a negative effect on the animal's survival but a positive effect on its mating chances, does the handicap principle come into consideration as a possibility.</p>\n<p>Unfortunately, before you can come close to concluding that's the reason, you have to look at all the other possibilities.  For example, maybe the reason larger animals have better mating success isn't because they signal being healthy enough to compensate for their size disadvantage.  Instead, if animals grow large BECAUSE they eat lot's of food, then perhaps the opposite sex will select them for mating because the animal sends a signal that they are good at finding food and thus will find a lot of food for the children they have together.  There is often a strong incentive to find a mate that can find enough food for your children.  There could also be genetic linkage between traits that control size and traits that control some other gene of interest.  For example, if the size genes are next to the genes for pheromone emissions, then maybe it's completely by luck that the larger animals also have genes that emit more mating pheromones to attract mates, and actually the opposite sex is selecting on that.  There could also be linkage between the gene for body size and gene for mate preference.  I don't want to write  a super long explanation, so look up &quot;runaway sexual selection.&quot;  And of course, there are many, many other possibilities.  For example, the sexy sons hypothesis posits that females will select sexy males not because they find the males attractive, but because other females do.  And they want their own male offspring to be found attractive, so therefore they decide to mate with a male that is considered handsome so that her sons which carry her genes will be able to mate a lot.  And there's a lot of complexity with any specific real world example.</p>\n<p>So this brings me to my second answer which is that while it's fun to think about these concepts, and its certainly useful to study these things in terms of being able to explain the natural world. That is, find evidence for the hypotheses, try to find examples, etc.  At the end of the day, I wouldn't put too much stock into these types of considerations.  It takes a lot of work than can actually be done in most cases to prove one specific reason is why a species has its mating habits, and once you do prove it, so what?  It was all just random to begin with, and other times, other random things will happen, so its not too impressive to say &quot;hey, this time the random thing that happened is the handicap principle because of all these interesting reasons, circumstances, and coincidences.&quot;  Biology is a very unsophisticated science, and evolution (my area of expertise) is probably the least sophisticated of all the fields within biology, so as long as you don't buy into these theories hook line and sinker, you can have a lot of fun bullshitting about what might or might not be and even trying to actually test these things when possible (which it usually isn't; I mean who's cruel enough to inject animals with growth hormone just to see if the opposite sex finds them more attractive?)</p>\n","answer_id":113199,"answer_text":"Let me give two separate answers.\n\n\n\n\nFirst, for your example specifically, you could design a test to see whether body size has any selective effect from your proposed mechanisms.  There are 4 tests, you'd need to do to establish the hypothesis. First you have to test whether the opposite sex finds your proposed trait attractive.  For example, inject half the animals with growth hormone so they become large and see if the opposite sex prefers them or not.  Second, stunt the growth of half the animals so they become small and again test to see whether the opposite sex actually finds them attractive or not. It's possible the opposite sex won't even notice the difference much less make mating choices based on them.  You need two more experiments to establish the cost of the trait in natural selection.  Test whether larger animals have more trouble surviving harsh winter by measuring the amount of food they each eat and seeing if animals that eat less food actually suffer health consequences.  Maybe they just hibernate an extra week and everything is fine.  Similarly with the small animals, test to see if small animals really do get caught and eaten by predators more often.  Only once you have shown that the trait of interest has a negative effect on the animal's survival but a positive effect on its mating chances, does the handicap principle come into consideration as a possibility.\n\n\n\n\nUnfortunately, before you can come close to concluding that's the reason, you have to look at all the other possibilities.  For example, maybe the reason larger animals have better mating success isn't because they signal being healthy enough to compensate for their size disadvantage.  Instead, if animals grow large BECAUSE they eat lot's of food, then perhaps the opposite sex will select them for mating because the animal sends a signal that they are good at finding food and thus will find a lot of food for the children they have together.  There is often a strong incentive to find a mate that can find enough food for your children.  There could also be genetic linkage between traits that control size and traits that control some other gene of interest.  For example, if the size genes are next to the genes for pheromone emissions, then maybe it's completely by luck that the larger animals also have genes that emit more mating pheromones to attract mates, and actually the opposite sex is selecting on that.  There could also be linkage between the gene for body size and gene for mate preference.  I don't want to write  a super long explanation, so look up \"runaway sexual selection.\"  And of course, there are many, many other possibilities.  For example, the sexy sons hypothesis posits that females will select sexy males not because they find the males attractive, but because other females do.  And they want their own male offspring to be found attractive, so therefore they decide to mate with a male that is considered handsome so that her sons which carry her genes will be able to mate a lot.  And there's a lot of complexity with any specific real world example.\n\n\n\n\nSo this brings me to my second answer which is that while it's fun to think about these concepts, and its certainly useful to study these things in terms of being able to explain the natural world. That is, find evidence for the hypotheses, try to find examples, etc.  At the end of the day, I wouldn't put too much stock into these types of considerations.  It takes a lot of work than can actually be done in most cases to prove one specific reason is why a species has its mating habits, and once you do prove it, so what?  It was all just random to begin with, and other times, other random things will happen, so its not too impressive to say \"hey, this time the random thing that happened is the handicap principle because of all these interesting reasons, circumstances, and coincidences.\"  Biology is a very unsophisticated science, and evolution (my area of expertise) is probably the least sophisticated of all the fields within biology, so as long as you don't buy into these theories hook line and sinker, you can have a lot of fun bullshitting about what might or might not be and even trying to actually test these things when possible (which it usually isn't; I mean who's cruel enough to inject animals with growth hormone just to see if the opposite sex finds them more attractive?)","answer_url":"https://biology.stackexchange.com/a/113199","author":"A Friendly Fish","author_url":"https://biology.stackexchange.com/users/77215/a-friendly-fish","content_license":"CC BY-SA 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yet.</p>\n","answer_id":114278,"answer_text":"Does this discredit individual applications of the handicap\nprinciple?\n\n\n\n\n\n\n\nBoth support the handicap principle.\n\n\n\n\n\n\n\nOr is there a way to measure the extent to which the handicap\nprinciple has affected selection of any given trait?\n\n\n\n\n\n\n\nNo, there is not a good way to do this yet.","answer_url":"https://biology.stackexchange.com/a/114278","author":"BigMistake","author_url":"https://biology.stackexchange.com/users/75355/bigmistake","content_license":"CC BY-SA 4.0","created_at":"2024-03-08T06:27:22+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 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Friendly Fish","author_url":"https://biology.stackexchange.com/users/77215/a-friendly-fish","content_license":"CC BY-SA 4.0","context_id":"113199","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"A Friendly Fish","profile_url":"https://biology.stackexchange.com/users/77215/a-friendly-fish","user_type":"registered"},"created_at":"2023-10-09T05:36:56+00:00","raw_file":"raw/codex_api_v1/6af9c7d042670008467ed73a4907cf5040455dcec44ada30c72785b8ae9c030c_1790824043634594200_0.json","raw_sha256":"86af78543bd42fa5daff5720e8d8724ccf27acfab275d042193c1f18cc524c18","revision_guid":"1EA0CABD-5153-4F7C-B1F2-DED34303A2F0","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/1EA0CABD-5153-4F7C-B1F2-DED34303A2F0/view-source"}],"url":"https://biology.stackexchange.com/a/113199"},{"author":"BigMistake","author_url":"https://biology.stackexchange.com/users/75355/bigmistake","content_license":"CC BY-SA 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However, it seems that this principle could be used to justify sexual selection of almost any trait. Consider the following examples justifying selection of two opposite traits:</p>\n<blockquote>\n<p>Assuming everything else equal, an individual with a larger body has higher nutritional requirements, which are harder to meet. Therefore individuals with larger body sizes were selected because that signals higher fitness.</p>\n</blockquote>\n<blockquote>\n<p>Assuming everything else equal, an individual with a smaller body can't protect itself as effectively. Therefore individuals with smaller body sizes were selected because that signals higher fitness.</p>\n</blockquote>\n<p>Does this discredit individual applications of the handicap principle? Or is there a way to measure the extent to which the handicap principle has affected selection of any given trait?</p>\n","text":"The handicap principle (https://en.wikipedia.org/wiki/Handicap_principle) is used as an explanation for some genetic traits, such as bright tails in male peacocks. However, it seems that this principle could be used to justify sexual selection of almost any trait. Consider the following examples justifying selection of two opposite traits:\n\n\n\n\n\n\n\nAssuming everything else equal, an individual with a larger body has higher nutritional requirements, which are harder to meet. Therefore individuals with larger body sizes were selected because that signals higher fitness.\n\n\n\n\n\n\n\n\n\n\nAssuming everything else equal, an individual with a smaller body can't protect itself as effectively. Therefore individuals with smaller body sizes were selected because that signals higher fitness.\n\n\n\n\n\n\n\nDoes this discredit individual applications of the handicap principle? Or is there a way to measure the extent to which the handicap principle has affected selection of any given trait?"},{"context_id":"113199","html":"<p>Let me give two separate answers.</p>\n<p>First, for your example specifically, you could design a test to see whether body size has any selective effect from your proposed mechanisms.  There are 4 tests, you'd need to do to establish the hypothesis. First you have to test whether the opposite sex finds your proposed trait attractive.  For example, inject half the animals with growth hormone so they become large and see if the opposite sex prefers them or not.  Second, stunt the growth of half the animals so they become small and again test to see whether the opposite sex actually finds them attractive or not. It's possible the opposite sex won't even notice the difference much less make mating choices based on them.  You need two more experiments to establish the cost of the trait in natural selection.  Test whether larger animals have more trouble surviving harsh winter by measuring the amount of food they each eat and seeing if animals that eat less food actually suffer health consequences.  Maybe they just hibernate an extra week and everything is fine.  Similarly with the small animals, test to see if small animals really do get caught and eaten by predators more often.  Only once you have shown that the trait of interest has a negative effect on the animal's survival but a positive effect on its mating chances, does the handicap principle come into consideration as a possibility.</p>\n<p>Unfortunately, before you can come close to concluding that's the reason, you have to look at all the other possibilities.  For example, maybe the reason larger animals have better mating success isn't because they signal being healthy enough to compensate for their size disadvantage.  Instead, if animals grow large BECAUSE they eat lot's of food, then perhaps the opposite sex will select them for mating because the animal sends a signal that they are good at finding food and thus will find a lot of food for the children they have together.  There is often a strong incentive to find a mate that can find enough food for your children.  There could also be genetic linkage between traits that control size and traits that control some other gene of interest.  For example, if the size genes are next to the genes for pheromone emissions, then maybe it's completely by luck that the larger animals also have genes that emit more mating pheromones to attract mates, and actually the opposite sex is selecting on that.  There could also be linkage between the gene for body size and gene for mate preference.  I don't want to write  a super long explanation, so look up &quot;runaway sexual selection.&quot;  And of course, there are many, many other possibilities.  For example, the sexy sons hypothesis posits that females will select sexy males not because they find the males attractive, but because other females do.  And they want their own male offspring to be found attractive, so therefore they decide to mate with a male that is considered handsome so that her sons which carry her genes will be able to mate a lot.  And there's a lot of complexity with any specific real world example.</p>\n<p>So this brings me to my second answer which is that while it's fun to think about these concepts, and its certainly useful to study these things in terms of being able to explain the natural world. That is, find evidence for the hypotheses, try to find examples, etc.  At the end of the day, I wouldn't put too much stock into these types of considerations.  It takes a lot of work than can actually be done in most cases to prove one specific reason is why a species has its mating habits, and once you do prove it, so what?  It was all just random to begin with, and other times, other random things will happen, so its not too impressive to say &quot;hey, this time the random thing that happened is the handicap principle because of all these interesting reasons, circumstances, and coincidences.&quot;  Biology is a very unsophisticated science, and evolution (my area of expertise) is probably the least sophisticated of all the fields within biology, so as long as you don't buy into these theories hook line and sinker, you can have a lot of fun bullshitting about what might or might not be and even trying to actually test these things when possible (which it usually isn't; I mean who's cruel enough to inject animals with growth hormone just to see if the opposite sex finds them more attractive?)</p>\n","text":"Let me give two separate answers.\n\n\n\n\nFirst, for your example specifically, you could design a test to see whether body size has any selective effect from your proposed mechanisms.  There are 4 tests, you'd need to do to establish the hypothesis. First you have to test whether the opposite sex finds your proposed trait attractive.  For example, inject half the animals with growth hormone so they become large and see if the opposite sex prefers them or not.  Second, stunt the growth of half the animals so they become small and again test to see whether the opposite sex actually finds them attractive or not. It's possible the opposite sex won't even notice the difference much less make mating choices based on them.  You need two more experiments to establish the cost of the trait in natural selection.  Test whether larger animals have more trouble surviving harsh winter by measuring the amount of food they each eat and seeing if animals that eat less food actually suffer health consequences.  Maybe they just hibernate an extra week and everything is fine.  Similarly with the small animals, test to see if small animals really do get caught and eaten by predators more often.  Only once you have shown that the trait of interest has a negative effect on the animal's survival but a positive effect on its mating chances, does the handicap principle come into consideration as a possibility.\n\n\n\n\nUnfortunately, before you can come close to concluding that's the reason, you have to look at all the other possibilities.  For example, maybe the reason larger animals have better mating success isn't because they signal being healthy enough to compensate for their size disadvantage.  Instead, if animals grow large BECAUSE they eat lot's of food, then perhaps the opposite sex will select them for mating because the animal sends a signal that they are good at finding food and thus will find a lot of food for the children they have together.  There is often a strong incentive to find a mate that can find enough food for your children.  There could also be genetic linkage between traits that control size and traits that control some other gene of interest.  For example, if the size genes are next to the genes for pheromone emissions, then maybe it's completely by luck that the larger animals also have genes that emit more mating pheromones to attract mates, and actually the opposite sex is selecting on that.  There could also be linkage between the gene for body size and gene for mate preference.  I don't want to write  a super long explanation, so look up \"runaway sexual selection.\"  And of course, there are many, many other possibilities.  For example, the sexy sons hypothesis posits that females will select sexy males not because they find the males attractive, but because other females do.  And they want their own male offspring to be found attractive, so therefore they decide to mate with a male that is considered handsome so that her sons which carry her genes will be able to mate a lot.  And there's a lot of complexity with any specific real world example.\n\n\n\n\nSo this brings me to my second answer which is that while it's fun to think about these concepts, and its certainly useful to study these things in terms of being able to explain the natural world. That is, find evidence for the hypotheses, try to find examples, etc.  At the end of the day, I wouldn't put too much stock into these types of considerations.  It takes a lot of work than can actually be done in most cases to prove one specific reason is why a species has its mating habits, and once you do prove it, so what?  It was all just random to begin with, and other times, other random things will happen, so its not too impressive to say \"hey, this time the random thing that happened is the handicap principle because of all these interesting reasons, circumstances, and coincidences.\"  Biology is a very unsophisticated science, and evolution (my area of expertise) is probably the least sophisticated of all the fields within biology, so as long as you don't buy into these theories hook line and sinker, you can have a lot of fun bullshitting about what might or might not be and even trying to actually test these things when possible (which it usually isn't; I mean who's cruel enough to inject animals with growth hormone just to see if the opposite sex finds them more attractive?)"},{"context_id":"114278","html":"<blockquote>\n<p>Does this discredit individual applications of the handicap\nprinciple?</p>\n</blockquote>\n<p>Both support the handicap principle.</p>\n<blockquote>\n<p>Or is there a way to measure the extent to which the handicap\nprinciple has affected selection of any given trait?</p>\n</blockquote>\n<p>No, there is not a good way to do this yet.</p>\n","text":"Does this discredit individual applications of the handicap\nprinciple?\n\n\n\n\n\n\n\nBoth support the handicap principle.\n\n\n\n\n\n\n\nOr is there a way to measure the extent to which the handicap\nprinciple has affected selection of any given trait?\n\n\n\n\n\n\n\nNo, there is not a good way to do this yet."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Handicap_principle"],"ground_truth_type":"metadata_grounded","group_id":"48a63eac33224c5b55ca973808e871fd9d46a68abd19538b1c2418a8b4d130e4","hard_case_family":["no_accepted_answer","multiple_answer_candidates"],"id":"RHM-1e5630ed30a8d632c94cf0d6","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 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However, it seems that this principle could be used to justify sexual selection of almost any trait. Consider the following examples justifying selection of two opposite traits:\n\n\n\n\n\n\n\nAssuming everything else equal, an individual with a larger body has higher nutritional requirements, which are harder to meet. Therefore individuals with larger body sizes were selected because that signals higher fitness.\n\n\n\n\n\n\n\n\n\n\nAssuming everything else equal, an individual with a smaller body can't protect itself as effectively. Therefore individuals with smaller body sizes were selected because that signals higher fitness.\n\n\n\n\n\n\n\nDoes this discredit individual applications of the handicap principle? Or is there a way to measure the extent to which the handicap principle has affected selection of any given trait?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113199,"score":0},{"answer_id":114278,"score":0}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>First, <a href=\"https://stats.stackexchange.com/questions/32925/perform-k-means-or-its-close-kin-clustering-with-only-a-distance-matrix-not-p\">there are versions of k-means that can handle k-medoids</a> from distance data.</p>\n<p>Second, there are plenty of clustering methods that are fine with distances (see e.g. <a href=\"https://en.wikipedia.org/wiki/Hierarchical_clustering\" rel=\"nofollow noreferrer\">hierarchical clustering</a>). Is there a reason you don't want to use this?</p>\n<p>Third, is there a reason that you need to cluster them based on their similarity?</p>\n<p>Fourth, you may be interested in approaches like <a href=\"https://www.nature.com/articles/s41587-023-01773-0\" rel=\"nofollow noreferrer\">FoldSeek</a> that describe differences between structures using a structural alphabet to yield a sequence, making it a lot easier to do structural comparisons. Your example is admittedly a lot simpler than what they are trying to do with full proteins, but nonetheless may hold some points of interest. It is being used for larger-scale protein clustering tools like <a href=\"https://research.arcadiascience.com/pub/resource-protein-cartography/release/4\" rel=\"nofollow noreferrer\">ProteinCartography</a>.</p>\n","answer_id":113140,"answer_text":"First, there are versions of k-means that can handle k-medoids (https://stats.stackexchange.com/questions/32925/perform-k-means-or-its-close-kin-clustering-with-only-a-distance-matrix-not-p) from distance data.\n\n\n\n\nSecond, there are plenty of clustering methods that are fine with distances (see e.g. hierarchical clustering (https://en.wikipedia.org/wiki/Hierarchical_clustering)). Is there a reason you don't want to use this?\n\n\n\n\nThird, is there a reason that you need to cluster them based on their similarity?\n\n\n\n\nFourth, you may be interested in approaches like FoldSeek (https://www.nature.com/articles/s41587-023-01773-0) that describe differences between structures using a structural alphabet to yield a sequence, making it a lot easier to do structural comparisons. Your example is admittedly a lot simpler than what they are trying to do with full proteins, but nonetheless may hold some points of interest. It is being used for larger-scale protein clustering tools like ProteinCartography (https://research.arcadiascience.com/pub/resource-protein-cartography/release/4).","answer_url":"https://biology.stackexchange.com/a/113140","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2023-10-02T00:06:59+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":113075,"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":"2023-10-02T00:06:59+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"443A263E-5448-4545-8D7E-014360ECB422","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/443A263E-5448-4545-8D7E-014360ECB422/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"user135580","author_url":"https://biology.stackexchange.com/users/38121/user135580","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user135580","profile_url":"https://biology.stackexchange.com/users/38121/user135580","user_type":"registered"},"created_at":"2023-09-25T06:17:14+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"6AEE2C10-1623-4B81-858D-8F36CEAE2508","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/6AEE2C10-1623-4B81-858D-8F36CEAE2508/view-source"}],"url":"https://biology.stackexchange.com/questions/113075/clustering-collection-of-pdb-files-based-on-3-dimensional-structural-similarity"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"113140","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":"2023-10-02T00:06:59+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"443A263E-5448-4545-8D7E-014360ECB422","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/443A263E-5448-4545-8D7E-014360ECB422/view-source"}],"url":"https://biology.stackexchange.com/a/113140"}],"contexts":[{"context_id":"question","html":"<p>I have generated a set of 3-dimensional structures of the peptide AGAGAG with different structures. Total number of PDB files are 300. I need to cluster the peptide structures based on their similarity. Is it possible to do Kmeans clustering and get the total number of clusters in Python? The issue is that the RMSD-based distance matrix requires reference PDB which is not available here. Kmeans does not do clustering based on the distance matrix.</p>\n","text":"I have generated a set of 3-dimensional structures of the peptide AGAGAG with different structures. Total number of PDB files are 300. I need to cluster the peptide structures based on their similarity. Is it possible to do Kmeans clustering and get the total number of clusters in Python? The issue is that the RMSD-based distance matrix requires reference PDB which is not available here. Kmeans does not do clustering based on the distance matrix."},{"context_id":"113140","html":"<p>First, <a href=\"https://stats.stackexchange.com/questions/32925/perform-k-means-or-its-close-kin-clustering-with-only-a-distance-matrix-not-p\">there are versions of k-means that can handle k-medoids</a> from distance data.</p>\n<p>Second, there are plenty of clustering methods that are fine with distances (see e.g. <a href=\"https://en.wikipedia.org/wiki/Hierarchical_clustering\" rel=\"nofollow noreferrer\">hierarchical clustering</a>). Is there a reason you don't want to use this?</p>\n<p>Third, is there a reason that you need to cluster them based on their similarity?</p>\n<p>Fourth, you may be interested in approaches like <a href=\"https://www.nature.com/articles/s41587-023-01773-0\" rel=\"nofollow noreferrer\">FoldSeek</a> that describe differences between structures using a structural alphabet to yield a sequence, making it a lot easier to do structural comparisons. Your example is admittedly a lot simpler than what they are trying to do with full proteins, but nonetheless may hold some points of interest. It is being used for larger-scale protein clustering tools like <a href=\"https://research.arcadiascience.com/pub/resource-protein-cartography/release/4\" rel=\"nofollow noreferrer\">ProteinCartography</a>.</p>\n","text":"First, there are versions of k-means that can handle k-medoids (https://stats.stackexchange.com/questions/32925/perform-k-means-or-its-close-kin-clustering-with-only-a-distance-matrix-not-p) from distance data.\n\n\n\n\nSecond, there are plenty of clustering methods that are fine with distances (see e.g. hierarchical clustering (https://en.wikipedia.org/wiki/Hierarchical_clustering)). Is there a reason you don't want to use this?\n\n\n\n\nThird, is there a reason that you need to cluster them based on their similarity?\n\n\n\n\nFourth, you may be interested in approaches like FoldSeek (https://www.nature.com/articles/s41587-023-01773-0) that describe differences between structures using a structural alphabet to yield a sequence, making it a lot easier to do structural comparisons. Your example is admittedly a lot simpler than what they are trying to do with full proteins, but nonetheless may hold some points of interest. It is being used for larger-scale protein clustering tools like ProteinCartography (https://research.arcadiascience.com/pub/resource-protein-cartography/release/4)."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Hierarchical_clustering","https://research.arcadiascience.com/pub/resource-protein-cartography/release/4","https://stats.stackexchange.com/questions/32925/perform-k-means-or-its-close-kin-clustering-with-only-a-distance-matrix-not-p","https://www.nature.com/articles/s41587-023-01773-0"],"ground_truth_type":"metadata_grounded","group_id":"774cfa223ea422fb1d5c11773055bd51b575b4b7413df47c703ba7b0254d060d","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-89f2f9b52f959919c629cd5a","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":"user135580","profile_url":"https://biology.stackexchange.com/users/38121/user135580","user_type":"registered"},"created_at":"2023-09-25T06:17:14+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"6AEE2C10-1623-4B81-858D-8F36CEAE2508","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/6AEE2C10-1623-4B81-858D-8F36CEAE2508/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":"113075","source_record_sha256":"2cb077ed78389b5ae2a334f21653e90cf9830f53a4b4e5d663da151d5362cd18","source_url":"https://biology.stackexchange.com/questions/113075/clustering-collection-of-pdb-files-based-on-3-dimensional-structural-similarity","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Clustering collection of PDB files based on 3 dimensional structural similarity in python\nI have generated a set of 3-dimensional structures of the peptide AGAGAG with different structures. Total number of PDB files are 300. I need to cluster the peptide structures based on their similarity. Is it possible to do Kmeans clustering and get the total number of clusters in Python? The issue is that the RMSD-based distance matrix requires reference PDB which is not available here. Kmeans does not do clustering based on the distance matrix.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113140,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Yes, interspecies adoptions have been observed. They're rare enough that study is limited to case reports, and the causes are guessed at but not fully understood. However, I think it's clear that there are strong biological drives towards participating in mothering for the species that do so, and it's not too surprising that these drives could be at times &quot;misplaced&quot; from a biological perspective and directed at non-offspring.</p>\n<p>A couple papers:</p>\n<p>Carzon, P., Delfour, F., Dudzinski, K., Oremus, M., &amp; Clua, É. (2019). Cross‐genus adoptions in delphinids: One example with taxonomic discussion. Ethology, 125(9), 669-676.</p>\n<p>Izar, P., Verderane, M. P., Visalberghi, E., Ottoni, E. B., Gomes De Oliveira, M., Shirley, J., &amp; Fragaszy, D. (2006). Cross‐genus adoption of a marmoset (Callithrix jacchus) by wild capuchin monkeys (Cebus libidinosus): Case report. American Journal of Primatology: Official Journal of the American Society of Primatologists, 68(7), 692-700.</p>\n","answer_id":113103,"answer_text":"Yes, interspecies adoptions have been observed. They're rare enough that study is limited to case reports, and the causes are guessed at but not fully understood. However, I think it's clear that there are strong biological drives towards participating in mothering for the species that do so, and it's not too surprising that these drives could be at times \"misplaced\" from a biological perspective and directed at non-offspring.\n\n\n\n\nA couple papers:\n\n\n\n\nCarzon, P., Delfour, F., Dudzinski, K., Oremus, M., & Clua, É. (2019). Cross‐genus adoptions in delphinids: One example with taxonomic discussion. Ethology, 125(9), 669-676.\n\n\n\n\nIzar, P., Verderane, M. P., Visalberghi, E., Ottoni, E. B., Gomes De Oliveira, M., Shirley, J., & Fragaszy, D. (2006). Cross‐genus adoption of a marmoset (Callithrix jacchus) by wild capuchin monkeys (Cebus libidinosus): Case report. American Journal of Primatology: Official Journal of the American Society of Primatologists, 68(7), 692-700.","answer_url":"https://biology.stackexchange.com/a/113103","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2023-09-28T15:46:52+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":113101,"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":"2023-09-28T15:46:52+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"581C3D0E-ACF0-4BF0-B60F-B57E1F489FE5","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/581C3D0E-ACF0-4BF0-B60F-B57E1F489FE5/view-source"}],"score":22},{"answer_html":"<p><a href=\"https://youtu.be/K83BKNxgg7w\" rel=\"nofollow noreferrer\">This video describes a cat feeding ducklings</a>, and shows the ducklings subsequently still having the emotional attachment to their foster mother even after growing up.</p>\n","answer_id":113124,"answer_text":"This video describes a cat feeding ducklings (https://youtu.be/K83BKNxgg7w), and shows the ducklings subsequently still having the emotional attachment to their foster mother even after growing up.","answer_url":"https://biology.stackexchange.com/a/113124","author":"user21820","author_url":"https://biology.stackexchange.com/users/19018/user21820","content_license":"CC BY-SA 4.0","created_at":"2023-09-30T04:45:22+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; 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They're rare enough that study is limited to case reports, and the causes are guessed at but not fully understood. However, I think it's clear that there are strong biological drives towards participating in mothering for the species that do so, and it's not too surprising that these drives could be at times &quot;misplaced&quot; from a biological perspective and directed at non-offspring.</p>\n<p>A couple papers:</p>\n<p>Carzon, P., Delfour, F., Dudzinski, K., Oremus, M., &amp; Clua, É. (2019). Cross‐genus adoptions in delphinids: One example with taxonomic discussion. Ethology, 125(9), 669-676.</p>\n<p>Izar, P., Verderane, M. P., Visalberghi, E., Ottoni, E. B., Gomes De Oliveira, M., Shirley, J., &amp; Fragaszy, D. (2006). Cross‐genus adoption of a marmoset (Callithrix jacchus) by wild capuchin monkeys (Cebus libidinosus): Case report. American Journal of Primatology: Official Journal of the American Society of Primatologists, 68(7), 692-700.</p>\n","text":"Yes, interspecies adoptions have been observed. They're rare enough that study is limited to case reports, and the causes are guessed at but not fully understood. However, I think it's clear that there are strong biological drives towards participating in mothering for the species that do so, and it's not too surprising that these drives could be at times \"misplaced\" from a biological perspective and directed at non-offspring.\n\n\n\n\nA couple papers:\n\n\n\n\nCarzon, P., Delfour, F., Dudzinski, K., Oremus, M., & Clua, É. (2019). Cross‐genus adoptions in delphinids: One example with taxonomic discussion. Ethology, 125(9), 669-676.\n\n\n\n\nIzar, P., Verderane, M. P., Visalberghi, E., Ottoni, E. B., Gomes De Oliveira, M., Shirley, J., & Fragaszy, D. (2006). Cross‐genus adoption of a marmoset (Callithrix jacchus) by wild capuchin monkeys (Cebus libidinosus): Case report. American Journal of Primatology: Official Journal of the American Society of Primatologists, 68(7), 692-700."},{"context_id":"113124","html":"<p><a href=\"https://youtu.be/K83BKNxgg7w\" rel=\"nofollow noreferrer\">This video describes a cat feeding ducklings</a>, and shows the ducklings subsequently still having the emotional attachment to their foster mother even after growing up.</p>\n","text":"This video describes a cat feeding ducklings (https://youtu.be/K83BKNxgg7w), and shows the ducklings subsequently still having the emotional attachment to their foster mother even after growing up."}],"domain":"biology","external_citations":["https://en.m.wikipedia.org/wiki/Human%E2%80%93animal_breastfeeding","https://youtu.be/K83BKNxgg7w"],"ground_truth_type":"metadata_grounded","group_id":"e6d4e1a5f878aa353ae0dfd85d1413030576db24cae3b5d207d25b8d4b008c1e","hard_case_family":["no_accepted_answer","multiple_sources","multiple_answer_candidates"],"id":"RHM-5d40c01b7bd35f7147170153","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":"Samid","profile_url":"https://biology.stackexchange.com/users/43350/samid","user_type":"registered"},"created_at":"2023-09-28T10:15:44+00:00","raw_file":"raw/codex_api_v1/7990290f44c327838228c7b3c3814c3a2aa21e981eefca82d28f255bb804f6fa_1790824034012716800_0.json","raw_sha256":"1938cd4833c1e706cad2a86a721cda79c53cf3432479a2d574c35bc2c5ebc71a","revision_guid":"9B489FD1-CECE-41A6-926C-DBC3FA43A0C7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9B489FD1-CECE-41A6-926C-DBC3FA43A0C7/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2023-09-28T18:18:18+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"F1187804-5D3D-407A-95A7-7C7914DBD2E9","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/F1187804-5D3D-407A-95A7-7C7914DBD2E9/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":"113101","source_record_sha256":"04a66d64bf59af0771a1ff7aec968e460db5c2edddd052a522dda3914152d743","source_url":"https://biology.stackexchange.com/questions/113101/does-interspecies-breastfeeding-occur-in-the-wild","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Does interspecies breastfeeding occur in the wild?\nDoes interspecies breastfeeding occur in the wild?\n\n\n\n\nSay, for example, a zebra feeding a wildebeest, or a bushbuck feeding a gazelle.\n\n\n\n\nThere is a Wikipedia page on this topic but it only shows animal-human and human-animal feeding.\nhttps://en.m.wikipedia.org/wiki/Human%E2%80%93animal_breastfeeding (https://en.m.wikipedia.org/wiki/Human%E2%80%93animal_breastfeeding)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113103,"score":22},{"answer_id":113124,"score":2}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":113107,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>There are direct enyzme-catalyzed pathways for reversible conversions among nucleoside diphosphates and triphosphates, via <a href=\"https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase\" rel=\"nofollow noreferrer\">nucleoside-diphosphate kinases</a>. See also <a href=\"https://archive.org/details/biochemistry200100jere/page/476/mode/2up\" rel=\"nofollow noreferrer\">https://archive.org/details/biochemistry200100jere/page/476/mode/2up</a> (link to Berg's Biochemistry from that Wikipedia page).</p>\n<p>Note that all of the triphosphates are used for some things in the cell, RNA synthesis in particular, so it's necessary for the cell to be able to generate them all.</p>\n","answer_id":113107,"answer_text":"There are direct enyzme-catalyzed pathways for reversible conversions among nucleoside diphosphates and triphosphates, via nucleoside-diphosphate kinases (https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase). See also https://archive.org/details/biochemistry200100jere/page/476/mode/2up (https://archive.org/details/biochemistry200100jere/page/476/mode/2up) (link to Berg's Biochemistry from that Wikipedia page).\n\n\n\n\nNote that all of the triphosphates are used for some things in the cell, RNA synthesis in particular, so it's necessary for the cell to be able to generate them all.","answer_url":"https://biology.stackexchange.com/a/113107","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2023-09-28T18:03:16+00:00","is_accepted":true,"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":113106,"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":"2023-09-28T18:03:16+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"423B5323-1F95-4F10-A347-5EF5D48B125E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/423B5323-1F95-4F10-A347-5EF5D48B125E/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Blue Various","author_url":"https://biology.stackexchange.com/users/53374/blue-various","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Blue Various","profile_url":"https://biology.stackexchange.com/users/53374/blue-various","user_type":"registered"},"created_at":"2023-09-28T17:49:29+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"376FEDEF-302E-490B-A84A-C346339ABD3A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/376FEDEF-302E-490B-A84A-C346339ABD3A/view-source"},{"content_license":null,"contributor":{"display_name":"Blue Various","profile_url":"https://biology.stackexchange.com/users/53374/blue-various","user_type":"registered"},"created_at":"2023-09-28T18:42:22+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"47035350-4FC6-4E56-96E8-226268065E12","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/47035350-4FC6-4E56-96E8-226268065E12/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2023-09-29T01:52:17+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"C3F54893-42FE-4B53-8AC3-AC1D1D559A95","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/C3F54893-42FE-4B53-8AC3-AC1D1D559A95/view-source"}],"url":"https://biology.stackexchange.com/questions/113106/fate-of-gtp-produced-in-the-tca-cycle"},{"author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","context_id":"113107","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":"2023-09-28T18:03:16+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"423B5323-1F95-4F10-A347-5EF5D48B125E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/423B5323-1F95-4F10-A347-5EF5D48B125E/view-source"}],"url":"https://biology.stackexchange.com/a/113107"}],"contexts":[{"context_id":"question","html":"<p>As someone already mentioned in one of the following questions, the TCA circuit generates GTP in addition to NADH and FADH2.　The fate of NADH and FADH2 is clear: they are used to pump protons in the electron transfer system.</p>\n<p><a href=\"https://biology.stackexchange.com/questions/53071/why-is-gtp-not-atp-produced-in-gluconeogenesis-tca-cycle\">Why is GTP, not ATP, produced in Gluconeogenesis &amp; TCA Cycle?</a></p>\n<p>However, the fate of GTP seems less clearly described. I have seen a weak statement that &quot;1 mol of GTP can produce 1 mol of ATP,&quot; but I do not know when, where, what, and how the energy of GTP is diverted to the production of ATP.</p>\n<p>So.</p>\n<blockquote>\n<p><strong>My question</strong>;<br>\nWhen, where, what and how GTP generated in the TCA circuit is used to generate ATP</p>\n</blockquote>\n","text":"As someone already mentioned in one of the following questions, the TCA circuit generates GTP in addition to NADH and FADH2.　The fate of NADH and FADH2 is clear: they are used to pump protons in the electron transfer system.\n\n\n\n\nWhy is GTP, not ATP, produced in Gluconeogenesis & TCA Cycle? (https://biology.stackexchange.com/questions/53071/why-is-gtp-not-atp-produced-in-gluconeogenesis-tca-cycle)\n\n\n\n\nHowever, the fate of GTP seems less clearly described. I have seen a weak statement that \"1 mol of GTP can produce 1 mol of ATP,\" but I do not know when, where, what, and how the energy of GTP is diverted to the production of ATP.\n\n\n\n\nSo.\n\n\n\n\n\n\n\nMy question;\n\nWhen, where, what and how GTP generated in the TCA circuit is used to generate ATP"},{"context_id":"113107","html":"<p>There are direct enyzme-catalyzed pathways for reversible conversions among nucleoside diphosphates and triphosphates, via <a href=\"https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase\" rel=\"nofollow noreferrer\">nucleoside-diphosphate kinases</a>. See also <a href=\"https://archive.org/details/biochemistry200100jere/page/476/mode/2up\" rel=\"nofollow noreferrer\">https://archive.org/details/biochemistry200100jere/page/476/mode/2up</a> (link to Berg's Biochemistry from that Wikipedia page).</p>\n<p>Note that all of the triphosphates are used for some things in the cell, RNA synthesis in particular, so it's necessary for the cell to be able to generate them all.</p>\n","text":"There are direct enyzme-catalyzed pathways for reversible conversions among nucleoside diphosphates and triphosphates, via nucleoside-diphosphate kinases (https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase). See also https://archive.org/details/biochemistry200100jere/page/476/mode/2up (https://archive.org/details/biochemistry200100jere/page/476/mode/2up) (link to Berg's Biochemistry from that Wikipedia page).\n\n\n\n\nNote that all of the triphosphates are used for some things in the cell, RNA synthesis in particular, so it's necessary for the cell to be able to generate them all."}],"domain":"biology","external_citations":["https://archive.org/details/biochemistry200100jere/page/476/mode/2up","https://biology.stackexchange.com/questions/53071/why-is-gtp-not-atp-produced-in-gluconeogenesis-tca-cycle","https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase"],"ground_truth_type":"metadata_grounded","group_id":"06d52d56a5904814c8ff9e87924304c01d27955b80fb93aa79f7c9d20483b979","hard_case_family":["multiple_sources"],"id":"RHM-cf1a0631a7e50ed6a3202c29","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":"Blue Various","profile_url":"https://biology.stackexchange.com/users/53374/blue-various","user_type":"registered"},"created_at":"2023-09-28T17:49:29+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"376FEDEF-302E-490B-A84A-C346339ABD3A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/376FEDEF-302E-490B-A84A-C346339ABD3A/view-source"},{"content_license":null,"contributor":{"display_name":"Blue Various","profile_url":"https://biology.stackexchange.com/users/53374/blue-various","user_type":"registered"},"created_at":"2023-09-28T18:42:22+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"47035350-4FC6-4E56-96E8-226268065E12","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/47035350-4FC6-4E56-96E8-226268065E12/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2023-09-29T01:52:17+00:00","raw_file":"raw/codex_api_v1/94d9f1e30b5dd1767475c05e1b94ebc9b51251f35d208b9800a4aa1aae1f7188_1790824031839073700_0.json","raw_sha256":"cce2a5f3b306f6a39571358a0439bc231c3ba14bee317be498ab1ef3965e7c77","revision_guid":"C3F54893-42FE-4B53-8AC3-AC1D1D559A95","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/C3F54893-42FE-4B53-8AC3-AC1D1D559A95/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":"113106","source_record_sha256":"fc83dbe458778a6961d574f23ae2d901cdeb943d9e857963498258fd29878a22","source_url":"https://biology.stackexchange.com/questions/113106/fate-of-gtp-produced-in-the-tca-cycle","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Fate of GTP produced in the TCA cycle\nAs someone already mentioned in one of the following questions, the TCA circuit generates GTP in addition to NADH and FADH2.　The fate of NADH and FADH2 is clear: they are used to pump protons in the electron transfer system.\n\n\n\n\nWhy is GTP, not ATP, produced in Gluconeogenesis & TCA Cycle? (https://biology.stackexchange.com/questions/53071/why-is-gtp-not-atp-produced-in-gluconeogenesis-tca-cycle)\n\n\n\n\nHowever, the fate of GTP seems less clearly described. I have seen a weak statement that \"1 mol of GTP can produce 1 mol of ATP,\" but I do not know when, where, what, and how the energy of GTP is diverted to the production of ATP.\n\n\n\n\nSo.\n\n\n\n\n\n\n\nMy question;\n\nWhen, where, what and how GTP generated in the TCA circuit is used to generate ATP","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113107,"score":3}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<ol>\n<li>No i don't think cells harden because dividing cells apply force on them, if that was true I think it would make more sense for a tree to compress every time more an more as it divides in vascular cambium. What happensn is that it grows in diametar, I think only a few cells of that mass simply can't act on a much more massive body like that. A small ball will hardly move a big wall( given it is not travelling at speed of space shuttle:). Even if that was the case, I still don't see which force would be behing it, there is no gravity in lateral direction. If increasing diametar would provide more an more preassure on the inside than wider trees would have stiffer and stronger middle than tiny ones. And I don't think that is the case.</li>\n</ol>\n<p>I am not an expert in botany, this is only my logic.</p>\n","answer_id":113222,"answer_text":"No i don't think cells harden because dividing cells apply force on them, if that was true I think it would make more sense for a tree to compress every time more an more as it divides in vascular cambium. What happensn is that it grows in diametar, I think only a few cells of that mass simply can't act on a much more massive body like that. A small ball will hardly move a big wall( given it is not travelling at speed of space shuttle:). Even if that was the case, I still don't see which force would be behing it, there is no gravity in lateral direction. If increasing diametar would provide more an more preassure on the inside than wider trees would have stiffer and stronger middle than tiny ones. And I don't think that is the case.\n\n\n\n\n\nI am not an expert in botany, this is only my logic.","answer_url":"https://biology.stackexchange.com/a/113222","author":"Captain popec","author_url":"https://biology.stackexchange.com/users/74443/captain-popec","content_license":"CC BY-SA 4.0","created_at":"2023-10-12T18:51:29+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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popec","profile_url":"https://biology.stackexchange.com/users/74443/captain-popec","user_type":"registered"},"created_at":"2023-10-12T18:55:49+00:00","raw_file":"raw/codex_api_v1/6af9c7d042670008467ed73a4907cf5040455dcec44ada30c72785b8ae9c030c_1790824043634594200_0.json","raw_sha256":"86af78543bd42fa5daff5720e8d8724ccf27acfab275d042193c1f18cc524c18","revision_guid":"2CEDA34F-0364-40FE-B5FA-766EF8C1CC2A","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2CEDA34F-0364-40FE-B5FA-766EF8C1CC2A/view-source"}],"url":"https://biology.stackexchange.com/a/113222"}],"contexts":[{"context_id":"question","html":"<p>I read in a textbook that the vascular cambium creates secondary xylem to its inside and outside. These cells, formerly conducting water, dry out and harden. Their cell walls get lignified creating wood, particularly in the cylinder between cork cambium and vascular cambium. This is actually three related questions.</p>\n<ol>\n<li><p>Is a force exerted on the secondary xylem by the vascular cambium? A force that compresses these cells?</p>\n</li>\n<li><p>If &quot;yes&quot; to number one, how can soft tissues that make up the vascular cambium press so hard on the previous layers of harder (dried out) secondary xykem? Are concentric cylinders staggered so hardness increases gradually, with a stiffer already compressed cylinder exerting more force than newer secondary xylem cylinders?</p>\n</li>\n<li><p>The secondary xylem (cortex) is living. Medullary rays traverse them and it is adjacent to the living cork cambium. As lignin is deposited in its cell walls, what biochemical processes continue to occur? The hard walls would deter intercellular transport but the cells must continue interacting.</p>\n</li>\n</ol>\n","text":"I read in a textbook that the vascular cambium creates secondary xylem to its inside and outside. These cells, formerly conducting water, dry out and harden. Their cell walls get lignified creating wood, particularly in the cylinder between cork cambium and vascular cambium. This is actually three related questions.\n\n\n\n\n\n\n\nIs a force exerted on the secondary xylem by the vascular cambium? A force that compresses these cells?\n\n\n\n\n\n\n\n\n\nIf \"yes\" to number one, how can soft tissues that make up the vascular cambium press so hard on the previous layers of harder (dried out) secondary xykem? Are concentric cylinders staggered so hardness increases gradually, with a stiffer already compressed cylinder exerting more force than newer secondary xylem cylinders?\n\n\n\n\n\n\n\n\n\nThe secondary xylem (cortex) is living. Medullary rays traverse them and it is adjacent to the living cork cambium. As lignin is deposited in its cell walls, what biochemical processes continue to occur? The hard walls would deter intercellular transport but the cells must continue interacting."},{"context_id":"113222","html":"<ol>\n<li>No i don't think cells harden because dividing cells apply force on them, if that was true I think it would make more sense for a tree to compress every time more an more as it divides in vascular cambium. What happensn is that it grows in diametar, I think only a few cells of that mass simply can't act on a much more massive body like that. A small ball will hardly move a big wall( given it is not travelling at speed of space shuttle:). Even if that was the case, I still don't see which force would be behing it, there is no gravity in lateral direction. If increasing diametar would provide more an more preassure on the inside than wider trees would have stiffer and stronger middle than tiny ones. And I don't think that is the case.</li>\n</ol>\n<p>I am not an expert in botany, this is only my logic.</p>\n","text":"No i don't think cells harden because dividing cells apply force on them, if that was true I think it would make more sense for a tree to compress every time more an more as it divides in vascular cambium. What happensn is that it grows in diametar, I think only a few cells of that mass simply can't act on a much more massive body like that. A small ball will hardly move a big wall( given it is not travelling at speed of space shuttle:). Even if that was the case, I still don't see which force would be behing it, there is no gravity in lateral direction. If increasing diametar would provide more an more preassure on the inside than wider trees would have stiffer and stronger middle than tiny ones. And I don't think that is the case.\n\n\n\n\n\nI am not an expert in botany, this is only my logic."}],"domain":"biology","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"399baa3cfb57d93546755252bfadd35fb0eecae5d4673bcf4d81e4170157fed3","hard_case_family":["no_accepted_answer"],"id":"RHM-bb4126f7f300946bd4c85c23","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 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BY-SA 4.0","source_record_id":"113218","source_record_sha256":"0caad0658eb3affb2176bf8caaa3d1ffe2bde0496797adb26a8ce07ac4288c52","source_url":"https://biology.stackexchange.com/questions/113218/other-than-lignification-how-does-secondary-xylem-attain-its-stiffness-then-bala","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Other than lignification how does secondary xylem attain its stiffness then balance that with remaining living processes?\nI read in a textbook that the vascular cambium creates secondary xylem to its inside and outside. These cells, formerly conducting water, dry out and harden. Their cell walls get lignified creating wood, particularly in the cylinder between cork cambium and vascular cambium. This is actually three related questions.\n\n\n\n\n\n\n\nIs a force exerted on the secondary xylem by the vascular cambium? A force that compresses these cells?\n\n\n\n\n\n\n\n\n\nIf \"yes\" to number one, how can soft tissues that make up the vascular cambium press so hard on the previous layers of harder (dried out) secondary xykem? Are concentric cylinders staggered so hardness increases gradually, with a stiffer already compressed cylinder exerting more force than newer secondary xylem cylinders?\n\n\n\n\n\n\n\n\n\nThe secondary xylem (cortex) is living. Medullary rays traverse them and it is adjacent to the living cork cambium. As lignin is deposited in its cell walls, what biochemical processes continue to occur? The hard walls would deter intercellular transport but the cells must continue interacting.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113222,"score":0}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The membrane allows movement of particles which will cause a balancing of the concentrations.\nThere is one hint in the text: &quot;Initially, the liquid levels on both sides are equal&quot; which gives away how this will happen.</p>\n<p>Water and glucose can freely move through the membrane and this is what will happen. Water will move through the membrane, the level in side A will rise until both concentrations of sucrose are equivalent. Glucose will also cross the membrane from B to A until the concentration is equal on both sides.</p>\n<p>You are right, the movement of water will lower the concentration of glucose in side A but since the glucose can move across the membrane as well, this will not affect the equilibrium.</p>\n","answer_id":113499,"answer_text":"The membrane allows movement of particles which will cause a balancing of the concentrations.\nThere is one hint in the text: \"Initially, the liquid levels on both sides are equal\" which gives away how this will happen.\n\n\n\n\nWater and glucose can freely move through the membrane and this is what will happen. Water will move through the membrane, the level in side A will rise until both concentrations of sucrose are equivalent. Glucose will also cross the membrane from B to A until the concentration is equal on both sides.\n\n\n\n\nYou are right, the movement of water will lower the concentration of glucose in side A but since the glucose can move across the membrane as well, this will not affect the equilibrium.","answer_url":"https://biology.stackexchange.com/a/113499","author":"Chris","author_url":"https://biology.stackexchange.com/users/5144/chris","content_license":"CC BY-SA 4.0","created_at":"2023-11-17T08:23:24+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":113498,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Chris","profile_url":"https://biology.stackexchange.com/users/5144/chris","user_type":"moderator"},"created_at":"2023-11-17T08:23:24+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"F15D2D5B-EDFC-48E8-AA79-C8E07170CAC3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F15D2D5B-EDFC-48E8-AA79-C8E07170CAC3/view-source"}],"score":4}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"geneticscodingnoob","author_url":"https://biology.stackexchange.com/users/70013/geneticscodingnoob","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"geneticscodingnoob","profile_url":"https://biology.stackexchange.com/users/70013/geneticscodingnoob","user_type":"registered"},"created_at":"2023-11-17T07:03:52+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"20F787BF-424B-4617-9A80-6D1BE0CBB297","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/20F787BF-424B-4617-9A80-6D1BE0CBB297/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"geneticscodingnoob","profile_url":"https://biology.stackexchange.com/users/70013/geneticscodingnoob","user_type":"registered"},"created_at":"2023-11-18T02:35:51+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"5FC9D3AE-B904-4FA0-A184-CE00D7D2147F","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5FC9D3AE-B904-4FA0-A184-CE00D7D2147F/view-source"}],"url":"https://biology.stackexchange.com/questions/113498/movement-of-solutes-across-a-semipermeable-membrane-in-a-u-shaped-tube"},{"author":"Chris","author_url":"https://biology.stackexchange.com/users/5144/chris","content_license":"CC BY-SA 4.0","context_id":"113499","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Chris","profile_url":"https://biology.stackexchange.com/users/5144/chris","user_type":"moderator"},"created_at":"2023-11-17T08:23:24+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"F15D2D5B-EDFC-48E8-AA79-C8E07170CAC3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F15D2D5B-EDFC-48E8-AA79-C8E07170CAC3/view-source"}],"url":"https://biology.stackexchange.com/a/113499"}],"contexts":[{"context_id":"question","html":"<p><a href=\"https://i.sstatic.net/XyBgJ.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/XyBgJ.png\" alt=\"Question\" /></a></p>\n<p>The solutions in the two arms of this U-tube are separated by a membrane that is permeable to water and glucose but not sucrose. Side A is half-filled with a solution of 2 M sucrose and 1 M glucose. Side b is half-filled with 1 M sucrose and 2 M glucose. Initially, the liquid levels on both sides are equal.</p>\n<p>When it reaches equilibrium, the sugar concentrations on both sides of the U-tube will be 1.5 M sucrose and 1.5 M glucose.</p>\n<p>Can somebody explain the answer (D) to me? My understanding is that the membrane is permeable to glucose, therefore glucose will reach equilibrium, with 1.5M on each side. Since the membrane is not permeable to sucrose, the concentration of sucrose will not change. Water will move from B to A. Does the movement of water causes the sucrose solution on both sides to be equal? But wouldn't that alter the glucose concentrations too? I'm sorry I just know what my bio teacher told me but I don't quite get the reasoning. Thanks.</p>\n","text":"[image: Question; source: https://i.sstatic.net/XyBgJ.png] (https://i.sstatic.net/XyBgJ.png)\n\n\n\n\nThe solutions in the two arms of this U-tube are separated by a membrane that is permeable to water and glucose but not sucrose. Side A is half-filled with a solution of 2 M sucrose and 1 M glucose. Side b is half-filled with 1 M sucrose and 2 M glucose. Initially, the liquid levels on both sides are equal.\n\n\n\n\nWhen it reaches equilibrium, the sugar concentrations on both sides of the U-tube will be 1.5 M sucrose and 1.5 M glucose.\n\n\n\n\nCan somebody explain the answer (D) to me? My understanding is that the membrane is permeable to glucose, therefore glucose will reach equilibrium, with 1.5M on each side. Since the membrane is not permeable to sucrose, the concentration of sucrose will not change. Water will move from B to A. Does the movement of water causes the sucrose solution on both sides to be equal? But wouldn't that alter the glucose concentrations too? I'm sorry I just know what my bio teacher told me but I don't quite get the reasoning. Thanks."},{"context_id":"113499","html":"<p>The membrane allows movement of particles which will cause a balancing of the concentrations.\nThere is one hint in the text: &quot;Initially, the liquid levels on both sides are equal&quot; which gives away how this will happen.</p>\n<p>Water and glucose can freely move through the membrane and this is what will happen. Water will move through the membrane, the level in side A will rise until both concentrations of sucrose are equivalent. Glucose will also cross the membrane from B to A until the concentration is equal on both sides.</p>\n<p>You are right, the movement of water will lower the concentration of glucose in side A but since the glucose can move across the membrane as well, this will not affect the equilibrium.</p>\n","text":"The membrane allows movement of particles which will cause a balancing of the concentrations.\nThere is one hint in the text: \"Initially, the liquid levels on both sides are equal\" which gives away how this will happen.\n\n\n\n\nWater and glucose can freely move through the membrane and this is what will happen. Water will move through the membrane, the level in side A will rise until both concentrations of sucrose are equivalent. Glucose will also cross the membrane from B to A until the concentration is equal on both sides.\n\n\n\n\nYou are right, the movement of water will lower the concentration of glucose in side A but since the glucose can move across the membrane as well, this will not affect the equilibrium."}],"domain":"biology","external_citations":["https://i.sstatic.net/XyBgJ.png"],"ground_truth_type":"metadata_grounded","group_id":"e3b35c96b7a91827a552ae6764a293eca28ada6e460e8a9013064c0009a1c17e","hard_case_family":["no_accepted_answer"],"id":"RHM-c75fa65759188d78619fd1dd","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":"geneticscodingnoob","profile_url":"https://biology.stackexchange.com/users/70013/geneticscodingnoob","user_type":"registered"},"created_at":"2023-11-17T07:03:52+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"20F787BF-424B-4617-9A80-6D1BE0CBB297","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/20F787BF-424B-4617-9A80-6D1BE0CBB297/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"geneticscodingnoob","profile_url":"https://biology.stackexchange.com/users/70013/geneticscodingnoob","user_type":"registered"},"created_at":"2023-11-18T02:35:51+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"5FC9D3AE-B904-4FA0-A184-CE00D7D2147F","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5FC9D3AE-B904-4FA0-A184-CE00D7D2147F/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":"113498","source_record_sha256":"4ab656103d3852919b41dbaf3ec30084e819c526b9a63ff3143dd8bfffc03ecd","source_url":"https://biology.stackexchange.com/questions/113498/movement-of-solutes-across-a-semipermeable-membrane-in-a-u-shaped-tube","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Movement of solutes across a semipermeable membrane in a U-shaped tube\n[image: Question; source: https://i.sstatic.net/XyBgJ.png] (https://i.sstatic.net/XyBgJ.png)\n\n\n\n\nThe solutions in the two arms of this U-tube are separated by a membrane that is permeable to water and glucose but not sucrose. Side A is half-filled with a solution of 2 M sucrose and 1 M glucose. Side b is half-filled with 1 M sucrose and 2 M glucose. Initially, the liquid levels on both sides are equal.\n\n\n\n\nWhen it reaches equilibrium, the sugar concentrations on both sides of the U-tube will be 1.5 M sucrose and 1.5 M glucose.\n\n\n\n\nCan somebody explain the answer (D) to me? My understanding is that the membrane is permeable to glucose, therefore glucose will reach equilibrium, with 1.5M on each side. Since the membrane is not permeable to sucrose, the concentration of sucrose will not change. Water will move from B to A. Does the movement of water causes the sucrose solution on both sides to be equal? But wouldn't that alter the glucose concentrations too? I'm sorry I just know what my bio teacher told me but I don't quite get the reasoning. Thanks.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113499,"score":4}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The answer to this strongly depends on the species of bacterium you are working with.</p>\n<p>The only ones that I know of that are capable of withstanding any dehydration process are those that form <a href=\"https://www.ncbi.nlm.nih.gov/books/NBK556071/\" rel=\"nofollow noreferrer\">spores</a>. The spores are tough, long-lasting structures that enable the bacterial species to resist environmental changes.</p>\n<p><em>Cupravidus metallidurans</em>, the species you are working on is not a spore-former, so it isn't possible to fully dehydrate them. However, it is possible to form long-term stocks of many, if not all, bacterial species in glycerol and frozen at -80 C (ultra-cold freezer) sort of temperatures.</p>\n","answer_id":113512,"answer_text":"The answer to this strongly depends on the species of bacterium you are working with.\n\n\n\n\nThe only ones that I know of that are capable of withstanding any dehydration process are those that form spores (https://www.ncbi.nlm.nih.gov/books/NBK556071/). The spores are tough, long-lasting structures that enable the bacterial species to resist environmental changes.\n\n\n\n\nCupravidus metallidurans, the species you are working on is not a spore-former, so it isn't possible to fully dehydrate them. However, it is possible to form long-term stocks of many, if not all, bacterial species in glycerol and frozen at -80 C (ultra-cold freezer) sort of temperatures.","answer_url":"https://biology.stackexchange.com/a/113512","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2023-11-19T21:39:17+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":113507,"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":"2023-11-19T21:39:17+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"0FC15442-25FB-45C8-B527-8BC81AFD9FD1","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0FC15442-25FB-45C8-B527-8BC81AFD9FD1/view-source"}],"score":1},{"answer_html":"<p>Lyophilization, aka <a href=\"https://en.wikipedia.org/wiki/Freeze_drying\" rel=\"nofollow noreferrer\">freeze-drying</a>, is probably the go-to method of microbial preservation without the need for cold storage. It's how bacterial strains purchased from commercial culture collections are typically shipped.</p>\n<p>The process consists of first freezing cultures in a lyophilization buffer containing a mixture of cryoprotectant and lyoprotectant excipients, which is exposed to a strong vacuum (while maintaining sub-freezing temperatures) to sublimate the frozen water out of the mixture (<a href=\"https://www.culturecollections.org.uk/news/nctc-news/lyophilisation-long-term-storage-for-bacterial-strains.aspx\" rel=\"nofollow noreferrer\">source</a>). The lyophilized powder is typically sealed in a glass ampoule filled with inert gas for long-term storage, but can also be packaged in any number of ways to for application-specific uses.</p>\n<p>Unfortunately, there's probably not a one-size-fits-all formula that works best for every organisms, but there may be some approaches that are &quot;good enough&quot; for most. Under the right conditions, lyophilized cultures can be stable for years with minimal loss of viability, but I wouldn't count on it without extensive optimization and process validation. Also would not recommend it as your sole method of long-term preservation. Best practice is to always keep glycerol stock backups at -70°C or colder, and to have a plan in place for how often these stocks should be assessed/renewed.</p>\n","answer_id":113519,"answer_text":"Lyophilization, aka freeze-drying (https://en.wikipedia.org/wiki/Freeze_drying), is probably the go-to method of microbial preservation without the need for cold storage. It's how bacterial strains purchased from commercial culture collections are typically shipped.\n\n\n\n\nThe process consists of first freezing cultures in a lyophilization buffer containing a mixture of cryoprotectant and lyoprotectant excipients, which is exposed to a strong vacuum (while maintaining sub-freezing temperatures) to sublimate the frozen water out of the mixture (source (https://www.culturecollections.org.uk/news/nctc-news/lyophilisation-long-term-storage-for-bacterial-strains.aspx)). The lyophilized powder is typically sealed in a glass ampoule filled with inert gas for long-term storage, but can also be packaged in any number of ways to for application-specific uses.\n\n\n\n\nUnfortunately, there's probably not a one-size-fits-all formula that works best for every organisms, but there may be some approaches that are \"good enough\" for most. Under the right conditions, lyophilized cultures can be stable for years with minimal loss of viability, but I wouldn't count on it without extensive optimization and process validation. Also would not recommend it as your sole method of long-term preservation. Best practice is to always keep glycerol stock backups at -70°C or colder, and to have a plan in place for how often these stocks should be assessed/renewed.","answer_url":"https://biology.stackexchange.com/a/113519","author":"MikeyC","author_url":"https://biology.stackexchange.com/users/56688/mikeyc","content_license":"CC BY-SA 4.0","created_at":"2023-11-20T16:22:26+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":113507,"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":"2023-11-20T16:22:26+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"FCA39277-F113-4CFC-B757-5610B4D65141","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FCA39277-F113-4CFC-B757-5610B4D65141/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Lee","author_url":"https://biology.stackexchange.com/users/77786/lee","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lee","profile_url":"https://biology.stackexchange.com/users/77786/lee","user_type":"registered"},"created_at":"2023-11-18T03:31:27+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"B1CED21D-9D97-489D-AA5C-7E0EFC8D1C81","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B1CED21D-9D97-489D-AA5C-7E0EFC8D1C81/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lee","profile_url":"https://biology.stackexchange.com/users/77786/lee","user_type":"registered"},"created_at":"2023-11-18T03:34:45+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"8893A347-1338-40E0-A42E-B3145AE5B4D9","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8893A347-1338-40E0-A42E-B3145AE5B4D9/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lee","profile_url":"https://biology.stackexchange.com/users/77786/lee","user_type":"registered"},"created_at":"2023-11-18T03:35:00+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"7008EEA5-2E76-44F2-BC1B-4455825FAFA8","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7008EEA5-2E76-44F2-BC1B-4455825FAFA8/view-source"}],"url":"https://biology.stackexchange.com/questions/113507/storing-bacteria-in-a-dry-room-temperature-long-term-storage-whilst-maintaining"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"113512","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":"2023-11-19T21:39:17+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"0FC15442-25FB-45C8-B527-8BC81AFD9FD1","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0FC15442-25FB-45C8-B527-8BC81AFD9FD1/view-source"}],"url":"https://biology.stackexchange.com/a/113512"},{"author":"MikeyC","author_url":"https://biology.stackexchange.com/users/56688/mikeyc","content_license":"CC BY-SA 4.0","context_id":"113519","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":"2023-11-20T16:22:26+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"FCA39277-F113-4CFC-B757-5610B4D65141","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FCA39277-F113-4CFC-B757-5610B4D65141/view-source"}],"url":"https://biology.stackexchange.com/a/113519"}],"contexts":[{"context_id":"question","html":"<p>I'm quite new to biology, but I'm wondering if there are any methods of storing bacteria in long-term, dry conditions with no climate control. Perhaps they could be dormant in a powder or granule-like form similar to yeast. The species that I'm trying to work with is a gram-negative bacteria called <a href=\"https://www.sciencedirect.com/topics/medicine-and-dentistry/cupriavidus-metallidurans\" rel=\"nofollow noreferrer\">C. Metallidurans</a>. What's pretty cool about this bacteria is its ability to survive in environments that are high in heavy metals and produce pure gold from gold chloride. Any advice helps, thank you.</p>\n","text":"I'm quite new to biology, but I'm wondering if there are any methods of storing bacteria in long-term, dry conditions with no climate control. Perhaps they could be dormant in a powder or granule-like form similar to yeast. The species that I'm trying to work with is a gram-negative bacteria called C. Metallidurans (https://www.sciencedirect.com/topics/medicine-and-dentistry/cupriavidus-metallidurans). What's pretty cool about this bacteria is its ability to survive in environments that are high in heavy metals and produce pure gold from gold chloride. Any advice helps, thank you."},{"context_id":"113512","html":"<p>The answer to this strongly depends on the species of bacterium you are working with.</p>\n<p>The only ones that I know of that are capable of withstanding any dehydration process are those that form <a href=\"https://www.ncbi.nlm.nih.gov/books/NBK556071/\" rel=\"nofollow noreferrer\">spores</a>. The spores are tough, long-lasting structures that enable the bacterial species to resist environmental changes.</p>\n<p><em>Cupravidus metallidurans</em>, the species you are working on is not a spore-former, so it isn't possible to fully dehydrate them. However, it is possible to form long-term stocks of many, if not all, bacterial species in glycerol and frozen at -80 C (ultra-cold freezer) sort of temperatures.</p>\n","text":"The answer to this strongly depends on the species of bacterium you are working with.\n\n\n\n\nThe only ones that I know of that are capable of withstanding any dehydration process are those that form spores (https://www.ncbi.nlm.nih.gov/books/NBK556071/). The spores are tough, long-lasting structures that enable the bacterial species to resist environmental changes.\n\n\n\n\nCupravidus metallidurans, the species you are working on is not a spore-former, so it isn't possible to fully dehydrate them. However, it is possible to form long-term stocks of many, if not all, bacterial species in glycerol and frozen at -80 C (ultra-cold freezer) sort of temperatures."},{"context_id":"113519","html":"<p>Lyophilization, aka <a href=\"https://en.wikipedia.org/wiki/Freeze_drying\" rel=\"nofollow noreferrer\">freeze-drying</a>, is probably the go-to method of microbial preservation without the need for cold storage. It's how bacterial strains purchased from commercial culture collections are typically shipped.</p>\n<p>The process consists of first freezing cultures in a lyophilization buffer containing a mixture of cryoprotectant and lyoprotectant excipients, which is exposed to a strong vacuum (while maintaining sub-freezing temperatures) to sublimate the frozen water out of the mixture (<a href=\"https://www.culturecollections.org.uk/news/nctc-news/lyophilisation-long-term-storage-for-bacterial-strains.aspx\" rel=\"nofollow noreferrer\">source</a>). The lyophilized powder is typically sealed in a glass ampoule filled with inert gas for long-term storage, but can also be packaged in any number of ways to for application-specific uses.</p>\n<p>Unfortunately, there's probably not a one-size-fits-all formula that works best for every organisms, but there may be some approaches that are &quot;good enough&quot; for most. Under the right conditions, lyophilized cultures can be stable for years with minimal loss of viability, but I wouldn't count on it without extensive optimization and process validation. Also would not recommend it as your sole method of long-term preservation. Best practice is to always keep glycerol stock backups at -70°C or colder, and to have a plan in place for how often these stocks should be assessed/renewed.</p>\n","text":"Lyophilization, aka freeze-drying (https://en.wikipedia.org/wiki/Freeze_drying), is probably the go-to method of microbial preservation without the need for cold storage. It's how bacterial strains purchased from commercial culture collections are typically shipped.\n\n\n\n\nThe process consists of first freezing cultures in a lyophilization buffer containing a mixture of cryoprotectant and lyoprotectant excipients, which is exposed to a strong vacuum (while maintaining sub-freezing temperatures) to sublimate the frozen water out of the mixture (source (https://www.culturecollections.org.uk/news/nctc-news/lyophilisation-long-term-storage-for-bacterial-strains.aspx)). The lyophilized powder is typically sealed in a glass ampoule filled with inert gas for long-term storage, but can also be packaged in any number of ways to for application-specific uses.\n\n\n\n\nUnfortunately, there's probably not a one-size-fits-all formula that works best for every organisms, but there may be some approaches that are \"good enough\" for most. Under the right conditions, lyophilized cultures can be stable for years with minimal loss of viability, but I wouldn't count on it without extensive optimization and process validation. Also would not recommend it as your sole method of long-term preservation. Best practice is to always keep glycerol stock backups at -70°C or colder, and to have a plan in place for how often these stocks should be assessed/renewed."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Freeze_drying","https://www.culturecollections.org.uk/news/nctc-news/lyophilisation-long-term-storage-for-bacterial-strains.aspx","https://www.ncbi.nlm.nih.gov/books/NBK556071/","https://www.sciencedirect.com/topics/medicine-and-dentistry/cupriavidus-metallidurans"],"ground_truth_type":"metadata_grounded","group_id":"361023ae7494bae1861a7c1138b32815228ba1d80ef8774c21fa98b6dec5c22c","hard_case_family":["no_accepted_answer","multiple_sources","multiple_answer_candidates"],"id":"RHM-74bd6e6a89de1a883337080b","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":"Lee","profile_url":"https://biology.stackexchange.com/users/77786/lee","user_type":"registered"},"created_at":"2023-11-18T03:31:27+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"B1CED21D-9D97-489D-AA5C-7E0EFC8D1C81","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B1CED21D-9D97-489D-AA5C-7E0EFC8D1C81/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lee","profile_url":"https://biology.stackexchange.com/users/77786/lee","user_type":"registered"},"created_at":"2023-11-18T03:34:45+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"8893A347-1338-40E0-A42E-B3145AE5B4D9","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8893A347-1338-40E0-A42E-B3145AE5B4D9/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Lee","profile_url":"https://biology.stackexchange.com/users/77786/lee","user_type":"registered"},"created_at":"2023-11-18T03:35:00+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"7008EEA5-2E76-44F2-BC1B-4455825FAFA8","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7008EEA5-2E76-44F2-BC1B-4455825FAFA8/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":"113507","source_record_sha256":"ecf749565cdeec5c4ecd72b70ed0002ed6ed302ef6e5a5fa4c8a6e2d156231ec","source_url":"https://biology.stackexchange.com/questions/113507/storing-bacteria-in-a-dry-room-temperature-long-term-storage-whilst-maintaining","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Storing bacteria in a dry, room temperature long-term storage whilst maintaining viability\nI'm quite new to biology, but I'm wondering if there are any methods of storing bacteria in long-term, dry conditions with no climate control. Perhaps they could be dormant in a powder or granule-like form similar to yeast. The species that I'm trying to work with is a gram-negative bacteria called C. Metallidurans (https://www.sciencedirect.com/topics/medicine-and-dentistry/cupriavidus-metallidurans). What's pretty cool about this bacteria is its ability to survive in environments that are high in heavy metals and produce pure gold from gold chloride. Any advice helps, thank you.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113512,"score":1},{"answer_id":113519,"score":2}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I linked to the paper above in a <a href=\"https://dornsife.usc.edu/assets/sites/496/docs/pubs/2009noplace.pdf\" rel=\"nofollow noreferrer\">comment</a>.</p>\n<p>I'm not a behavioral scientist. So interpret with a grain of salt.</p>\n<p>The study analyzes language used after tours of homes, to evaluate how stressful the homes appear to be. So it's an imperfect measurement probably, but in direct reference to their homes. It probably does reflect something about how stressful they feel their homes to be, but IDK.</p>\n<p>Assuming that the slope of the diurnal cortisol curve is a meaningful measure (seems to be somewhat true based on my non-exhaustive search), and that the sample is adequately powered (n=30 couples, which is not too awful but not great either given the number of hypothesis tests). If you look at Tables 1 and 2, it does look like women are affected by a &quot;stressful home&quot; to a degree that men are not. Men also seem vaguely unhappy about stressful homes, though not as strongly as women. Granted, they only present regression tables, which is not always very helpful for understanding causal or statistical relationships.</p>\n<p>Nonetheless, the paper seems well-cited in the literature (as might be expected if it made it into a book). A lot of the work citing it is saying things along the lines of &quot;we need more work in this area to examine this effect&quot;. A small number of studies seem to confirm qualitatively that messy homes are stressful for women, see for example <a href=\"https://www.sciencedirect.com/science/article/abs/pii/S0272494421000062\" rel=\"nofollow noreferrer\">here</a> or <a href=\"https://journals.sagepub.com/doi/abs/10.1177/10775595221081795\" rel=\"nofollow noreferrer\">here</a>. It is less clear that the same isn't true for men, but then the majority of housework and caregiving responsibility is concentrated on women.</p>\n<p>Furthermore, it does seem like <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120613/\" rel=\"nofollow noreferrer\">global cortisol differences in men and women are not surprising</a>, and that cortisol-induced stress may affect women and men <a href=\"https://www.uc.edu/news/articles/legacy/healthnews/2005/11/chronic-stress-might-harm-women-more-than-it-does-men.html\" rel=\"nofollow noreferrer\">differently</a>.</p>\n<p>Generally, this study seems ok if not great. It fits into a broadly supportive narrative of (partially qualitative) research. The sum of the literature that I've skimmed very briefly cites this paper with approval, if perhaps making more of the results than is merited given the level 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=2ahUKEwiZvoeF1_eCAxWhPUQIHRe9Cd0QFnoECCIQAQ&amp;url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FPower_of_a_test&amp;usg=AOvVaw0a3pod09DZxufF6bshKtiA&amp;opi=89978449\" rel=\"nofollow noreferrer\">power</a> for the study. No one has posted on pubpeer about it or found anything dodgy about the study, in spite of its relatively high profile, so it's not obviously awful. I don't love the linguistic analysis either, but clutter is itself subjective I guess.</p>\n<p>There remains the issue that you raise that perhaps a person under stress will react more strongly than someone who is more relaxed. But it's a bit circular of course- in either case, it seems like women are more stressed, and they also get more stressed out about domestic clutter.</p>\n<p>Interested to hear more from a real behavioral science professional. I hope that my answer doesn't discourage anyone with more credentials from posting.</p>\n","answer_id":113624,"answer_text":"I linked to the paper above in a comment (https://dornsife.usc.edu/assets/sites/496/docs/pubs/2009noplace.pdf).\n\n\n\n\nI'm not a behavioral scientist. So interpret with a grain of salt.\n\n\n\n\nThe study analyzes language used after tours of homes, to evaluate how stressful the homes appear to be. So it's an imperfect measurement probably, but in direct reference to their homes. It probably does reflect something about how stressful they feel their homes to be, but IDK.\n\n\n\n\nAssuming that the slope of the diurnal cortisol curve is a meaningful measure (seems to be somewhat true based on my non-exhaustive search), and that the sample is adequately powered (n=30 couples, which is not too awful but not great either given the number of hypothesis tests). If you look at Tables 1 and 2, it does look like women are affected by a \"stressful home\" to a degree that men are not. Men also seem vaguely unhappy about stressful homes, though not as strongly as women. Granted, they only present regression tables, which is not always very helpful for understanding causal or statistical relationships.\n\n\n\n\nNonetheless, the paper seems well-cited in the literature (as might be expected if it made it into a book). A lot of the work citing it is saying things along the lines of \"we need more work in this area to examine this effect\". A small number of studies seem to confirm qualitatively that messy homes are stressful for women, see for example here (https://www.sciencedirect.com/science/article/abs/pii/S0272494421000062) or here (https://journals.sagepub.com/doi/abs/10.1177/10775595221081795). It is less clear that the same isn't true for men, but then the majority of housework and caregiving responsibility is concentrated on women.\n\n\n\n\nFurthermore, it does seem like global cortisol differences in men and women are not surprising (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120613/), and that cortisol-induced stress may affect women and men differently (https://www.uc.edu/news/articles/legacy/healthnews/2005/11/chronic-stress-might-harm-women-more-than-it-does-men.html).\n\n\n\n\nGenerally, this study seems ok if not great. It fits into a broadly supportive narrative of (partially qualitative) research. The sum of the literature that I've skimmed very briefly cites this paper with approval, if perhaps making more of the results than is merited given the level of power (https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwiZvoeF1_eCAxWhPUQIHRe9Cd0QFnoECCIQAQ&url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FPower_of_a_test&usg=AOvVaw0a3pod09DZxufF6bshKtiA&opi=89978449) for the study. No one has posted on pubpeer about it or found anything dodgy about the study, in spite of its relatively high profile, so it's not obviously awful. I don't love the linguistic analysis either, but clutter is itself subjective I guess.\n\n\n\n\nThere remains the issue that you raise that perhaps a person under stress will react more strongly than someone who is more relaxed. But it's a bit circular of course- in either case, it seems like women are more stressed, and they also get more stressed out about domestic clutter.\n\n\n\n\nInterested to hear more from a real behavioral science professional. I hope that my answer doesn't discourage anyone with more credentials from posting.","answer_url":"https://biology.stackexchange.com/a/113624","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2023-12-05T06:47:39+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":113531,"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":"2023-12-05T06:47:39+00:00","raw_file":"raw/codex_api_v1/4b31ece29d49640766904acfb09f413caa800382e2048749dca713fe1c36c614_1790824046659275600_0.json","raw_sha256":"d34fed5816d7a26a5c9619cd4bcaa8f6e5ab3886f8bed7f16f08fb06ee93b82d","revision_guid":"B1929C25-57E4-4EED-B28E-E59B48542218","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B1929C25-57E4-4EED-B28E-E59B48542218/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"user46147","author_url":"https://biology.stackexchange.com/users/18858/user46147","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user46147","profile_url":"https://biology.stackexchange.com/users/18858/user46147","user_type":"registered"},"created_at":"2023-11-22T19:41:14+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"9A8E76F4-FFDA-4B7A-B2F7-75A2B151AC19","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9A8E76F4-FFDA-4B7A-B2F7-75A2B151AC19/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":"2023-12-05T23:21:40+00:00","raw_file":"raw/codex_api_v1/4b31ece29d49640766904acfb09f413caa800382e2048749dca713fe1c36c614_1790824046659275600_0.json","raw_sha256":"d34fed5816d7a26a5c9619cd4bcaa8f6e5ab3886f8bed7f16f08fb06ee93b82d","revision_guid":"699C7F0C-4E7A-422F-B234-A3F15422C5F0","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/699C7F0C-4E7A-422F-B234-A3F15422C5F0/view-source"}],"url":"https://biology.stackexchange.com/questions/113531/what-is-the-evidence-that-women-experience-a-larger-cortisol-spike-than-men-whe"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"113624","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":"2023-12-05T06:47:39+00:00","raw_file":"raw/codex_api_v1/4b31ece29d49640766904acfb09f413caa800382e2048749dca713fe1c36c614_1790824046659275600_0.json","raw_sha256":"d34fed5816d7a26a5c9619cd4bcaa8f6e5ab3886f8bed7f16f08fb06ee93b82d","revision_guid":"B1929C25-57E4-4EED-B28E-E59B48542218","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B1929C25-57E4-4EED-B28E-E59B48542218/view-source"}],"url":"https://biology.stackexchange.com/a/113624"}],"contexts":[{"context_id":"question","html":"<p>I'm reading a book &quot;The Organized Mind: Thinking Straight in the Age of Information Overload&quot; by Daniel Levitin.</p>\n<p>At the beginning of chapter &quot;Organizing our homes&quot; he says that compared to men, women experience larger cortisol spike when they see mess. I googled that statement, and the source of that claim seems to come from <a href=\"https://doi.org/10.1177/0146167209352864\" rel=\"nofollow noreferrer\">https://doi.org/10.1177/0146167209352864</a></p>\n<p>I don't have the access to the journal, but the abstract doesn't say much about how cluttered is the home. It just seems to correlate linguistic patterns with cortisol level.\nBut someone stressed for sure has different way of speaking than someone chill. No clutter scale is mentioned. The person might be stressed by something unaccounted in the research.</p>\n<p>So please, can someone with journal access and proper qualifications tell me:</p>\n<ol>\n<li>Was my googling attempt succesfull, or are there better sources?</li>\n<li>If this is the most relevant paper... is it of quality? Or my remarks on it are valid?</li>\n</ol>\n","text":"I'm reading a book \"The Organized Mind: Thinking Straight in the Age of Information Overload\" by Daniel Levitin.\n\n\n\n\nAt the beginning of chapter \"Organizing our homes\" he says that compared to men, women experience larger cortisol spike when they see mess. I googled that statement, and the source of that claim seems to come from https://doi.org/10.1177/0146167209352864 (https://doi.org/10.1177/0146167209352864)\n\n\n\n\nI don't have the access to the journal, but the abstract doesn't say much about how cluttered is the home. It just seems to correlate linguistic patterns with cortisol level.\nBut someone stressed for sure has different way of speaking than someone chill. No clutter scale is mentioned. The person might be stressed by something unaccounted in the research.\n\n\n\n\nSo please, can someone with journal access and proper qualifications tell me:\n\n\n\n\n\nWas my googling attempt succesfull, or are there better sources?\n\n\n\n\nIf this is the most relevant paper... is it of quality? Or my remarks on it are valid?"},{"context_id":"113624","html":"<p>I linked to the paper above in a <a href=\"https://dornsife.usc.edu/assets/sites/496/docs/pubs/2009noplace.pdf\" rel=\"nofollow noreferrer\">comment</a>.</p>\n<p>I'm not a behavioral scientist. So interpret with a grain of salt.</p>\n<p>The study analyzes language used after tours of homes, to evaluate how stressful the homes appear to be. So it's an imperfect measurement probably, but in direct reference to their homes. It probably does reflect something about how stressful they feel their homes to be, but IDK.</p>\n<p>Assuming that the slope of the diurnal cortisol curve is a meaningful measure (seems to be somewhat true based on my non-exhaustive search), and that the sample is adequately powered (n=30 couples, which is not too awful but not great either given the number of hypothesis tests). If you look at Tables 1 and 2, it does look like women are affected by a &quot;stressful home&quot; to a degree that men are not. Men also seem vaguely unhappy about stressful homes, though not as strongly as women. Granted, they only present regression tables, which is not always very helpful for understanding causal or statistical relationships.</p>\n<p>Nonetheless, the paper seems well-cited in the literature (as might be expected if it made it into a book). A lot of the work citing it is saying things along the lines of &quot;we need more work in this area to examine this effect&quot;. A small number of studies seem to confirm qualitatively that messy homes are stressful for women, see for example <a href=\"https://www.sciencedirect.com/science/article/abs/pii/S0272494421000062\" rel=\"nofollow noreferrer\">here</a> or <a href=\"https://journals.sagepub.com/doi/abs/10.1177/10775595221081795\" rel=\"nofollow noreferrer\">here</a>. It is less clear that the same isn't true for men, but then the majority of housework and caregiving responsibility is concentrated on women.</p>\n<p>Furthermore, it does seem like <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120613/\" rel=\"nofollow noreferrer\">global cortisol differences in men and women are not surprising</a>, and that cortisol-induced stress may affect women and men <a href=\"https://www.uc.edu/news/articles/legacy/healthnews/2005/11/chronic-stress-might-harm-women-more-than-it-does-men.html\" rel=\"nofollow noreferrer\">differently</a>.</p>\n<p>Generally, this study seems ok if not great. It fits into a broadly supportive narrative of (partially qualitative) research. The sum of the literature that I've skimmed very briefly cites this paper with approval, if perhaps making more of the results than is merited given the level 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=2ahUKEwiZvoeF1_eCAxWhPUQIHRe9Cd0QFnoECCIQAQ&amp;url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FPower_of_a_test&amp;usg=AOvVaw0a3pod09DZxufF6bshKtiA&amp;opi=89978449\" rel=\"nofollow noreferrer\">power</a> for the study. No one has posted on pubpeer about it or found anything dodgy about the study, in spite of its relatively high profile, so it's not obviously awful. I don't love the linguistic analysis either, but clutter is itself subjective I guess.</p>\n<p>There remains the issue that you raise that perhaps a person under stress will react more strongly than someone who is more relaxed. But it's a bit circular of course- in either case, it seems like women are more stressed, and they also get more stressed out about domestic clutter.</p>\n<p>Interested to hear more from a real behavioral science professional. I hope that my answer doesn't discourage anyone with more credentials from posting.</p>\n","text":"I linked to the paper above in a comment (https://dornsife.usc.edu/assets/sites/496/docs/pubs/2009noplace.pdf).\n\n\n\n\nI'm not a behavioral scientist. So interpret with a grain of salt.\n\n\n\n\nThe study analyzes language used after tours of homes, to evaluate how stressful the homes appear to be. So it's an imperfect measurement probably, but in direct reference to their homes. It probably does reflect something about how stressful they feel their homes to be, but IDK.\n\n\n\n\nAssuming that the slope of the diurnal cortisol curve is a meaningful measure (seems to be somewhat true based on my non-exhaustive search), and that the sample is adequately powered (n=30 couples, which is not too awful but not great either given the number of hypothesis tests). If you look at Tables 1 and 2, it does look like women are affected by a \"stressful home\" to a degree that men are not. Men also seem vaguely unhappy about stressful homes, though not as strongly as women. Granted, they only present regression tables, which is not always very helpful for understanding causal or statistical relationships.\n\n\n\n\nNonetheless, the paper seems well-cited in the literature (as might be expected if it made it into a book). A lot of the work citing it is saying things along the lines of \"we need more work in this area to examine this effect\". A small number of studies seem to confirm qualitatively that messy homes are stressful for women, see for example here (https://www.sciencedirect.com/science/article/abs/pii/S0272494421000062) or here (https://journals.sagepub.com/doi/abs/10.1177/10775595221081795). It is less clear that the same isn't true for men, but then the majority of housework and caregiving responsibility is concentrated on women.\n\n\n\n\nFurthermore, it does seem like global cortisol differences in men and women are not surprising (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120613/), and that cortisol-induced stress may affect women and men differently (https://www.uc.edu/news/articles/legacy/healthnews/2005/11/chronic-stress-might-harm-women-more-than-it-does-men.html).\n\n\n\n\nGenerally, this study seems ok if not great. It fits into a broadly supportive narrative of (partially qualitative) research. The sum of the literature that I've skimmed very briefly cites this paper with approval, if perhaps making more of the results than is merited given the level of power (https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwiZvoeF1_eCAxWhPUQIHRe9Cd0QFnoECCIQAQ&url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FPower_of_a_test&usg=AOvVaw0a3pod09DZxufF6bshKtiA&opi=89978449) for the study. No one has posted on pubpeer about it or found anything dodgy about the study, in spite of its relatively high profile, so it's not obviously awful. I don't love the linguistic analysis either, but clutter is itself subjective I guess.\n\n\n\n\nThere remains the issue that you raise that perhaps a person under stress will react more strongly than someone who is more relaxed. But it's a bit circular of course- in either case, it seems like women are more stressed, and they also get more stressed out about domestic clutter.\n\n\n\n\nInterested to hear more from a real behavioral science professional. I hope that my answer doesn't discourage anyone with more credentials from posting."}],"domain":"biology","external_citations":["https://doi.org/10.1177/0146167209352864","https://dornsife.usc.edu/assets/sites/496/docs/pubs/2009noplace.pdf","https://journals.sagepub.com/doi/abs/10.1177/10775595221081795","https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwiZvoeF1_eCAxWhPUQIHRe9Cd0QFnoECCIQAQ&url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FPower_of_a_test&usg=AOvVaw0a3pod09DZxufF6bshKtiA&opi=89978449","https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120613/","https://www.sciencedirect.com/science/article/abs/pii/S0272494421000062","https://www.uc.edu/news/articles/legacy/healthnews/2005/11/chronic-stress-might-harm-women-more-than-it-does-men.html"],"ground_truth_type":"metadata_grounded","group_id":"9c314080349d180f73f765517e975e16e1f2863ffda7572a9c41eb32d15c2fe2","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-88b76a6520280caeb9052cfb","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":"user46147","profile_url":"https://biology.stackexchange.com/users/18858/user46147","user_type":"registered"},"created_at":"2023-11-22T19:41:14+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"9A8E76F4-FFDA-4B7A-B2F7-75A2B151AC19","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9A8E76F4-FFDA-4B7A-B2F7-75A2B151AC19/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":"2023-12-05T23:21:40+00:00","raw_file":"raw/codex_api_v1/4b31ece29d49640766904acfb09f413caa800382e2048749dca713fe1c36c614_1790824046659275600_0.json","raw_sha256":"d34fed5816d7a26a5c9619cd4bcaa8f6e5ab3886f8bed7f16f08fb06ee93b82d","revision_guid":"699C7F0C-4E7A-422F-B234-A3F15422C5F0","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/699C7F0C-4E7A-422F-B234-A3F15422C5F0/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":"113531","source_record_sha256":"4aae004c103eaeb57fe06b324ee2afba8acc689c540720fd52217e9fa58fbd36","source_url":"https://biology.stackexchange.com/questions/113531/what-is-the-evidence-that-women-experience-a-larger-cortisol-spike-than-men-whe","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What is the evidence that women experience a larger cortisol spike than men, when they see domestic clutter?\nI'm reading a book \"The Organized Mind: Thinking Straight in the Age of Information Overload\" by Daniel Levitin.\n\n\n\n\nAt the beginning of chapter \"Organizing our homes\" he says that compared to men, women experience larger cortisol spike when they see mess. I googled that statement, and the source of that claim seems to come from https://doi.org/10.1177/0146167209352864 (https://doi.org/10.1177/0146167209352864)\n\n\n\n\nI don't have the access to the journal, but the abstract doesn't say much about how cluttered is the home. It just seems to correlate linguistic patterns with cortisol level.\nBut someone stressed for sure has different way of speaking than someone chill. No clutter scale is mentioned. The person might be stressed by something unaccounted in the research.\n\n\n\n\nSo please, can someone with journal access and proper qualifications tell me:\n\n\n\n\n\nWas my googling attempt succesfull, or are there better sources?\n\n\n\n\nIf this is the most relevant paper... is it of quality? Or my remarks on it are valid?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113624,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":113535,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Two other kingdoms contain unicellular organisms.</p>\n<p>Some fungi, such as <a href=\"https://en.wikipedia.org/wiki/Yeast\" rel=\"nofollow noreferrer\">yeasts</a> are unicellular.</p>\n<p>Many algal (Plantae) species are unicellular, including the spectacular <em><a href=\"https://en.wikipedia.org/wiki/Valonia_ventricosa\" rel=\"nofollow noreferrer\">Valonia ventricosa</a></em>, which is up to 5 cm (2 inches) in diameter. There is also a genus of seaweed <em><a href=\"https://en.wikipedia.org/wiki/Caulerpa\" rel=\"nofollow noreferrer\">Caulerpa</a></em>, which is unicellular, though multi-nucleate that is thought to be the largest single-celled organism, being up to about 3 m (10 feet) long.</p>\n","answer_id":113535,"answer_text":"Two other kingdoms contain unicellular organisms.\n\n\n\n\nSome fungi, such as yeasts (https://en.wikipedia.org/wiki/Yeast) are unicellular.\n\n\n\n\nMany algal (Plantae) species are unicellular, including the spectacular Valonia ventricosa (https://en.wikipedia.org/wiki/Valonia_ventricosa), which is up to 5 cm (2 inches) in diameter. There is also a genus of seaweed Caulerpa (https://en.wikipedia.org/wiki/Caulerpa), which is unicellular, though multi-nucleate that is thought to be the largest single-celled organism, being up to about 3 m (10 feet) long.","answer_url":"https://biology.stackexchange.com/a/113535","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2023-11-23T02:38:25+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":113534,"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":"2023-11-23T02:38:25+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"C94573E9-5290-4F36-95E0-D1B702E6B5E3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C94573E9-5290-4F36-95E0-D1B702E6B5E3/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Kunj Parikh","author_url":"https://biology.stackexchange.com/users/77862/kunj-parikh","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Kunj Parikh","profile_url":"https://biology.stackexchange.com/users/77862/kunj-parikh","user_type":"registered"},"created_at":"2023-11-22T23:59:23+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"D39925FF-AB4A-46B2-A1C7-2BD0B45864FE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D39925FF-AB4A-46B2-A1C7-2BD0B45864FE/view-source"}],"url":"https://biology.stackexchange.com/questions/113534/are-all-unicellular-eukaryotic-organisms-protists"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"113535","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":"2023-11-23T02:38:25+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"C94573E9-5290-4F36-95E0-D1B702E6B5E3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C94573E9-5290-4F36-95E0-D1B702E6B5E3/view-source"}],"url":"https://biology.stackexchange.com/a/113535"}],"contexts":[{"context_id":"question","html":"<p>I know that the Protists are in Domain Eukarya, and that some protists are unicellular. Are there any other eukaryotic group of creatures that are not protists that are unicellular?</p>\n","text":"I know that the Protists are in Domain Eukarya, and that some protists are unicellular. Are there any other eukaryotic group of creatures that are not protists that are unicellular?"},{"context_id":"113535","html":"<p>Two other kingdoms contain unicellular organisms.</p>\n<p>Some fungi, such as <a href=\"https://en.wikipedia.org/wiki/Yeast\" rel=\"nofollow noreferrer\">yeasts</a> are unicellular.</p>\n<p>Many algal (Plantae) species are unicellular, including the spectacular <em><a href=\"https://en.wikipedia.org/wiki/Valonia_ventricosa\" rel=\"nofollow noreferrer\">Valonia ventricosa</a></em>, which is up to 5 cm (2 inches) in diameter. There is also a genus of seaweed <em><a href=\"https://en.wikipedia.org/wiki/Caulerpa\" rel=\"nofollow noreferrer\">Caulerpa</a></em>, which is unicellular, though multi-nucleate that is thought to be the largest single-celled organism, being up to about 3 m (10 feet) long.</p>\n","text":"Two other kingdoms contain unicellular organisms.\n\n\n\n\nSome fungi, such as yeasts (https://en.wikipedia.org/wiki/Yeast) are unicellular.\n\n\n\n\nMany algal (Plantae) species are unicellular, including the spectacular Valonia ventricosa (https://en.wikipedia.org/wiki/Valonia_ventricosa), which is up to 5 cm (2 inches) in diameter. There is also a genus of seaweed Caulerpa (https://en.wikipedia.org/wiki/Caulerpa), which is unicellular, though multi-nucleate that is thought to be the largest single-celled organism, being up to about 3 m (10 feet) long."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Caulerpa","https://en.wikipedia.org/wiki/Valonia_ventricosa","https://en.wikipedia.org/wiki/Yeast"],"ground_truth_type":"metadata_grounded","group_id":"e1da058ed72ed45f09c05fb0dee0346395cab79c6046fbdf5280d9fdddf78151","hard_case_family":["multiple_sources"],"id":"RHM-9840ca138b6e8511ea5f0e48","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":"Kunj Parikh","profile_url":"https://biology.stackexchange.com/users/77862/kunj-parikh","user_type":"registered"},"created_at":"2023-11-22T23:59:23+00:00","raw_file":"raw/codex_api_v1/dd2ec40a5fd89c86baf1df900910393bf6ce6ec67fd07493fc5fb9dcd3e21d06_1790824048829330400_0.json","raw_sha256":"543debf5d698aa4490d105f431e8f442c0f067237add2fc696b1bcaa58d49ecd","revision_guid":"D39925FF-AB4A-46B2-A1C7-2BD0B45864FE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D39925FF-AB4A-46B2-A1C7-2BD0B45864FE/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":"113534","source_record_sha256":"cffd91380e7dee0a3e9f8b0a4cab6e3f2d78c22e554618c0fabbf3b3f86692f5","source_url":"https://biology.stackexchange.com/questions/113534/are-all-unicellular-eukaryotic-organisms-protists","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Are all unicellular eukaryotic organisms protists?\nI know that the Protists are in Domain Eukarya, and that some protists are unicellular. Are there any other eukaryotic group of creatures that are not protists that are unicellular?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113535,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The eukaryotic initiation factor (eIF) proteins are necessary for the ribosome to translate the mRNA. The main benefit is that they, when present, make it easier for the ribosome to find the AUG sequence, which is the start of the protein (as shown in this <a href=\"https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9/figures/1\" rel=\"nofollow noreferrer\">diagram</a>) by &quot;helping&quot; the Methionine t-RNA find said sequence.</p>\n<p>The reason why the mRNA doesn't bind to the PABP directly is for translation regulation. If the mRNA needed to just bind to the PABP and the mRNA for a protein is made when there is more than enough protein, then amino acids are being wasted to make the already abundant protein. If there exist some factors that can control the translation of protein, then the cell can better control protein translation.</p>\n<p>Why 4E-BP1 is phosphorylated instead of PABP is because it evolved that way. I know that isn't a satisfying answer, but cells don't really evolve for efficiency, but for &quot;good enough&quot;. If it is enough to survive, then why bother changing it?</p>\n<p>I hope this answers your question!</p>\n<p>Citation for Paper with Diagram: <a href=\"https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9\" rel=\"nofollow noreferrer\">https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9</a></p>\n","answer_id":113971,"answer_text":"The eukaryotic initiation factor (eIF) proteins are necessary for the ribosome to translate the mRNA. The main benefit is that they, when present, make it easier for the ribosome to find the AUG sequence, which is the start of the protein (as shown in this diagram (https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9/figures/1)) by \"helping\" the Methionine t-RNA find said sequence.\n\n\n\n\nThe reason why the mRNA doesn't bind to the PABP directly is for translation regulation. If the mRNA needed to just bind to the PABP and the mRNA for a protein is made when there is more than enough protein, then amino acids are being wasted to make the already abundant protein. If there exist some factors that can control the translation of protein, then the cell can better control protein translation.\n\n\n\n\nWhy 4E-BP1 is phosphorylated instead of PABP is because it evolved that way. I know that isn't a satisfying answer, but cells don't really evolve for efficiency, but for \"good enough\". If it is enough to survive, then why bother changing it?\n\n\n\n\nI hope this answers your question!\n\n\n\n\nCitation for Paper with Diagram: https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9 (https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9)","answer_url":"https://biology.stackexchange.com/a/113971","author":"RoyGenesis","author_url":"https://biology.stackexchange.com/users/35570/roygenesis","content_license":"CC BY-SA 4.0","created_at":"2024-01-26T01:40:34+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":113965,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"RoyGenesis","profile_url":"https://biology.stackexchange.com/users/35570/roygenesis","user_type":"registered"},"created_at":"2024-01-26T01:40:34+00:00","raw_file":"raw/codex_api_v1/7731e95f5b86805dcc210d6fef6f1ae90aedbea29d6d8084621d880fcd44e459_1790824059333573800_0.json","raw_sha256":"75346ea86ff90b8db1427552949ecffb611214a9308b4f99afbdda87d5df239e","revision_guid":"FB5266FF-F740-4016-862C-059ECD65715B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FB5266FF-F740-4016-862C-059ECD65715B/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"RoyGenesis","profile_url":"https://biology.stackexchange.com/users/35570/roygenesis","user_type":"registered"},"created_at":"2024-01-31T03:13:17+00:00","raw_file":"raw/codex_api_v1/7731e95f5b86805dcc210d6fef6f1ae90aedbea29d6d8084621d880fcd44e459_1790824059333573800_0.json","raw_sha256":"75346ea86ff90b8db1427552949ecffb611214a9308b4f99afbdda87d5df239e","revision_guid":"4222EE60-363B-4587-885A-0E77BD290FB5","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4222EE60-363B-4587-885A-0E77BD290FB5/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Dion Silverman","author_url":"https://biology.stackexchange.com/users/78685/dion-silverman","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Dion Silverman","profile_url":"https://biology.stackexchange.com/users/78685/dion-silverman","user_type":"registered"},"created_at":"2024-01-25T06:07:37+00:00","raw_file":"raw/codex_api_v1/7731e95f5b86805dcc210d6fef6f1ae90aedbea29d6d8084621d880fcd44e459_1790824059333573800_0.json","raw_sha256":"75346ea86ff90b8db1427552949ecffb611214a9308b4f99afbdda87d5df239e","revision_guid":"9FF1FC43-6FBD-4342-B7C6-AE92A7D3C06C","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9FF1FC43-6FBD-4342-B7C6-AE92A7D3C06C/view-source"}],"url":"https://biology.stackexchange.com/questions/113965/in-mrna-translation-why-are-there-so-many-factors"},{"author":"RoyGenesis","author_url":"https://biology.stackexchange.com/users/35570/roygenesis","content_license":"CC BY-SA 4.0","context_id":"113971","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"RoyGenesis","profile_url":"https://biology.stackexchange.com/users/35570/roygenesis","user_type":"registered"},"created_at":"2024-01-26T01:40:34+00:00","raw_file":"raw/codex_api_v1/7731e95f5b86805dcc210d6fef6f1ae90aedbea29d6d8084621d880fcd44e459_1790824059333573800_0.json","raw_sha256":"75346ea86ff90b8db1427552949ecffb611214a9308b4f99afbdda87d5df239e","revision_guid":"FB5266FF-F740-4016-862C-059ECD65715B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FB5266FF-F740-4016-862C-059ECD65715B/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"RoyGenesis","profile_url":"https://biology.stackexchange.com/users/35570/roygenesis","user_type":"registered"},"created_at":"2024-01-31T03:13:17+00:00","raw_file":"raw/codex_api_v1/7731e95f5b86805dcc210d6fef6f1ae90aedbea29d6d8084621d880fcd44e459_1790824059333573800_0.json","raw_sha256":"75346ea86ff90b8db1427552949ecffb611214a9308b4f99afbdda87d5df239e","revision_guid":"4222EE60-363B-4587-885A-0E77BD290FB5","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4222EE60-363B-4587-885A-0E77BD290FB5/view-source"}],"url":"https://biology.stackexchange.com/a/113971"}],"contexts":[{"context_id":"question","html":"<p>When the small ribosomal subunit binds to mRNA’s 5’-cap, it looks for the complex of three eLFs bound to the poly-A-binding protein (PABP), which circularises the mRNA.  It is then this circular mRNA that the small ribosomal subunit binds to.\n<a href=\"https://i.sstatic.net/Gr7WU.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/Gr7WU.png\" alt=\"Transcription Initiation Complex\" /></a></p>\n<p>In low-nutrient environments, 4E-BP1 binds to PABP, inhibiting it from binding to the 5’-cap complex. I high nutrient environments 4E-BP1 is phosphorylated.\n<a href=\"https://i.sstatic.net/ajgG6.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/ajgG6.png\" alt=\"4E-BP1 Inhibition of PABP\" /></a></p>\n<p>Why (what benefit is conferred?) are the eLFs there?  Why not just have the PABP bind to the 5’-cap to initiate transcription?  And why 4E-BP1?   Why not just phosphorylate PABP directly?</p>\n<p>I mean I know that as is, PABP isn’t set up to be usefully phosphorylated, but why is it this way?  It seems a whole bunch energy and resources wasted making these extra proteins, and more room for things to go wrong, more DNA that has to be made and carried around with no mutations and transcribed and translated correctly.</p>\n","text":"When the small ribosomal subunit binds to mRNA’s 5’-cap, it looks for the complex of three eLFs bound to the poly-A-binding protein (PABP), which circularises the mRNA.  It is then this circular mRNA that the small ribosomal subunit binds to.\n[image: Transcription Initiation Complex; source: https://i.sstatic.net/Gr7WU.png] (https://i.sstatic.net/Gr7WU.png)\n\n\n\n\nIn low-nutrient environments, 4E-BP1 binds to PABP, inhibiting it from binding to the 5’-cap complex. I high nutrient environments 4E-BP1 is phosphorylated.\n[image: 4E-BP1 Inhibition of PABP; source: https://i.sstatic.net/ajgG6.png] (https://i.sstatic.net/ajgG6.png)\n\n\n\n\nWhy (what benefit is conferred?) are the eLFs there?  Why not just have the PABP bind to the 5’-cap to initiate transcription?  And why 4E-BP1?   Why not just phosphorylate PABP directly?\n\n\n\n\nI mean I know that as is, PABP isn’t set up to be usefully phosphorylated, but why is it this way?  It seems a whole bunch energy and resources wasted making these extra proteins, and more room for things to go wrong, more DNA that has to be made and carried around with no mutations and transcribed and translated correctly."},{"context_id":"113971","html":"<p>The eukaryotic initiation factor (eIF) proteins are necessary for the ribosome to translate the mRNA. The main benefit is that they, when present, make it easier for the ribosome to find the AUG sequence, which is the start of the protein (as shown in this <a href=\"https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9/figures/1\" rel=\"nofollow noreferrer\">diagram</a>) by &quot;helping&quot; the Methionine t-RNA find said sequence.</p>\n<p>The reason why the mRNA doesn't bind to the PABP directly is for translation regulation. If the mRNA needed to just bind to the PABP and the mRNA for a protein is made when there is more than enough protein, then amino acids are being wasted to make the already abundant protein. If there exist some factors that can control the translation of protein, then the cell can better control protein translation.</p>\n<p>Why 4E-BP1 is phosphorylated instead of PABP is because it evolved that way. I know that isn't a satisfying answer, but cells don't really evolve for efficiency, but for &quot;good enough&quot;. If it is enough to survive, then why bother changing it?</p>\n<p>I hope this answers your question!</p>\n<p>Citation for Paper with Diagram: <a href=\"https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9\" rel=\"nofollow noreferrer\">https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9</a></p>\n","text":"The eukaryotic initiation factor (eIF) proteins are necessary for the ribosome to translate the mRNA. The main benefit is that they, when present, make it easier for the ribosome to find the AUG sequence, which is the start of the protein (as shown in this diagram (https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9/figures/1)) by \"helping\" the Methionine t-RNA find said sequence.\n\n\n\n\nThe reason why the mRNA doesn't bind to the PABP directly is for translation regulation. If the mRNA needed to just bind to the PABP and the mRNA for a protein is made when there is more than enough protein, then amino acids are being wasted to make the already abundant protein. If there exist some factors that can control the translation of protein, then the cell can better control protein translation.\n\n\n\n\nWhy 4E-BP1 is phosphorylated instead of PABP is because it evolved that way. I know that isn't a satisfying answer, but cells don't really evolve for efficiency, but for \"good enough\". If it is enough to survive, then why bother changing it?\n\n\n\n\nI hope this answers your question!\n\n\n\n\nCitation for Paper with Diagram: https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9 (https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9)"}],"domain":"biology","external_citations":["https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9","https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9/figures/1","https://i.sstatic.net/Gr7WU.png","https://i.sstatic.net/ajgG6.png"],"ground_truth_type":"metadata_grounded","group_id":"225936032c9454d462b6aedd9c5fc3a287ab98491b562c82f75162667e796246","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-0f49aff14ee9cb1ef201b79b","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":"Dion Silverman","profile_url":"https://biology.stackexchange.com/users/78685/dion-silverman","user_type":"registered"},"created_at":"2024-01-25T06:07:37+00:00","raw_file":"raw/codex_api_v1/7731e95f5b86805dcc210d6fef6f1ae90aedbea29d6d8084621d880fcd44e459_1790824059333573800_0.json","raw_sha256":"75346ea86ff90b8db1427552949ecffb611214a9308b4f99afbdda87d5df239e","revision_guid":"9FF1FC43-6FBD-4342-B7C6-AE92A7D3C06C","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9FF1FC43-6FBD-4342-B7C6-AE92A7D3C06C/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":"113965","source_record_sha256":"98d1762bb0e5f653d8b2440ebf7b0ae150c245567e749781a938b3da7d504bb6","source_url":"https://biology.stackexchange.com/questions/113965/in-mrna-translation-why-are-there-so-many-factors","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"In mRNA translation, why are there so many factors?\nWhen the small ribosomal subunit binds to mRNA’s 5’-cap, it looks for the complex of three eLFs bound to the poly-A-binding protein (PABP), which circularises the mRNA.  It is then this circular mRNA that the small ribosomal subunit binds to.\n[image: Transcription Initiation Complex; source: https://i.sstatic.net/Gr7WU.png] (https://i.sstatic.net/Gr7WU.png)\n\n\n\n\nIn low-nutrient environments, 4E-BP1 binds to PABP, inhibiting it from binding to the 5’-cap complex. I high nutrient environments 4E-BP1 is phosphorylated.\n[image: 4E-BP1 Inhibition of PABP; source: https://i.sstatic.net/ajgG6.png] (https://i.sstatic.net/ajgG6.png)\n\n\n\n\nWhy (what benefit is conferred?) are the eLFs there?  Why not just have the PABP bind to the 5’-cap to initiate transcription?  And why 4E-BP1?   Why not just phosphorylate PABP directly?\n\n\n\n\nI mean I know that as is, PABP isn’t set up to be usefully phosphorylated, but why is it this way?  It seems a whole bunch energy and resources wasted making these extra proteins, and more room for things to go wrong, more DNA that has to be made and carried around with no mutations and transcribed and translated correctly.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":113971,"score":2}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":114165,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Answering my own question:</p>\n<p><strong>Yes, cells can straddle anatomical systems in the body.</strong></p>\n<p>In particular, the spinal cord is part of the central nervous system while spinal nerves are part of the peripheral nervous system, as described in <a href=\"https://biology.stackexchange.com/questions/80780/why-are-spinal-nerves-considered-a-part-of-pns-while-the-spinal-cord-is-a-part-o\">this question</a>. And nerves are <a href=\"https://en.wikipedia.org/wiki/Nerve\" rel=\"nofollow noreferrer\">bundles of axons, supported and held together by additional cells</a>. The cell body to which the axon belongs is not part of the nerve. Instead, for spinal nerves, it's a part of the spinal cord and hence in the CNS.</p>\n<p>It was surprising to me that the boundaries of anatomical structure don't always correspond to the boundaries between cells, but that makes sense when I consider that the field of anatomy began as a macroscopic endeavor, a scale on which it makes sense to treat the boundary between nerve and spinal cord as the point where they meet.</p>\n<p>Thanks to anongoodnurse who basically led me to this answer in the comments.</p>\n","answer_id":114165,"answer_text":"Answering my own question:\n\n\n\n\nYes, cells can straddle anatomical systems in the body.\n\n\n\n\nIn particular, the spinal cord is part of the central nervous system while spinal nerves are part of the peripheral nervous system, as described in this question (https://biology.stackexchange.com/questions/80780/why-are-spinal-nerves-considered-a-part-of-pns-while-the-spinal-cord-is-a-part-o). And nerves are bundles of axons, supported and held together by additional cells (https://en.wikipedia.org/wiki/Nerve). The cell body to which the axon belongs is not part of the nerve. Instead, for spinal nerves, it's a part of the spinal cord and hence in the CNS.\n\n\n\n\nIt was surprising to me that the boundaries of anatomical structure don't always correspond to the boundaries between cells, but that makes sense when I consider that the field of anatomy began as a macroscopic endeavor, a scale on which it makes sense to treat the boundary between nerve and spinal cord as the point where they meet.\n\n\n\n\nThanks to anongoodnurse who basically led me to this answer in the comments.","answer_url":"https://biology.stackexchange.com/a/114165","author":"Mark Foskey","author_url":"https://biology.stackexchange.com/users/15605/mark-foskey","content_license":"CC BY-SA 4.0","created_at":"2024-02-24T02:26:49+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":114055,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Mark Foskey","profile_url":"https://biology.stackexchange.com/users/15605/mark-foskey","user_type":"registered"},"created_at":"2024-02-24T02:26:49+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"C23ABC56-C14B-4B76-AE04-9D7DAECF353A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C23ABC56-C14B-4B76-AE04-9D7DAECF353A/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Mark Foskey","author_url":"https://biology.stackexchange.com/users/15605/mark-foskey","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Mark Foskey","profile_url":"https://biology.stackexchange.com/users/15605/mark-foskey","user_type":"registered"},"created_at":"2024-02-07T19:45:35+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"31272345-8987-458D-8852-16F3D757D0A9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/31272345-8987-458D-8852-16F3D757D0A9/view-source"}],"url":"https://biology.stackexchange.com/questions/114055/can-cells-straddle-different-anatomical-systems-in-the-body"},{"author":"Mark Foskey","author_url":"https://biology.stackexchange.com/users/15605/mark-foskey","content_license":"CC BY-SA 4.0","context_id":"114165","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Mark Foskey","profile_url":"https://biology.stackexchange.com/users/15605/mark-foskey","user_type":"registered"},"created_at":"2024-02-24T02:26:49+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"C23ABC56-C14B-4B76-AE04-9D7DAECF353A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C23ABC56-C14B-4B76-AE04-9D7DAECF353A/view-source"}],"url":"https://biology.stackexchange.com/a/114165"}],"contexts":[{"context_id":"question","html":"<p>I'm reading <em>Periphery</em> by Moses V. Chao, and the author explains that the peripheral nervous system consists of the portion of the nervous system outside the brain and spinal cord. But, if I understand correctly, the cell bodies of motor neurons are in the spinal cord (or even further upstream?), whereas the nerve fibers themselves are just bundles of really long myelinated axons going all the way from the spinal cord to the nerve endings. So these seem to be cells whose cell bodies are part of the central nervous system, but whose axons are part of the peripheral nervous system. Is that how neurologists think about it? I would have thought things would be subdivided in a way that each cell is in one system or another.</p>\n<p>I see <a href=\"https://biology.stackexchange.com/questions/80780/why-are-spinal-nerves-considered-a-part-of-pns-while-the-spinal-cord-is-a-part-o\">this related question</a>, but I don't think its answer is a clear answer for this question. That answer does seem to <em>suggest</em> that the cell bodies of the motor neurons are part of the PNS, not the CNS, even though they're physically in the spinal cord, but it's not really explicit about that point.</p>\n<p>Alternatively, it's perfectly reasonable to have overlapping systems. I'd just like to know the way the lines are drawn.</p>\n","text":"I'm reading Periphery by Moses V. Chao, and the author explains that the peripheral nervous system consists of the portion of the nervous system outside the brain and spinal cord. But, if I understand correctly, the cell bodies of motor neurons are in the spinal cord (or even further upstream?), whereas the nerve fibers themselves are just bundles of really long myelinated axons going all the way from the spinal cord to the nerve endings. So these seem to be cells whose cell bodies are part of the central nervous system, but whose axons are part of the peripheral nervous system. Is that how neurologists think about it? I would have thought things would be subdivided in a way that each cell is in one system or another.\n\n\n\n\nI see this related question (https://biology.stackexchange.com/questions/80780/why-are-spinal-nerves-considered-a-part-of-pns-while-the-spinal-cord-is-a-part-o), but I don't think its answer is a clear answer for this question. That answer does seem to suggest that the cell bodies of the motor neurons are part of the PNS, not the CNS, even though they're physically in the spinal cord, but it's not really explicit about that point.\n\n\n\n\nAlternatively, it's perfectly reasonable to have overlapping systems. I'd just like to know the way the lines are drawn."},{"context_id":"114165","html":"<p>Answering my own question:</p>\n<p><strong>Yes, cells can straddle anatomical systems in the body.</strong></p>\n<p>In particular, the spinal cord is part of the central nervous system while spinal nerves are part of the peripheral nervous system, as described in <a href=\"https://biology.stackexchange.com/questions/80780/why-are-spinal-nerves-considered-a-part-of-pns-while-the-spinal-cord-is-a-part-o\">this question</a>. And nerves are <a href=\"https://en.wikipedia.org/wiki/Nerve\" rel=\"nofollow noreferrer\">bundles of axons, supported and held together by additional cells</a>. The cell body to which the axon belongs is not part of the nerve. Instead, for spinal nerves, it's a part of the spinal cord and hence in the CNS.</p>\n<p>It was surprising to me that the boundaries of anatomical structure don't always correspond to the boundaries between cells, but that makes sense when I consider that the field of anatomy began as a macroscopic endeavor, a scale on which it makes sense to treat the boundary between nerve and spinal cord as the point where they meet.</p>\n<p>Thanks to anongoodnurse who basically led me to this answer in the comments.</p>\n","text":"Answering my own question:\n\n\n\n\nYes, cells can straddle anatomical systems in the body.\n\n\n\n\nIn particular, the spinal cord is part of the central nervous system while spinal nerves are part of the peripheral nervous system, as described in this question (https://biology.stackexchange.com/questions/80780/why-are-spinal-nerves-considered-a-part-of-pns-while-the-spinal-cord-is-a-part-o). And nerves are bundles of axons, supported and held together by additional cells (https://en.wikipedia.org/wiki/Nerve). The cell body to which the axon belongs is not part of the nerve. Instead, for spinal nerves, it's a part of the spinal cord and hence in the CNS.\n\n\n\n\nIt was surprising to me that the boundaries of anatomical structure don't always correspond to the boundaries between cells, but that makes sense when I consider that the field of anatomy began as a macroscopic endeavor, a scale on which it makes sense to treat the boundary between nerve and spinal cord as the point where they meet.\n\n\n\n\nThanks to anongoodnurse who basically led me to this answer in the comments."}],"domain":"biology","external_citations":["https://biology.stackexchange.com/questions/80780/why-are-spinal-nerves-considered-a-part-of-pns-while-the-spinal-cord-is-a-part-o","https://en.wikipedia.org/wiki/Nerve"],"ground_truth_type":"metadata_grounded","group_id":"2f4c2da96c6008be207ea01555cd7689c9b8296ad4fd91220d7abcf8f4bc24f3","hard_case_family":["multiple_sources"],"id":"RHM-2f4bf0655e8b7a198552819f","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":"Mark Foskey","profile_url":"https://biology.stackexchange.com/users/15605/mark-foskey","user_type":"registered"},"created_at":"2024-02-07T19:45:35+00:00","raw_file":"raw/codex_api_v1/4aa156cabb1f3edbc4e0a74ff84deb30f9cd06be13c7d021adab58e209db850d_1790824057164545000_0.json","raw_sha256":"42ee08c1af6f231bf4bd10a51fd8384910e076e5d887f51c6dd79384012b46ec","revision_guid":"31272345-8987-458D-8852-16F3D757D0A9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/31272345-8987-458D-8852-16F3D757D0A9/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":"114055","source_record_sha256":"04fd89c5af78722c014ddf29179b7f79415813d4f3e02f39554fcd14cfcc5135","source_url":"https://biology.stackexchange.com/questions/114055/can-cells-straddle-different-anatomical-systems-in-the-body","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Can cells straddle different anatomical systems in the body?\nI'm reading Periphery by Moses V. Chao, and the author explains that the peripheral nervous system consists of the portion of the nervous system outside the brain and spinal cord. But, if I understand correctly, the cell bodies of motor neurons are in the spinal cord (or even further upstream?), whereas the nerve fibers themselves are just bundles of really long myelinated axons going all the way from the spinal cord to the nerve endings. So these seem to be cells whose cell bodies are part of the central nervous system, but whose axons are part of the peripheral nervous system. Is that how neurologists think about it? I would have thought things would be subdivided in a way that each cell is in one system or another.\n\n\n\n\nI see this related question (https://biology.stackexchange.com/questions/80780/why-are-spinal-nerves-considered-a-part-of-pns-while-the-spinal-cord-is-a-part-o), but I don't think its answer is a clear answer for this question. That answer does seem to suggest that the cell bodies of the motor neurons are part of the PNS, not the CNS, even though they're physically in the spinal cord, but it's not really explicit about that point.\n\n\n\n\nAlternatively, it's perfectly reasonable to have overlapping systems. I'd just like to know the way the lines are drawn.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114165,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":114160,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Theoretically, for CFU determination the volume of the inoculum shouldn't matter as long as you plate a dilution series and find the plate with a countable number of colonies. It also shouldn't matter if you use the spread-plate method or the pour plate method or something else (like drop plates or spiral plates). But all of that assumes ideal conditions where you are able to get a perfect and uniform spread over the whole plate every time. In the real world there are practical limitations on the range of usable inoculum volumes when spreading liquid onto agar plates.</p>\n<p>When making spread plates it's best to maintain continuous spreading motion until all (or almost all) of the liquid from the inoculum has been absorbed by the agar medium. If you don't, you can end up with unevenly distributed colonies, which can make otherwise countable dilutions difficult or impossible to count accurately. If the volume is too large, it may take an impractical amount of time for the liquid to absorb. On the flip side, the volume still needs to be large enough to cover the whole plate evenly. If it's too small (say 10µL) you may have trouble spreading it evenly across the entire surface.</p>\n<p>There's also some potential for variation in consistency when dispensing different volumes. Most micropipettes are slightly more accurate at the high end of their range than the low end. So, IF you were using the same p1000 pipette, your replicates could be slightly more consistent with larger volumes than small ones. But, properly calibrated, the dispensed volume should vary by less than 10% even at the lowest setting of most pipettes, and if this were a concern, it could be remedied by switching to a more appropriately sized pipette.</p>\n<p>Lastly, if you are trying to make a bacterial lawn, for something like a Kirby-Bauer test, changing the inoculum volume can affect the outcome of the test. McFarland standards aren't always perfectly calibrated for every organism, but overloading the plate with 5x the standard inoculum certainly has the potential of skewing the test results. The methods for these tests are standardized to improve repeatability between labs. Essentially, a denser inoculum will reduce the size of the inhibition zone, while a reduced inoculum will increase the inhibition zone. Since the inhibition zone determines whether a particular isolate is classified as resistant or susceptible to a given drug, inoculation protocols are standardized to make sure patients receive the appropriate care.</p>\n<p>Source: <a href=\"https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Disk_test_documents/2021_manuals/Manual_v_9.0_EUCAST_Disk_Test_2021.pdf\" rel=\"nofollow noreferrer\">EUCAST Disk Diffusion Method for Antimicrobial Susceptibility Testing  - Version 9.0 (January 2021)</a></p>\n","answer_id":114160,"answer_text":"Theoretically, for CFU determination the volume of the inoculum shouldn't matter as long as you plate a dilution series and find the plate with a countable number of colonies. It also shouldn't matter if you use the spread-plate method or the pour plate method or something else (like drop plates or spiral plates). But all of that assumes ideal conditions where you are able to get a perfect and uniform spread over the whole plate every time. In the real world there are practical limitations on the range of usable inoculum volumes when spreading liquid onto agar plates.\n\n\n\n\nWhen making spread plates it's best to maintain continuous spreading motion until all (or almost all) of the liquid from the inoculum has been absorbed by the agar medium. If you don't, you can end up with unevenly distributed colonies, which can make otherwise countable dilutions difficult or impossible to count accurately. If the volume is too large, it may take an impractical amount of time for the liquid to absorb. On the flip side, the volume still needs to be large enough to cover the whole plate evenly. If it's too small (say 10µL) you may have trouble spreading it evenly across the entire surface.\n\n\n\n\nThere's also some potential for variation in consistency when dispensing different volumes. Most micropipettes are slightly more accurate at the high end of their range than the low end. So, IF you were using the same p1000 pipette, your replicates could be slightly more consistent with larger volumes than small ones. But, properly calibrated, the dispensed volume should vary by less than 10% even at the lowest setting of most pipettes, and if this were a concern, it could be remedied by switching to a more appropriately sized pipette.\n\n\n\n\nLastly, if you are trying to make a bacterial lawn, for something like a Kirby-Bauer test, changing the inoculum volume can affect the outcome of the test. McFarland standards aren't always perfectly calibrated for every organism, but overloading the plate with 5x the standard inoculum certainly has the potential of skewing the test results. The methods for these tests are standardized to improve repeatability between labs. Essentially, a denser inoculum will reduce the size of the inhibition zone, while a reduced inoculum will increase the inhibition zone. Since the inhibition zone determines whether a particular isolate is classified as resistant or susceptible to a given drug, inoculation protocols are standardized to make sure patients receive the appropriate care.\n\n\n\n\nSource: EUCAST Disk Diffusion Method for Antimicrobial Susceptibility Testing  - Version 9.0 (January 2021) (https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Disk_test_documents/2021_manuals/Manual_v_9.0_EUCAST_Disk_Test_2021.pdf)","answer_url":"https://biology.stackexchange.com/a/114160","author":"MikeyC","author_url":"https://biology.stackexchange.com/users/56688/mikeyc","content_license":"CC BY-SA 4.0","created_at":"2024-02-23T16:11:23+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":114135,"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":"2024-02-23T16:11:23+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"B77FB29F-27E3-4342-B269-03C1BA052F9A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B77FB29F-27E3-4342-B269-03C1BA052F9A/view-source"},{"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":"2024-02-23T18:57:57+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"D0AA6BF4-982B-4B80-BA12-DAA30B697C12","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D0AA6BF4-982B-4B80-BA12-DAA30B697C12/view-source"}],"score":3},{"answer_html":"<p>To add to the answer by @MikeyC . The spread plate technique for calculation of colony forming units has volume plated as a variable:</p>\n<p>CFU/ml = (number of colonies x dilution factor) / volume of culture plated</p>\n<p>This means that you account for the volume in the calculation performed after doing your counting.</p>\n<p>Of course, as MikeyC mentioned, the volume matters to some extent as if you add too much of too high a density suspension, then you will have an uncountable plate. To compensate for this, what is usually done is a dilution series, where you choose which dilution is used for the calculation This also provides a secondary check on your count, as a plate below (lower dilution) the countable dilution should be TMTC and the one above should have approximately 1/(dilution factor) fewer colonies. For example, in a 10-fold dilution factor series, your countable plate might have 50 colonies, the one below should have ~500 (TMTC) and the one above should have about 5.</p>\n<p>You should also note that the dilution factor is also compensated for in the equation.</p>\n","answer_id":114171,"answer_text":"To add to the answer by @MikeyC . The spread plate technique for calculation of colony forming units has volume plated as a variable:\n\n\n\n\nCFU/ml = (number of colonies x dilution factor) / volume of culture plated\n\n\n\n\nThis means that you account for the volume in the calculation performed after doing your counting.\n\n\n\n\nOf course, as MikeyC mentioned, the volume matters to some extent as if you add too much of too high a density suspension, then you will have an uncountable plate. To compensate for this, what is usually done is a dilution series, where you choose which dilution is used for the calculation This also provides a secondary check on your count, as a plate below (lower dilution) the countable dilution should be TMTC and the one above should have approximately 1/(dilution factor) fewer colonies. For example, in a 10-fold dilution factor series, your countable plate might have 50 colonies, the one below should have ~500 (TMTC) and the one above should have about 5.\n\n\n\n\nYou should also note that the dilution factor is also compensated for in the equation.","answer_url":"https://biology.stackexchange.com/a/114171","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2024-02-25T19:55:26+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":114135,"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":"2024-02-25T19:55:26+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"203CF5D0-CE50-40F6-9053-72EFC53BC9E3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/203CF5D0-CE50-40F6-9053-72EFC53BC9E3/view-source"}],"score":0}],"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":"2024-02-20T20:25:24+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"52E0004F-8D19-4D3D-9D0C-1EE48E40F897","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/52E0004F-8D19-4D3D-9D0C-1EE48E40F897/view-source"}],"url":"https://biology.stackexchange.com/questions/114135/does-inoculum-volume-affect-spread-plate-outcome"},{"author":"MikeyC","author_url":"https://biology.stackexchange.com/users/56688/mikeyc","content_license":"CC BY-SA 4.0","context_id":"114160","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":"2024-02-23T16:11:23+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"B77FB29F-27E3-4342-B269-03C1BA052F9A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B77FB29F-27E3-4342-B269-03C1BA052F9A/view-source"},{"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":"2024-02-23T18:57:57+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"D0AA6BF4-982B-4B80-BA12-DAA30B697C12","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D0AA6BF4-982B-4B80-BA12-DAA30B697C12/view-source"}],"url":"https://biology.stackexchange.com/a/114160"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"114171","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":"2024-02-25T19:55:26+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"203CF5D0-CE50-40F6-9053-72EFC53BC9E3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/203CF5D0-CE50-40F6-9053-72EFC53BC9E3/view-source"}],"url":"https://biology.stackexchange.com/a/114171"}],"contexts":[{"context_id":"question","html":"<h2>Background</h2>\n<p>The <strong>spread plate</strong> method is a technique used in microbiology to enumerate and isolate bacteria or other microorganisms present in a sample. It involves evenly spreading a liquid sample containing microorganisms onto the surface of a solid agar medium in a Petri dish.</p>\n<p><strong>Inoculum Density</strong>: Inoculum density refers to the concentration or density of microorganisms (bacteria, fungi, etc.) present in the sample that is being plated onto the agar surface. It is typically measured as the number of colony-forming units (CFUs) per unit volume of the sample.</p>\n<p><strong>Inoculum Volume</strong>: Inoculum volume refers to the volume of the sample that is spread or plated onto the surface of the agar medium during the spread plate method. It is typically measured in microliters (µL) or milliliters (mL).</p>\n<h2>Question</h2>\n<p>Does inoculum volume affect spread plate outcome?\nIf I pipetted 0.1ml 0.5 McFarland of bacteria into the agar plate before spreading, would it differ from pipetting 0.5ml of the same density?</p>\n","text":"Background\n\n\n\n\nThe spread plate method is a technique used in microbiology to enumerate and isolate bacteria or other microorganisms present in a sample. It involves evenly spreading a liquid sample containing microorganisms onto the surface of a solid agar medium in a Petri dish.\n\n\n\n\nInoculum Density: Inoculum density refers to the concentration or density of microorganisms (bacteria, fungi, etc.) present in the sample that is being plated onto the agar surface. It is typically measured as the number of colony-forming units (CFUs) per unit volume of the sample.\n\n\n\n\nInoculum Volume: Inoculum volume refers to the volume of the sample that is spread or plated onto the surface of the agar medium during the spread plate method. It is typically measured in microliters (µL) or milliliters (mL).\n\n\n\n\nQuestion\n\n\n\n\nDoes inoculum volume affect spread plate outcome?\nIf I pipetted 0.1ml 0.5 McFarland of bacteria into the agar plate before spreading, would it differ from pipetting 0.5ml of the same density?"},{"context_id":"114160","html":"<p>Theoretically, for CFU determination the volume of the inoculum shouldn't matter as long as you plate a dilution series and find the plate with a countable number of colonies. It also shouldn't matter if you use the spread-plate method or the pour plate method or something else (like drop plates or spiral plates). But all of that assumes ideal conditions where you are able to get a perfect and uniform spread over the whole plate every time. In the real world there are practical limitations on the range of usable inoculum volumes when spreading liquid onto agar plates.</p>\n<p>When making spread plates it's best to maintain continuous spreading motion until all (or almost all) of the liquid from the inoculum has been absorbed by the agar medium. If you don't, you can end up with unevenly distributed colonies, which can make otherwise countable dilutions difficult or impossible to count accurately. If the volume is too large, it may take an impractical amount of time for the liquid to absorb. On the flip side, the volume still needs to be large enough to cover the whole plate evenly. If it's too small (say 10µL) you may have trouble spreading it evenly across the entire surface.</p>\n<p>There's also some potential for variation in consistency when dispensing different volumes. Most micropipettes are slightly more accurate at the high end of their range than the low end. So, IF you were using the same p1000 pipette, your replicates could be slightly more consistent with larger volumes than small ones. But, properly calibrated, the dispensed volume should vary by less than 10% even at the lowest setting of most pipettes, and if this were a concern, it could be remedied by switching to a more appropriately sized pipette.</p>\n<p>Lastly, if you are trying to make a bacterial lawn, for something like a Kirby-Bauer test, changing the inoculum volume can affect the outcome of the test. McFarland standards aren't always perfectly calibrated for every organism, but overloading the plate with 5x the standard inoculum certainly has the potential of skewing the test results. The methods for these tests are standardized to improve repeatability between labs. Essentially, a denser inoculum will reduce the size of the inhibition zone, while a reduced inoculum will increase the inhibition zone. Since the inhibition zone determines whether a particular isolate is classified as resistant or susceptible to a given drug, inoculation protocols are standardized to make sure patients receive the appropriate care.</p>\n<p>Source: <a href=\"https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Disk_test_documents/2021_manuals/Manual_v_9.0_EUCAST_Disk_Test_2021.pdf\" rel=\"nofollow noreferrer\">EUCAST Disk Diffusion Method for Antimicrobial Susceptibility Testing  - Version 9.0 (January 2021)</a></p>\n","text":"Theoretically, for CFU determination the volume of the inoculum shouldn't matter as long as you plate a dilution series and find the plate with a countable number of colonies. It also shouldn't matter if you use the spread-plate method or the pour plate method or something else (like drop plates or spiral plates). But all of that assumes ideal conditions where you are able to get a perfect and uniform spread over the whole plate every time. In the real world there are practical limitations on the range of usable inoculum volumes when spreading liquid onto agar plates.\n\n\n\n\nWhen making spread plates it's best to maintain continuous spreading motion until all (or almost all) of the liquid from the inoculum has been absorbed by the agar medium. If you don't, you can end up with unevenly distributed colonies, which can make otherwise countable dilutions difficult or impossible to count accurately. If the volume is too large, it may take an impractical amount of time for the liquid to absorb. On the flip side, the volume still needs to be large enough to cover the whole plate evenly. If it's too small (say 10µL) you may have trouble spreading it evenly across the entire surface.\n\n\n\n\nThere's also some potential for variation in consistency when dispensing different volumes. Most micropipettes are slightly more accurate at the high end of their range than the low end. So, IF you were using the same p1000 pipette, your replicates could be slightly more consistent with larger volumes than small ones. But, properly calibrated, the dispensed volume should vary by less than 10% even at the lowest setting of most pipettes, and if this were a concern, it could be remedied by switching to a more appropriately sized pipette.\n\n\n\n\nLastly, if you are trying to make a bacterial lawn, for something like a Kirby-Bauer test, changing the inoculum volume can affect the outcome of the test. McFarland standards aren't always perfectly calibrated for every organism, but overloading the plate with 5x the standard inoculum certainly has the potential of skewing the test results. The methods for these tests are standardized to improve repeatability between labs. Essentially, a denser inoculum will reduce the size of the inhibition zone, while a reduced inoculum will increase the inhibition zone. Since the inhibition zone determines whether a particular isolate is classified as resistant or susceptible to a given drug, inoculation protocols are standardized to make sure patients receive the appropriate care.\n\n\n\n\nSource: EUCAST Disk Diffusion Method for Antimicrobial Susceptibility Testing  - Version 9.0 (January 2021) (https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Disk_test_documents/2021_manuals/Manual_v_9.0_EUCAST_Disk_Test_2021.pdf)"},{"context_id":"114171","html":"<p>To add to the answer by @MikeyC . The spread plate technique for calculation of colony forming units has volume plated as a variable:</p>\n<p>CFU/ml = (number of colonies x dilution factor) / volume of culture plated</p>\n<p>This means that you account for the volume in the calculation performed after doing your counting.</p>\n<p>Of course, as MikeyC mentioned, the volume matters to some extent as if you add too much of too high a density suspension, then you will have an uncountable plate. To compensate for this, what is usually done is a dilution series, where you choose which dilution is used for the calculation This also provides a secondary check on your count, as a plate below (lower dilution) the countable dilution should be TMTC and the one above should have approximately 1/(dilution factor) fewer colonies. For example, in a 10-fold dilution factor series, your countable plate might have 50 colonies, the one below should have ~500 (TMTC) and the one above should have about 5.</p>\n<p>You should also note that the dilution factor is also compensated for in the equation.</p>\n","text":"To add to the answer by @MikeyC . The spread plate technique for calculation of colony forming units has volume plated as a variable:\n\n\n\n\nCFU/ml = (number of colonies x dilution factor) / volume of culture plated\n\n\n\n\nThis means that you account for the volume in the calculation performed after doing your counting.\n\n\n\n\nOf course, as MikeyC mentioned, the volume matters to some extent as if you add too much of too high a density suspension, then you will have an uncountable plate. To compensate for this, what is usually done is a dilution series, where you choose which dilution is used for the calculation This also provides a secondary check on your count, as a plate below (lower dilution) the countable dilution should be TMTC and the one above should have approximately 1/(dilution factor) fewer colonies. For example, in a 10-fold dilution factor series, your countable plate might have 50 colonies, the one below should have ~500 (TMTC) and the one above should have about 5.\n\n\n\n\nYou should also note that the dilution factor is also compensated for in the equation."}],"domain":"biology","external_citations":["https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Disk_test_documents/2021_manuals/Manual_v_9.0_EUCAST_Disk_Test_2021.pdf"],"ground_truth_type":"metadata_grounded","group_id":"0454eea2f48a874f2e79bf52f71d88987abb402e1079f0c03bbd988f09aeffa4","hard_case_family":["multiple_answer_candidates"],"id":"RHM-d6000f58b13b03c1eb0222c2","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":"Freezing Soul","profile_url":"https://biology.stackexchange.com/users/71062/freezing-soul","user_type":"registered"},"created_at":"2024-02-20T20:25:24+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"52E0004F-8D19-4D3D-9D0C-1EE48E40F897","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/52E0004F-8D19-4D3D-9D0C-1EE48E40F897/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":"114135","source_record_sha256":"4c47e98fb768d760c672534d4bc532ca724cb328ee49e1bb5a00ccdda2524690","source_url":"https://biology.stackexchange.com/questions/114135/does-inoculum-volume-affect-spread-plate-outcome","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Does inoculum volume affect spread plate outcome?\nBackground\n\n\n\n\nThe spread plate method is a technique used in microbiology to enumerate and isolate bacteria or other microorganisms present in a sample. It involves evenly spreading a liquid sample containing microorganisms onto the surface of a solid agar medium in a Petri dish.\n\n\n\n\nInoculum Density: Inoculum density refers to the concentration or density of microorganisms (bacteria, fungi, etc.) present in the sample that is being plated onto the agar surface. It is typically measured as the number of colony-forming units (CFUs) per unit volume of the sample.\n\n\n\n\nInoculum Volume: Inoculum volume refers to the volume of the sample that is spread or plated onto the surface of the agar medium during the spread plate method. It is typically measured in microliters (µL) or milliliters (mL).\n\n\n\n\nQuestion\n\n\n\n\nDoes inoculum volume affect spread plate outcome?\nIf I pipetted 0.1ml 0.5 McFarland of bacteria into the agar plate before spreading, would it differ from pipetting 0.5ml of the same density?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114160,"score":3},{"answer_id":114171,"score":0}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Check your assumptions.</p>\n<p>It looks like you're using a formula that assumes linear, additive variance. Your data suggest a system that does not follow these assumptions, so the equations are not valid for the situation you describe.</p>\n<p>See also <a href=\"https://en.m.wikipedia.org/wiki/All_models_are_wrong\" rel=\"nofollow noreferrer\">https://en.m.wikipedia.org/wiki/All_models_are_wrong</a> - much of the difficulty in applying simple mathematical formulae to real world data is in deciding/recognizing when your model is sufficiently wrong that it's no longer useful.</p>\n","answer_id":114208,"answer_text":"Check your assumptions.\n\n\n\n\nIt looks like you're using a formula that assumes linear, additive variance. Your data suggest a system that does not follow these assumptions, so the equations are not valid for the situation you describe.\n\n\n\n\nSee also https://en.m.wikipedia.org/wiki/All_models_are_wrong (https://en.m.wikipedia.org/wiki/All_models_are_wrong) - much of the difficulty in applying simple mathematical formulae to real world data is in deciding/recognizing when your model is sufficiently wrong that it's no longer useful.","answer_url":"https://biology.stackexchange.com/a/114208","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2024-02-29T04:29:34+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":114207,"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":"2024-02-29T04:29:34+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"F56112DE-B89E-4603-A0F8-388A12ED9A46","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F56112DE-B89E-4603-A0F8-388A12ED9A46/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user438383","profile_url":"https://biology.stackexchange.com/users/27357/user438383","user_type":"registered"},"created_at":"2024-04-01T09:41:44+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"87407451-524F-4F50-91E7-9C2FDC0C1E39","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/87407451-524F-4F50-91E7-9C2FDC0C1E39/view-source"}],"score":1},{"answer_html":"<p>From <a href=\"https://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2010.02084.x\" rel=\"nofollow noreferrer\">this paper</a> discussing the pitfalls of using the breeder's equation:</p>\n<blockquote>\n<p>The breeder's equation provides a useful framework for conceptualizing the process of adaptive evolution by natural selection: selection causes phenotypic changes in a population, and genetic variation transmits these changes to future generations. This is not wrong, but given the assumptions we have discussed, it may generally be very inappropriate to apply this framework as a predictive tool in nature. There is consequently a problem with the enthusiastic way in which evolutionary biologists, ourselves included, have transferred this model from being a tool to conceptualise trait evolution and analyse artificial selection experiments (a context in which the inherent assumptions can be more readily approximated) to a predictive model in the field. Estimates of selection based on selection gradients are undoubtedly a conceptual step forward, but they do not escape reliance on the assumption that all traits and environmental factors that jointly influence studied traits and fitness have been identified, meaningfully measured and adequately modelled.</p>\n</blockquote>\n<p>So if this is indeed an artificial selection experiment and you have actually designed the experiment to control for all possible sources of e.g. environmental variation, then it may be appropriate to use the breeder's equation model. However, we don't know anything about the source of your data, so it's difficult to evaluate whether your data are from an adequately controlled e.g. common garden style experiment.</p>\n<p>Moreover:</p>\n<blockquote>\n<p>No model can be expected to provide accurate predictions if its assumptions are seriously violated. The simple approaches we discuss here for predicting evolutionary change actually make many simplifying assumptions (<strong>e.g. constant population demography, discrete generations, constant environmental conditions</strong>; Merilä et al., 2001a), and we are certainly not the first to highlight the potential for predictions to fail when when these models are applied to natural systems (Hadfield, 2008; Price et al., 1988; van Tienderen &amp; de Jong, 1994) or to call for caution in this regard.</p>\n</blockquote>\n<p>They are clearly focusing on natural populations, which I don't <em>think</em> you are. But on the off chance that your &quot;selected&quot; parental population is not selected explicitly on your height measurement, then that is probably the reason why your estimates are wonky.</p>\n<p>If you are in fact doing an artificial selection experiment, your estimates are probably wonky because some of those bolded factors were not controlled for.</p>\n<p>For example, if these are bean plants, the parental and offspring generations may have been grown in different years with different climatic conditions. Even in a laboratory environment with well controlled conditions, unless the parents and offspring are grown at literally the exact same time side by side (which presents obvious logistical challenges) with positional rotation and constant care, it can be hard to fully reject the hypothesis of some unknown environmental factor impacting your data.</p>\n","answer_id":114420,"answer_text":"From this paper (https://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2010.02084.x) discussing the pitfalls of using the breeder's equation:\n\n\n\n\n\n\n\nThe breeder's equation provides a useful framework for conceptualizing the process of adaptive evolution by natural selection: selection causes phenotypic changes in a population, and genetic variation transmits these changes to future generations. This is not wrong, but given the assumptions we have discussed, it may generally be very inappropriate to apply this framework as a predictive tool in nature. There is consequently a problem with the enthusiastic way in which evolutionary biologists, ourselves included, have transferred this model from being a tool to conceptualise trait evolution and analyse artificial selection experiments (a context in which the inherent assumptions can be more readily approximated) to a predictive model in the field. Estimates of selection based on selection gradients are undoubtedly a conceptual step forward, but they do not escape reliance on the assumption that all traits and environmental factors that jointly influence studied traits and fitness have been identified, meaningfully measured and adequately modelled.\n\n\n\n\n\n\n\nSo if this is indeed an artificial selection experiment and you have actually designed the experiment to control for all possible sources of e.g. environmental variation, then it may be appropriate to use the breeder's equation model. However, we don't know anything about the source of your data, so it's difficult to evaluate whether your data are from an adequately controlled e.g. common garden style experiment.\n\n\n\n\nMoreover:\n\n\n\n\n\n\n\nNo model can be expected to provide accurate predictions if its assumptions are seriously violated. The simple approaches we discuss here for predicting evolutionary change actually make many simplifying assumptions (e.g. constant population demography, discrete generations, constant environmental conditions; Merilä et al., 2001a), and we are certainly not the first to highlight the potential for predictions to fail when when these models are applied to natural systems (Hadfield, 2008; Price et al., 1988; van Tienderen & de Jong, 1994) or to call for caution in this regard.\n\n\n\n\n\n\n\nThey are clearly focusing on natural populations, which I don't think you are. But on the off chance that your \"selected\" parental population is not selected explicitly on your height measurement, then that is probably the reason why your estimates are wonky.\n\n\n\n\nIf you are in fact doing an artificial selection experiment, your estimates are probably wonky because some of those bolded factors were not controlled for.\n\n\n\n\nFor example, if these are bean plants, the parental and offspring generations may have been grown in different years with different climatic conditions. Even in a laboratory environment with well controlled conditions, unless the parents and offspring are grown at literally the exact same time side by side (which presents obvious logistical challenges) with positional rotation and constant care, it can be hard to fully reject the hypothesis of some unknown environmental factor impacting your data.","answer_url":"https://biology.stackexchange.com/a/114420","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2024-04-01T18:40:03+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 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Krause","profile_url":"https://biology.stackexchange.com/users/27148/bryan-krause","user_type":"moderator"},"created_at":"2024-02-29T04:29:34+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"F56112DE-B89E-4603-A0F8-388A12ED9A46","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F56112DE-B89E-4603-A0F8-388A12ED9A46/view-source"},{"content_license":"CC BY-SA 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Press","profile_url":"https://biology.stackexchange.com/users/22392/maximilian-press","user_type":"registered"},"created_at":"2024-04-01T18:40:03+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"6FCA9402-4994-4682-A01B-EF960A0D14BF","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/6FCA9402-4994-4682-A01B-EF960A0D14BF/view-source"}],"url":"https://biology.stackexchange.com/a/114420"}],"contexts":[{"context_id":"question","html":"<p>Here is my data:</p>\n<p>Mean height score of the total parental population: 5.2</p>\n<p>Mean height score of selected parents (those chosen for breeding due to their higher height): 6.4</p>\n<p>Mean height score of the offspring (resulting from the selected parents): 7.8</p>\n<p>Selection differential (S) for height:\nS = Mean height score of selected parents - Mean height score of the total parental population\nS = 6.4 - 5.2 = 1.2</p>\n<p>Response to selection (R):\nR = 7.8 - 5.2 = 2.6</p>\n<p>h^2 = R / S</p>\n<p>h^2 = 2.6 / 1.2 = 2.167</p>\n<p>I confirmed that the data are not wrong. What is the interpretation of this h^2 value?</p>\n<p>I am looking for explanations for why h^2 would be above one.</p>\n","text":"Here is my data:\n\n\n\n\nMean height score of the total parental population: 5.2\n\n\n\n\nMean height score of selected parents (those chosen for breeding due to their higher height): 6.4\n\n\n\n\nMean height score of the offspring (resulting from the selected parents): 7.8\n\n\n\n\nSelection differential (S) for height:\nS = Mean height score of selected parents - Mean height score of the total parental population\nS = 6.4 - 5.2 = 1.2\n\n\n\n\nResponse to selection (R):\nR = 7.8 - 5.2 = 2.6\n\n\n\n\nh^2 = R / S\n\n\n\n\nh^2 = 2.6 / 1.2 = 2.167\n\n\n\n\nI confirmed that the data are not wrong. What is the interpretation of this h^2 value?\n\n\n\n\nI am looking for explanations for why h^2 would be above one."},{"context_id":"114208","html":"<p>Check your assumptions.</p>\n<p>It looks like you're using a formula that assumes linear, additive variance. Your data suggest a system that does not follow these assumptions, so the equations are not valid for the situation you describe.</p>\n<p>See also <a href=\"https://en.m.wikipedia.org/wiki/All_models_are_wrong\" rel=\"nofollow noreferrer\">https://en.m.wikipedia.org/wiki/All_models_are_wrong</a> - much of the difficulty in applying simple mathematical formulae to real world data is in deciding/recognizing when your model is sufficiently wrong that it's no longer useful.</p>\n","text":"Check your assumptions.\n\n\n\n\nIt looks like you're using a formula that assumes linear, additive variance. Your data suggest a system that does not follow these assumptions, so the equations are not valid for the situation you describe.\n\n\n\n\nSee also https://en.m.wikipedia.org/wiki/All_models_are_wrong (https://en.m.wikipedia.org/wiki/All_models_are_wrong) - much of the difficulty in applying simple mathematical formulae to real world data is in deciding/recognizing when your model is sufficiently wrong that it's no longer useful."},{"context_id":"114420","html":"<p>From <a href=\"https://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2010.02084.x\" rel=\"nofollow noreferrer\">this paper</a> discussing the pitfalls of using the breeder's equation:</p>\n<blockquote>\n<p>The breeder's equation provides a useful framework for conceptualizing the process of adaptive evolution by natural selection: selection causes phenotypic changes in a population, and genetic variation transmits these changes to future generations. This is not wrong, but given the assumptions we have discussed, it may generally be very inappropriate to apply this framework as a predictive tool in nature. There is consequently a problem with the enthusiastic way in which evolutionary biologists, ourselves included, have transferred this model from being a tool to conceptualise trait evolution and analyse artificial selection experiments (a context in which the inherent assumptions can be more readily approximated) to a predictive model in the field. Estimates of selection based on selection gradients are undoubtedly a conceptual step forward, but they do not escape reliance on the assumption that all traits and environmental factors that jointly influence studied traits and fitness have been identified, meaningfully measured and adequately modelled.</p>\n</blockquote>\n<p>So if this is indeed an artificial selection experiment and you have actually designed the experiment to control for all possible sources of e.g. environmental variation, then it may be appropriate to use the breeder's equation model. However, we don't know anything about the source of your data, so it's difficult to evaluate whether your data are from an adequately controlled e.g. common garden style experiment.</p>\n<p>Moreover:</p>\n<blockquote>\n<p>No model can be expected to provide accurate predictions if its assumptions are seriously violated. The simple approaches we discuss here for predicting evolutionary change actually make many simplifying assumptions (<strong>e.g. constant population demography, discrete generations, constant environmental conditions</strong>; Merilä et al., 2001a), and we are certainly not the first to highlight the potential for predictions to fail when when these models are applied to natural systems (Hadfield, 2008; Price et al., 1988; van Tienderen &amp; de Jong, 1994) or to call for caution in this regard.</p>\n</blockquote>\n<p>They are clearly focusing on natural populations, which I don't <em>think</em> you are. But on the off chance that your &quot;selected&quot; parental population is not selected explicitly on your height measurement, then that is probably the reason why your estimates are wonky.</p>\n<p>If you are in fact doing an artificial selection experiment, your estimates are probably wonky because some of those bolded factors were not controlled for.</p>\n<p>For example, if these are bean plants, the parental and offspring generations may have been grown in different years with different climatic conditions. Even in a laboratory environment with well controlled conditions, unless the parents and offspring are grown at literally the exact same time side by side (which presents obvious logistical challenges) with positional rotation and constant care, it can be hard to fully reject the hypothesis of some unknown environmental factor impacting your data.</p>\n","text":"From this paper (https://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2010.02084.x) discussing the pitfalls of using the breeder's equation:\n\n\n\n\n\n\n\nThe breeder's equation provides a useful framework for conceptualizing the process of adaptive evolution by natural selection: selection causes phenotypic changes in a population, and genetic variation transmits these changes to future generations. This is not wrong, but given the assumptions we have discussed, it may generally be very inappropriate to apply this framework as a predictive tool in nature. There is consequently a problem with the enthusiastic way in which evolutionary biologists, ourselves included, have transferred this model from being a tool to conceptualise trait evolution and analyse artificial selection experiments (a context in which the inherent assumptions can be more readily approximated) to a predictive model in the field. Estimates of selection based on selection gradients are undoubtedly a conceptual step forward, but they do not escape reliance on the assumption that all traits and environmental factors that jointly influence studied traits and fitness have been identified, meaningfully measured and adequately modelled.\n\n\n\n\n\n\n\nSo if this is indeed an artificial selection experiment and you have actually designed the experiment to control for all possible sources of e.g. environmental variation, then it may be appropriate to use the breeder's equation model. However, we don't know anything about the source of your data, so it's difficult to evaluate whether your data are from an adequately controlled e.g. common garden style experiment.\n\n\n\n\nMoreover:\n\n\n\n\n\n\n\nNo model can be expected to provide accurate predictions if its assumptions are seriously violated. The simple approaches we discuss here for predicting evolutionary change actually make many simplifying assumptions (e.g. constant population demography, discrete generations, constant environmental conditions; Merilä et al., 2001a), and we are certainly not the first to highlight the potential for predictions to fail when when these models are applied to natural systems (Hadfield, 2008; Price et al., 1988; van Tienderen & de Jong, 1994) or to call for caution in this regard.\n\n\n\n\n\n\n\nThey are clearly focusing on natural populations, which I don't think you are. But on the off chance that your \"selected\" parental population is not selected explicitly on your height measurement, then that is probably the reason why your estimates are wonky.\n\n\n\n\nIf you are in fact doing an artificial selection experiment, your estimates are probably wonky because some of those bolded factors were not controlled for.\n\n\n\n\nFor example, if these are bean plants, the parental and offspring generations may have been grown in different years with different climatic conditions. Even in a laboratory environment with well controlled conditions, unless the parents and offspring are grown at literally the exact same time side by side (which presents obvious logistical challenges) with positional rotation and constant care, it can be hard to fully reject the hypothesis of some unknown environmental factor impacting your data."}],"domain":"biology","external_citations":["https://en.m.wikipedia.org/wiki/All_models_are_wrong","https://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2010.02084.x"],"ground_truth_type":"metadata_grounded","group_id":"559b641fc26c0da1f94a9dfc5d01a1266a78276bb0e8025d7973bbcce7b5ccd7","hard_case_family":["no_accepted_answer","multiple_sources","multiple_answer_candidates"],"id":"RHM-3001d476ab22bcad10b84b02","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":"2024-02-29T03:22:02+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"74F74F3B-968B-409B-B758-97AB1EA345FD","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/74F74F3B-968B-409B-B758-97AB1EA345FD/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":"2024-02-29T03:36:09+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"A4B13087-186F-45EC-A427-DB662578DFE4","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A4B13087-186F-45EC-A427-DB662578DFE4/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":"2024-02-29T05:58:53+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"D447808C-D7D4-4241-B7C2-A11211A08284","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D447808C-D7D4-4241-B7C2-A11211A08284/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2024-03-30T06:01:20+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"4D22225F-33D8-4050-B18C-2EF52C62B49C","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/4D22225F-33D8-4050-B18C-2EF52C62B49C/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":"2024-04-01T18:13:32+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"9642B35B-D8E9-4203-AA2F-11D0813C78C9","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9642B35B-D8E9-4203-AA2F-11D0813C78C9/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":"114207","source_record_sha256":"5a695f2caf409d9ca23a51325b35c826cb9485b395cc76cf51c6309f01dd62c5","source_url":"https://biology.stackexchange.com/questions/114207/interpretation-of-narrow-sense-heritability-over-one-using-r-s-h2","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Interpretation of narrow-sense heritability over one (using R/S = h^2)\nHere is my data:\n\n\n\n\nMean height score of the total parental population: 5.2\n\n\n\n\nMean height score of selected parents (those chosen for breeding due to their higher height): 6.4\n\n\n\n\nMean height score of the offspring (resulting from the selected parents): 7.8\n\n\n\n\nSelection differential (S) for height:\nS = Mean height score of selected parents - Mean height score of the total parental population\nS = 6.4 - 5.2 = 1.2\n\n\n\n\nResponse to selection (R):\nR = 7.8 - 5.2 = 2.6\n\n\n\n\nh^2 = R / S\n\n\n\n\nh^2 = 2.6 / 1.2 = 2.167\n\n\n\n\nI confirmed that the data are not wrong. What is the interpretation of this h^2 value?\n\n\n\n\nI am looking for explanations for why h^2 would be above one.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114208,"score":1},{"answer_id":114420,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":114214,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Forming a <a href=\"https://dictionary.cambridge.org/dictionary/english/pool\" rel=\"nofollow noreferrer\">pool</a> (second definition in link); forming a small amount of liquid on a surface. <em>A la</em> &quot;<em>I knocked my cup over and the coffee formed a small pool on my bench</em>&quot;</p>\n<p>Basically this results in a concentration of the organisms in one area, rather than an evenly distributed spread.</p>\n","answer_id":114214,"answer_text":"Forming a pool (https://dictionary.cambridge.org/dictionary/english/pool) (second definition in link); forming a small amount of liquid on a surface. A la \"I knocked my cup over and the coffee formed a small pool on my bench\"\n\n\n\n\nBasically this results in a concentration of the organisms in one area, rather than an evenly distributed spread.","answer_url":"https://biology.stackexchange.com/a/114214","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2024-02-29T20:28:50+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":114213,"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":"2024-02-29T20:28:50+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"58BB3358-C320-4407-9DDE-823AA7636AE6","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/58BB3358-C320-4407-9DDE-823AA7636AE6/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":"2024-02-29T20:10:18+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"9D4E8FC4-1B76-45DC-9C3C-CA102AE25535","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9D4E8FC4-1B76-45DC-9C3C-CA102AE25535/view-source"}],"url":"https://biology.stackexchange.com/questions/114213/whats-pooling-in-the-spread-plate-technique"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"114214","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":"2024-02-29T20:28:50+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"58BB3358-C320-4407-9DDE-823AA7636AE6","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/58BB3358-C320-4407-9DDE-823AA7636AE6/view-source"}],"url":"https://biology.stackexchange.com/a/114214"}],"contexts":[{"context_id":"question","html":"<p>&quot;Distributing the organisms by rotating the spreader rather than the plate tends to cause more pooling of the inoculum.&quot;\n<a href=\"https://asm.org/ASM/media/Protocol-Images/Preparing-Spread-Plates-Protocols.pdf?ext=.pdf\" rel=\"nofollow noreferrer\">https://asm.org/ASM/media/Protocol-Images/Preparing-Spread-Plates-Protocols.pdf?ext=.pdf</a></p>\n","text":"\"Distributing the organisms by rotating the spreader rather than the plate tends to cause more pooling of the inoculum.\"\nhttps://asm.org/ASM/media/Protocol-Images/Preparing-Spread-Plates-Protocols.pdf?ext=.pdf (https://asm.org/ASM/media/Protocol-Images/Preparing-Spread-Plates-Protocols.pdf?ext=.pdf)"},{"context_id":"114214","html":"<p>Forming a <a href=\"https://dictionary.cambridge.org/dictionary/english/pool\" rel=\"nofollow noreferrer\">pool</a> (second definition in link); forming a small amount of liquid on a surface. <em>A la</em> &quot;<em>I knocked my cup over and the coffee formed a small pool on my bench</em>&quot;</p>\n<p>Basically this results in a concentration of the organisms in one area, rather than an evenly distributed spread.</p>\n","text":"Forming a pool (https://dictionary.cambridge.org/dictionary/english/pool) (second definition in link); forming a small amount of liquid on a surface. A la \"I knocked my cup over and the coffee formed a small pool on my bench\"\n\n\n\n\nBasically this results in a concentration of the organisms in one area, rather than an evenly distributed spread."}],"domain":"biology","external_citations":["https://asm.org/ASM/media/Protocol-Images/Preparing-Spread-Plates-Protocols.pdf?ext=.pdf","https://dictionary.cambridge.org/dictionary/english/pool"],"ground_truth_type":"metadata_grounded","group_id":"4ea741b1e5a705c07793a6b62bde42a29834d00b934733d28848e097663d1fda","hard_case_family":["multiple_sources"],"id":"RHM-b7a1a8999b628bd6197f9257","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":"Freezing Soul","profile_url":"https://biology.stackexchange.com/users/71062/freezing-soul","user_type":"registered"},"created_at":"2024-02-29T20:10:18+00:00","raw_file":"raw/codex_api_v1/20c6382e006dfc70ceae89b5b384391a51cd420854d2e23edb6c44d00de6688e_1790824066738015300_0.json","raw_sha256":"4baa513e3d4757eb58cf2dd23c824e0e27e58aa0c4e8ec570c22801fd30dcaa7","revision_guid":"9D4E8FC4-1B76-45DC-9C3C-CA102AE25535","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9D4E8FC4-1B76-45DC-9C3C-CA102AE25535/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":"114213","source_record_sha256":"26b64bdf321bee54ca9ab1fd2e6c9896fcf5b476491f3e4e220e7d02ba1c0400","source_url":"https://biology.stackexchange.com/questions/114213/whats-pooling-in-the-spread-plate-technique","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What's pooling in the spread plate technique?\n\"Distributing the organisms by rotating the spreader rather than the plate tends to cause more pooling of the inoculum.\"\nhttps://asm.org/ASM/media/Protocol-Images/Preparing-Spread-Plates-Protocols.pdf?ext=.pdf (https://asm.org/ASM/media/Protocol-Images/Preparing-Spread-Plates-Protocols.pdf?ext=.pdf)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114214,"score":2}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Phylogenies are an attempt to answer precisely the question of what things are most similar, where &quot;similar&quot; can mean one of a number of things. In statistical terms, <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6705769/\" rel=\"nofollow noreferrer\">a phylogeny is a hierarchical clustering of available organisms</a> based on some similarity criterion. This attempts to make use of second-order information to make guesses about closest relatives based on more than just pairwise similarity; pairwise similarity can give you incorrect answers due to <a href=\"https://en.wikipedia.org/wiki/Convergent_evolution\" rel=\"nofollow noreferrer\">convergent evolution / homoplasy</a>.</p>\n<p>A phylogeny based on mitochondrial DNA only will differ from a phylogeny based on full proteome sequences, will differ from a phylogeny based on morphological characters, and so on and so forth. These are all different measures of similarity with advantages and disadvantages. We can further pass these data through one or more <a href=\"https://en.wikipedia.org/wiki/Models_of_DNA_evolution\" rel=\"nofollow noreferrer\"><em>models</em> of how the data in question might evolve</a> through the tree. These might include the maximum parsimony model based on Jukes-Cantor distance, maximum likelihood based on the F84 model, or something else.</p>\n<p><strong>I believe that the specific measurement that you would be most interested in is the <a href=\"https://www.ebi.ac.uk/training/online/courses/introduction-to-phylogenetics/what-is-a-phylogeny/aspects-of-phylogenies/branches/\" rel=\"nofollow noreferrer\">branch length</a>.</strong> Branches in phylogenetic cladograms are calibrated to show evolutionary distances according to the evolutionary model fit to the available data.</p>\n<p>If you are interested in the nearest relative, you may therefore simply measure the length of the branches differentiating any two tips of the tree. Whatever path is shortest from a tip (organism) <span class=\"math-container\">$A$</span> to any other tip will be the nearest relative of tip <span class=\"math-container\">$A$</span>.</p>\n<p>This provides an unambiguous method of identifying a closest relative in a tree. Of course, it does not account for organisms that may be missing from the tree that you consider!</p>\n<p>For a clearer guide on reading phylogenetic cladograms, I would suggest <a href=\"https://artic.network/how-to-read-a-tree.html\" rel=\"nofollow noreferrer\">this resource</a>.</p>\n","answer_id":114296,"answer_text":"Phylogenies are an attempt to answer precisely the question of what things are most similar, where \"similar\" can mean one of a number of things. In statistical terms, a phylogeny is a hierarchical clustering of available organisms (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6705769/) based on some similarity criterion. This attempts to make use of second-order information to make guesses about closest relatives based on more than just pairwise similarity; pairwise similarity can give you incorrect answers due to convergent evolution / homoplasy (https://en.wikipedia.org/wiki/Convergent_evolution).\n\n\n\n\nA phylogeny based on mitochondrial DNA only will differ from a phylogeny based on full proteome sequences, will differ from a phylogeny based on morphological characters, and so on and so forth. These are all different measures of similarity with advantages and disadvantages. We can further pass these data through one or more models of how the data in question might evolve (https://en.wikipedia.org/wiki/Models_of_DNA_evolution) through the tree. These might include the maximum parsimony model based on Jukes-Cantor distance, maximum likelihood based on the F84 model, or something else.\n\n\n\n\nI believe that the specific measurement that you would be most interested in is the branch length (https://www.ebi.ac.uk/training/online/courses/introduction-to-phylogenetics/what-is-a-phylogeny/aspects-of-phylogenies/branches/). Branches in phylogenetic cladograms are calibrated to show evolutionary distances according to the evolutionary model fit to the available data.\n\n\n\n\nIf you are interested in the nearest relative, you may therefore simply measure the length of the branches differentiating any two tips of the tree. Whatever path is shortest from a tip (organism) $A$ to any other tip will be the nearest relative of tip $A$.\n\n\n\n\nThis provides an unambiguous method of identifying a closest relative in a tree. Of course, it does not account for organisms that may be missing from the tree that you consider!\n\n\n\n\nFor a clearer guide on reading phylogenetic cladograms, I would suggest this resource (https://artic.network/how-to-read-a-tree.html).","answer_url":"https://biology.stackexchange.com/a/114296","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2024-03-11T19:26:47+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":114295,"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":"2024-03-11T19:26:47+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"3731C1CB-738E-40EC-B4D8-8CC06CBD44C6","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3731C1CB-738E-40EC-B4D8-8CC06CBD44C6/view-source"}],"score":2},{"answer_html":"<p>The common scientific figure of speech is <em>&quot;The closest living relative&quot;</em>, because the species are like a puzzling family tree, a phylogenetic tree. We can also theorize about a well documented fossil as &quot;<em>the closest known relative</em>&quot;.</p>\n<p>We can also use close relatives in a plural and general sense:</p>\n<p>The closest living relatives of hyenas are mongooses and civets.</p>\n<p>The red panda is most closely related to skunks and raccoons.</p>\n<p>Armadillos are most closely related to sloths and anteaters.</p>\n<p>It's an interesting and practical way to reason about the tree of life. It is best measured with genetic similarity.</p>\n<p>Some species have mysterious ancestry, sea cows, red pandas, hyenas, and so it's useful and interesting to know what family of species they belong to.</p>\n<p>The notion of relatedness can be referred to as <a href=\"https://en.wikipedia.org/wiki/Genetic_distance\" rel=\"nofollow noreferrer\">genetic distance</a>. To research biology trees on the web it's usually best to search images i.e. &quot;amphibian phylogeny&quot;</p>\n<p>This notion indicates the evolutionary relationship and genetic similarity between organisms, highlighting their proximity on the evolutionary tree.</p>\n","answer_id":114297,"answer_text":"The common scientific figure of speech is \"The closest living relative\", because the species are like a puzzling family tree, a phylogenetic tree. We can also theorize about a well documented fossil as \"the closest known relative\".\n\n\n\n\nWe can also use close relatives in a plural and general sense:\n\n\n\n\nThe closest living relatives of hyenas are mongooses and civets.\n\n\n\n\nThe red panda is most closely related to skunks and raccoons.\n\n\n\n\nArmadillos are most closely related to sloths and anteaters.\n\n\n\n\nIt's an interesting and practical way to reason about the tree of life. It is best measured with genetic similarity.\n\n\n\n\nSome species have mysterious ancestry, sea cows, red pandas, hyenas, and so it's useful and interesting to know what family of species they belong to.\n\n\n\n\nThe notion of relatedness can be referred to as genetic distance (https://en.wikipedia.org/wiki/Genetic_distance). To research biology trees on the web it's usually best to search images i.e. \"amphibian phylogeny\"\n\n\n\n\nThis notion indicates the evolutionary relationship and genetic similarity between organisms, highlighting their proximity on the evolutionary tree.","answer_url":"https://biology.stackexchange.com/a/114297","author":"bandybabboon","author_url":"https://biology.stackexchange.com/users/8952/bandybabboon","content_license":"CC BY-SA 4.0","created_at":"2024-03-11T19:46:26+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":114295,"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":"2024-03-11T19:46:26+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"356031B0-0E6F-48FE-B335-19521EB991F3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/356031B0-0E6F-48FE-B335-19521EB991F3/view-source"},{"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":"2024-03-11T19:52:14+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"BD4522DD-1970-4944-8D02-4D845FF0ECC8","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/BD4522DD-1970-4944-8D02-4D845FF0ECC8/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"toothandsticks","author_url":"https://biology.stackexchange.com/users/63124/toothandsticks","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"toothandsticks","profile_url":"https://biology.stackexchange.com/users/63124/toothandsticks","user_type":"registered"},"created_at":"2024-03-11T18:10:54+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"53B28058-5A8B-4B10-A28F-2E96B367755F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/53B28058-5A8B-4B10-A28F-2E96B367755F/view-source"}],"url":"https://biology.stackexchange.com/questions/114295/what-most-closely-related-to-means-in-phylogenetic-trees"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"114296","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":"2024-03-11T19:26:47+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"3731C1CB-738E-40EC-B4D8-8CC06CBD44C6","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3731C1CB-738E-40EC-B4D8-8CC06CBD44C6/view-source"}],"url":"https://biology.stackexchange.com/a/114296"},{"author":"bandybabboon","author_url":"https://biology.stackexchange.com/users/8952/bandybabboon","content_license":"CC BY-SA 4.0","context_id":"114297","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":"2024-03-11T19:46:26+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"356031B0-0E6F-48FE-B335-19521EB991F3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/356031B0-0E6F-48FE-B335-19521EB991F3/view-source"},{"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":"2024-03-11T19:52:14+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"BD4522DD-1970-4944-8D02-4D845FF0ECC8","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/BD4522DD-1970-4944-8D02-4D845FF0ECC8/view-source"}],"url":"https://biology.stackexchange.com/a/114297"}],"contexts":[{"context_id":"question","html":"<p>Here is a sample phylogenetic tree from a textbook publisher:</p>\n<p><a href=\"https://i.sstatic.net/jyiP3.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/jyiP3.png\" alt=\"enter image description here\" /></a></p>\n<p>We often ask questions like &quot;Which organism is most closely related to the pig, the hedgehog or the cow?&quot; I don't like these particular questions, and maybe that's because I misunderstand what &quot;most closely related&quot; means in phylogeny.</p>\n<p>I have been told and have read that the most closest relatives share the most recent common ancestor.  For my question, we would have to say the cow is the closest relative of the pig.  My gut feeling says we cannot say that is truly the case unless we have sufficient DNA evidence.  For example, what if we compare the pig and hedgehog genomes and find, say, 80% match.  We might then compare the pig and cow genomes and find, say, a 78% match.  Would this not mean that the hedgehog is more closely related to the pig than the cow is to the pig, despite the heuristics we have been handing students about reading phylogenetic trees?</p>\n<p>Here is an extreme example to make my case:  Is the oldest species of archaea more closely related to humans or to the species of bacteria which most recently preceded the archaea?  If we use the &quot;most recent common ancestor&quot; answer, we must say the archaea is more closely related to the human, but I would find its temporal proximity (and thus likely % of shared DNA) to the bacterium to be a much more convincing argument for relatedness.</p>\n<p><strong>Question:</strong>  How should we interpret and approach these sorts of questions, or are they bad questions due to their lack of context?</p>\n","text":"Here is a sample phylogenetic tree from a textbook publisher:\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/jyiP3.png] (https://i.sstatic.net/jyiP3.png)\n\n\n\n\nWe often ask questions like \"Which organism is most closely related to the pig, the hedgehog or the cow?\" I don't like these particular questions, and maybe that's because I misunderstand what \"most closely related\" means in phylogeny.\n\n\n\n\nI have been told and have read that the most closest relatives share the most recent common ancestor.  For my question, we would have to say the cow is the closest relative of the pig.  My gut feeling says we cannot say that is truly the case unless we have sufficient DNA evidence.  For example, what if we compare the pig and hedgehog genomes and find, say, 80% match.  We might then compare the pig and cow genomes and find, say, a 78% match.  Would this not mean that the hedgehog is more closely related to the pig than the cow is to the pig, despite the heuristics we have been handing students about reading phylogenetic trees?\n\n\n\n\nHere is an extreme example to make my case:  Is the oldest species of archaea more closely related to humans or to the species of bacteria which most recently preceded the archaea?  If we use the \"most recent common ancestor\" answer, we must say the archaea is more closely related to the human, but I would find its temporal proximity (and thus likely % of shared DNA) to the bacterium to be a much more convincing argument for relatedness.\n\n\n\n\nQuestion:  How should we interpret and approach these sorts of questions, or are they bad questions due to their lack of context?"},{"context_id":"114296","html":"<p>Phylogenies are an attempt to answer precisely the question of what things are most similar, where &quot;similar&quot; can mean one of a number of things. In statistical terms, <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6705769/\" rel=\"nofollow noreferrer\">a phylogeny is a hierarchical clustering of available organisms</a> based on some similarity criterion. This attempts to make use of second-order information to make guesses about closest relatives based on more than just pairwise similarity; pairwise similarity can give you incorrect answers due to <a href=\"https://en.wikipedia.org/wiki/Convergent_evolution\" rel=\"nofollow noreferrer\">convergent evolution / homoplasy</a>.</p>\n<p>A phylogeny based on mitochondrial DNA only will differ from a phylogeny based on full proteome sequences, will differ from a phylogeny based on morphological characters, and so on and so forth. These are all different measures of similarity with advantages and disadvantages. We can further pass these data through one or more <a href=\"https://en.wikipedia.org/wiki/Models_of_DNA_evolution\" rel=\"nofollow noreferrer\"><em>models</em> of how the data in question might evolve</a> through the tree. These might include the maximum parsimony model based on Jukes-Cantor distance, maximum likelihood based on the F84 model, or something else.</p>\n<p><strong>I believe that the specific measurement that you would be most interested in is the <a href=\"https://www.ebi.ac.uk/training/online/courses/introduction-to-phylogenetics/what-is-a-phylogeny/aspects-of-phylogenies/branches/\" rel=\"nofollow noreferrer\">branch length</a>.</strong> Branches in phylogenetic cladograms are calibrated to show evolutionary distances according to the evolutionary model fit to the available data.</p>\n<p>If you are interested in the nearest relative, you may therefore simply measure the length of the branches differentiating any two tips of the tree. Whatever path is shortest from a tip (organism) <span class=\"math-container\">$A$</span> to any other tip will be the nearest relative of tip <span class=\"math-container\">$A$</span>.</p>\n<p>This provides an unambiguous method of identifying a closest relative in a tree. Of course, it does not account for organisms that may be missing from the tree that you consider!</p>\n<p>For a clearer guide on reading phylogenetic cladograms, I would suggest <a href=\"https://artic.network/how-to-read-a-tree.html\" rel=\"nofollow noreferrer\">this resource</a>.</p>\n","text":"Phylogenies are an attempt to answer precisely the question of what things are most similar, where \"similar\" can mean one of a number of things. In statistical terms, a phylogeny is a hierarchical clustering of available organisms (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6705769/) based on some similarity criterion. This attempts to make use of second-order information to make guesses about closest relatives based on more than just pairwise similarity; pairwise similarity can give you incorrect answers due to convergent evolution / homoplasy (https://en.wikipedia.org/wiki/Convergent_evolution).\n\n\n\n\nA phylogeny based on mitochondrial DNA only will differ from a phylogeny based on full proteome sequences, will differ from a phylogeny based on morphological characters, and so on and so forth. These are all different measures of similarity with advantages and disadvantages. We can further pass these data through one or more models of how the data in question might evolve (https://en.wikipedia.org/wiki/Models_of_DNA_evolution) through the tree. These might include the maximum parsimony model based on Jukes-Cantor distance, maximum likelihood based on the F84 model, or something else.\n\n\n\n\nI believe that the specific measurement that you would be most interested in is the branch length (https://www.ebi.ac.uk/training/online/courses/introduction-to-phylogenetics/what-is-a-phylogeny/aspects-of-phylogenies/branches/). Branches in phylogenetic cladograms are calibrated to show evolutionary distances according to the evolutionary model fit to the available data.\n\n\n\n\nIf you are interested in the nearest relative, you may therefore simply measure the length of the branches differentiating any two tips of the tree. Whatever path is shortest from a tip (organism) $A$ to any other tip will be the nearest relative of tip $A$.\n\n\n\n\nThis provides an unambiguous method of identifying a closest relative in a tree. Of course, it does not account for organisms that may be missing from the tree that you consider!\n\n\n\n\nFor a clearer guide on reading phylogenetic cladograms, I would suggest this resource (https://artic.network/how-to-read-a-tree.html)."},{"context_id":"114297","html":"<p>The common scientific figure of speech is <em>&quot;The closest living relative&quot;</em>, because the species are like a puzzling family tree, a phylogenetic tree. We can also theorize about a well documented fossil as &quot;<em>the closest known relative</em>&quot;.</p>\n<p>We can also use close relatives in a plural and general sense:</p>\n<p>The closest living relatives of hyenas are mongooses and civets.</p>\n<p>The red panda is most closely related to skunks and raccoons.</p>\n<p>Armadillos are most closely related to sloths and anteaters.</p>\n<p>It's an interesting and practical way to reason about the tree of life. It is best measured with genetic similarity.</p>\n<p>Some species have mysterious ancestry, sea cows, red pandas, hyenas, and so it's useful and interesting to know what family of species they belong to.</p>\n<p>The notion of relatedness can be referred to as <a href=\"https://en.wikipedia.org/wiki/Genetic_distance\" rel=\"nofollow noreferrer\">genetic distance</a>. To research biology trees on the web it's usually best to search images i.e. &quot;amphibian phylogeny&quot;</p>\n<p>This notion indicates the evolutionary relationship and genetic similarity between organisms, highlighting their proximity on the evolutionary tree.</p>\n","text":"The common scientific figure of speech is \"The closest living relative\", because the species are like a puzzling family tree, a phylogenetic tree. We can also theorize about a well documented fossil as \"the closest known relative\".\n\n\n\n\nWe can also use close relatives in a plural and general sense:\n\n\n\n\nThe closest living relatives of hyenas are mongooses and civets.\n\n\n\n\nThe red panda is most closely related to skunks and raccoons.\n\n\n\n\nArmadillos are most closely related to sloths and anteaters.\n\n\n\n\nIt's an interesting and practical way to reason about the tree of life. It is best measured with genetic similarity.\n\n\n\n\nSome species have mysterious ancestry, sea cows, red pandas, hyenas, and so it's useful and interesting to know what family of species they belong to.\n\n\n\n\nThe notion of relatedness can be referred to as genetic distance (https://en.wikipedia.org/wiki/Genetic_distance). To research biology trees on the web it's usually best to search images i.e. \"amphibian phylogeny\"\n\n\n\n\nThis notion indicates the evolutionary relationship and genetic similarity between organisms, highlighting their proximity on the evolutionary tree."}],"domain":"biology","external_citations":["https://artic.network/how-to-read-a-tree.html","https://en.wikipedia.org/wiki/Convergent_evolution","https://en.wikipedia.org/wiki/Genetic_distance","https://en.wikipedia.org/wiki/Models_of_DNA_evolution","https://i.sstatic.net/jyiP3.png","https://www.ebi.ac.uk/training/online/courses/introduction-to-phylogenetics/what-is-a-phylogeny/aspects-of-phylogenies/branches/","https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6705769/"],"ground_truth_type":"metadata_grounded","group_id":"28c602bf4b1b3112242eaad9de02be825d10f53b028cbdfe8296747a3264b51e","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-691b825b4c6073b6327ee6c9","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":"toothandsticks","profile_url":"https://biology.stackexchange.com/users/63124/toothandsticks","user_type":"registered"},"created_at":"2024-03-11T18:10:54+00:00","raw_file":"raw/codex_api_v1/c09c25974111e465f43435e13249e671865a3c492931b0256ef7f890bfa5e2e0_1790824064569681800_0.json","raw_sha256":"0b302246b77e7a9d8782e0c9b89ad24379ff8e65cc316aa696d777ef4a6f718d","revision_guid":"53B28058-5A8B-4B10-A28F-2E96B367755F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/53B28058-5A8B-4B10-A28F-2E96B367755F/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":"114295","source_record_sha256":"ccb4904f06d9b35fd0816effd061470615c53ef21c3d3632eecc8921fc54ba91","source_url":"https://biology.stackexchange.com/questions/114295/what-most-closely-related-to-means-in-phylogenetic-trees","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What \"most closely related to\" means in phylogenetic trees?\nHere is a sample phylogenetic tree from a textbook publisher:\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/jyiP3.png] (https://i.sstatic.net/jyiP3.png)\n\n\n\n\nWe often ask questions like \"Which organism is most closely related to the pig, the hedgehog or the cow?\" I don't like these particular questions, and maybe that's because I misunderstand what \"most closely related\" means in phylogeny.\n\n\n\n\nI have been told and have read that the most closest relatives share the most recent common ancestor.  For my question, we would have to say the cow is the closest relative of the pig.  My gut feeling says we cannot say that is truly the case unless we have sufficient DNA evidence.  For example, what if we compare the pig and hedgehog genomes and find, say, 80% match.  We might then compare the pig and cow genomes and find, say, a 78% match.  Would this not mean that the hedgehog is more closely related to the pig than the cow is to the pig, despite the heuristics we have been handing students about reading phylogenetic trees?\n\n\n\n\nHere is an extreme example to make my case:  Is the oldest species of archaea more closely related to humans or to the species of bacteria which most recently preceded the archaea?  If we use the \"most recent common ancestor\" answer, we must say the archaea is more closely related to the human, but I would find its temporal proximity (and thus likely % of shared DNA) to the bacterium to be a much more convincing argument for relatedness.\n\n\n\n\nQuestion:  How should we interpret and approach these sorts of questions, or are they bad questions due to their lack of context?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114296,"score":2},{"answer_id":114297,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>In skeletal muscles, depolarization occurs via opening of voltage-gated sodium channels, leading to influx of sodium ions, and opening of potassium channels. However, in the case of cardiac muscles, during depolarization, voltage-gated sodium channels open, and influx of sodium ions leads to closure of potassium channels, which eventually leads to the long action potential and plateau phase. In cardiac muscles, co-occurrence of calcium channels also occurs.</p>\n<p>You can find more details <a href=\"https://doi.org/10.1080%2F19336950.2015.1076597\" rel=\"nofollow noreferrer\">here</a></p>\n","answer_id":114406,"answer_text":"In skeletal muscles, depolarization occurs via opening of voltage-gated sodium channels, leading to influx of sodium ions, and opening of potassium channels. However, in the case of cardiac muscles, during depolarization, voltage-gated sodium channels open, and influx of sodium ions leads to closure of potassium channels, which eventually leads to the long action potential and plateau phase. In cardiac muscles, co-occurrence of calcium channels also occurs.\n\n\n\n\nYou can find more details here (https://doi.org/10.1080%2F19336950.2015.1076597)","answer_url":"https://biology.stackexchange.com/a/114406","author":"user80416","author_url":null,"content_license":"CC BY-SA 4.0","created_at":"2024-03-30T01:37:36+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 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=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114370,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user80416","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-03-30T01:37:36+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"AEE1C46D-7A70-4AD7-9C56-6C1150EDD6B3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AEE1C46D-7A70-4AD7-9C56-6C1150EDD6B3/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user80416","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-04-04T19:52:05+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"BF313B31-58EE-4D97-B6CC-B3856E1FBBAF","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/BF313B31-58EE-4D97-B6CC-B3856E1FBBAF/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Mason Shah","author_url":"https://biology.stackexchange.com/users/79003/mason-shah","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Mason Shah","profile_url":"https://biology.stackexchange.com/users/79003/mason-shah","user_type":"registered"},"created_at":"2024-03-25T10:57:51+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"832732AB-1AE8-43AC-ADC5-5CEF8D9CAA3F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/832732AB-1AE8-43AC-ADC5-5CEF8D9CAA3F/view-source"}],"url":"https://biology.stackexchange.com/questions/114370/potassium-permeability-in-cardiac-muscle-cells"},{"author":"user80416","author_url":null,"content_license":"CC BY-SA 4.0","context_id":"114406","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user80416","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-03-30T01:37:36+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"AEE1C46D-7A70-4AD7-9C56-6C1150EDD6B3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/AEE1C46D-7A70-4AD7-9C56-6C1150EDD6B3/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user80416","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-04-04T19:52:05+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"BF313B31-58EE-4D97-B6CC-B3856E1FBBAF","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/BF313B31-58EE-4D97-B6CC-B3856E1FBBAF/view-source"}],"url":"https://biology.stackexchange.com/a/114406"}],"contexts":[{"context_id":"question","html":"<p>From my research it seems as though there's a difference between cardiac and skeletal muscle cells in that during depolarisation, the permeability of potassium actually decreases for cardiac muscle cells. How does this occur? I imagine it would be due to the closure of potassium channels but if this is the case, then how is the inwards current of calcium balanced during the plateau phase?</p>\n","text":"From my research it seems as though there's a difference between cardiac and skeletal muscle cells in that during depolarisation, the permeability of potassium actually decreases for cardiac muscle cells. How does this occur? I imagine it would be due to the closure of potassium channels but if this is the case, then how is the inwards current of calcium balanced during the plateau phase?"},{"context_id":"114406","html":"<p>In skeletal muscles, depolarization occurs via opening of voltage-gated sodium channels, leading to influx of sodium ions, and opening of potassium channels. However, in the case of cardiac muscles, during depolarization, voltage-gated sodium channels open, and influx of sodium ions leads to closure of potassium channels, which eventually leads to the long action potential and plateau phase. In cardiac muscles, co-occurrence of calcium channels also occurs.</p>\n<p>You can find more details <a href=\"https://doi.org/10.1080%2F19336950.2015.1076597\" rel=\"nofollow noreferrer\">here</a></p>\n","text":"In skeletal muscles, depolarization occurs via opening of voltage-gated sodium channels, leading to influx of sodium ions, and opening of potassium channels. However, in the case of cardiac muscles, during depolarization, voltage-gated sodium channels open, and influx of sodium ions leads to closure of potassium channels, which eventually leads to the long action potential and plateau phase. In cardiac muscles, co-occurrence of calcium channels also occurs.\n\n\n\n\nYou can find more details here (https://doi.org/10.1080%2F19336950.2015.1076597)"}],"domain":"biology","external_citations":["https://doi.org/10.1080%2F19336950.2015.1076597"],"ground_truth_type":"metadata_grounded","group_id":"5eec5763612de64dff711882ca09212ef819c04eafcb1832f10662f3e15a6a6c","hard_case_family":["no_accepted_answer"],"id":"RHM-817bf2042c75836b05a2b160","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":"Mason Shah","profile_url":"https://biology.stackexchange.com/users/79003/mason-shah","user_type":"registered"},"created_at":"2024-03-25T10:57:51+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"832732AB-1AE8-43AC-ADC5-5CEF8D9CAA3F","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/832732AB-1AE8-43AC-ADC5-5CEF8D9CAA3F/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":"114370","source_record_sha256":"07b64fa014c539a6deeb187e57648960a52e49643592f27a58685097171d4769","source_url":"https://biology.stackexchange.com/questions/114370/potassium-permeability-in-cardiac-muscle-cells","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Potassium Permeability in Cardiac Muscle Cells\nFrom my research it seems as though there's a difference between cardiac and skeletal muscle cells in that during depolarisation, the permeability of potassium actually decreases for cardiac muscle cells. How does this occur? I imagine it would be due to the closure of potassium channels but if this is the case, then how is the inwards current of calcium balanced during the plateau phase?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114406,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Proteins tend to denature on hydrophobic surfaces, which &quot;changes&quot; the binding modes in that it abolishes them completely. I found a <a href=\"https://www.sciencedirect.com/science/article/pii/S0008622320304243\" rel=\"nofollow noreferrer\">study on BSA binding affinity when adsorbed to reduced graphene oxide</a> (rGO), which should have very similar behavior to graphene itself.</p>\n<blockquote>\n<p>The biochemical functionality of adsorbed BSA was investigated through the interaction with its anti-BSA antibody counterpart. BSA on GO can retain its binding sites while, in contrast, a denatured ad-layer of BSA forms on the rGO followed by further binding of active BSA molecules, depending on the concentration of the protein.</p>\n</blockquote>\n","answer_id":114404,"answer_text":"Proteins tend to denature on hydrophobic surfaces, which \"changes\" the binding modes in that it abolishes them completely. I found a study on BSA binding affinity when adsorbed to reduced graphene oxide (https://www.sciencedirect.com/science/article/pii/S0008622320304243) (rGO), which should have very similar behavior to graphene itself.\n\n\n\n\n\n\n\nThe biochemical functionality of adsorbed BSA was investigated through the interaction with its anti-BSA antibody counterpart. BSA on GO can retain its binding sites while, in contrast, a denatured ad-layer of BSA forms on the rGO followed by further binding of active BSA molecules, depending on the concentration of the protein.","answer_url":"https://biology.stackexchange.com/a/114404","author":"timeskull","author_url":"https://biology.stackexchange.com/users/55506/timeskull","content_license":"CC BY-SA 4.0","created_at":"2024-03-29T21:54:49+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 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=2&pagesize=100&site=biology&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":114385,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"timeskull","profile_url":"https://biology.stackexchange.com/users/55506/timeskull","user_type":"registered"},"created_at":"2024-03-29T21:54:49+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"2BA3DB12-6478-4966-9907-61F9287DF1DB","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2BA3DB12-6478-4966-9907-61F9287DF1DB/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Roshan Shrestha","author_url":"https://biology.stackexchange.com/users/15413/roshan-shrestha","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Roshan Shrestha","profile_url":"https://biology.stackexchange.com/users/15413/roshan-shrestha","user_type":"registered"},"created_at":"2024-03-27T07:36:09+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"9DD23F05-1F31-48AF-B00E-B1533B226851","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9DD23F05-1F31-48AF-B00E-B1533B226851/view-source"}],"url":"https://biology.stackexchange.com/questions/114385/binding-modes-of-a-protein-on-a-planar-surface-graphene"},{"author":"timeskull","author_url":"https://biology.stackexchange.com/users/55506/timeskull","content_license":"CC BY-SA 4.0","context_id":"114404","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"timeskull","profile_url":"https://biology.stackexchange.com/users/55506/timeskull","user_type":"registered"},"created_at":"2024-03-29T21:54:49+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"2BA3DB12-6478-4966-9907-61F9287DF1DB","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2BA3DB12-6478-4966-9907-61F9287DF1DB/view-source"}],"url":"https://biology.stackexchange.com/a/114404"}],"contexts":[{"context_id":"question","html":"<p>Can a protein have different binding modes on a flat even surface like graphene? For a surface like Graphene oxide I can understand, since it has several oxygenated groups on its surface that makes it easier for a protein to have different binding modes, but what for a homogenous aromatic surface like graphene?</p>\n","text":"Can a protein have different binding modes on a flat even surface like graphene? For a surface like Graphene oxide I can understand, since it has several oxygenated groups on its surface that makes it easier for a protein to have different binding modes, but what for a homogenous aromatic surface like graphene?"},{"context_id":"114404","html":"<p>Proteins tend to denature on hydrophobic surfaces, which &quot;changes&quot; the binding modes in that it abolishes them completely. I found a <a href=\"https://www.sciencedirect.com/science/article/pii/S0008622320304243\" rel=\"nofollow noreferrer\">study on BSA binding affinity when adsorbed to reduced graphene oxide</a> (rGO), which should have very similar behavior to graphene itself.</p>\n<blockquote>\n<p>The biochemical functionality of adsorbed BSA was investigated through the interaction with its anti-BSA antibody counterpart. BSA on GO can retain its binding sites while, in contrast, a denatured ad-layer of BSA forms on the rGO followed by further binding of active BSA molecules, depending on the concentration of the protein.</p>\n</blockquote>\n","text":"Proteins tend to denature on hydrophobic surfaces, which \"changes\" the binding modes in that it abolishes them completely. I found a study on BSA binding affinity when adsorbed to reduced graphene oxide (https://www.sciencedirect.com/science/article/pii/S0008622320304243) (rGO), which should have very similar behavior to graphene itself.\n\n\n\n\n\n\n\nThe biochemical functionality of adsorbed BSA was investigated through the interaction with its anti-BSA antibody counterpart. BSA on GO can retain its binding sites while, in contrast, a denatured ad-layer of BSA forms on the rGO followed by further binding of active BSA molecules, depending on the concentration of the protein."}],"domain":"biology","external_citations":["https://www.sciencedirect.com/science/article/pii/S0008622320304243"],"ground_truth_type":"metadata_grounded","group_id":"ce8af23ead3ae81f7fcedf7bce939e610c51c891f9c235fbacc61151a4596970","hard_case_family":["no_accepted_answer"],"id":"RHM-a082825de2720af08967a1d8","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":"Roshan Shrestha","profile_url":"https://biology.stackexchange.com/users/15413/roshan-shrestha","user_type":"registered"},"created_at":"2024-03-27T07:36:09+00:00","raw_file":"raw/codex_api_v1/22e8417b315063b6d3b906d11f4422eb4ac33f788b9058bddc9dd7bfc046cafc_1790824071906161300_0.json","raw_sha256":"84dcb0018b97f3e9f1f4320ffea98714a55b6054974fc678a4c6cac9e312e078","revision_guid":"9DD23F05-1F31-48AF-B00E-B1533B226851","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9DD23F05-1F31-48AF-B00E-B1533B226851/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":"114385","source_record_sha256":"033249092b33d479b0c8f9d8661392f9a03b9479b349103bd1f88cc57360a953","source_url":"https://biology.stackexchange.com/questions/114385/binding-modes-of-a-protein-on-a-planar-surface-graphene","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Binding modes of a protein on a planar surface graphene\nCan a protein have different binding modes on a flat even surface like graphene? For a surface like Graphene oxide I can understand, since it has several oxygenated groups on its surface that makes it easier for a protein to have different binding modes, but what for a homogenous aromatic surface like graphene?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114404,"score":2}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":114583,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The answer must be an unequivocal yes and you only need to focus on one object. However, it's not quite how you describe the problem, so not quite what you mean.</p>\n<p>If you look at a single object off to one side of your face, but within the &quot;infinity&quot; distance of our eyes (about <a href=\"https://biology.stackexchange.com/questions/15981/whats-the-minimum-distance-of-focus-for-the-lens-of-a-human-eye-to-reach-maximu\">six meters/19.7 feet</a>), the path lengths between the object and each eye must be different lengths, therefore they must have different focal distances. Obviously the difference isn't massive but the decision to focus on that object is intentional and therefore you have the ability to have different focus points for each eye in an intentional system.</p>\n<p>The ability to focus on different objects with each eye is another matter. As far as I am aware, people with <a href=\"https://en.wikipedia.org/wiki/Amblyopia\" rel=\"nofollow noreferrer\">Amblyopia</a> (AKA &quot;lazy eye&quot;) are not able to focus or not able to focus well with the amblyopic eye and suffer loss of vision control in that eye if not treated. I don't know if anyone has looked at the abilities of people who can independently control their eyes. We have dominant eyes (just as we have dominant hands), so I suspect that we would ignore the input from one eye in a situation where you were looking at two separate objects with two eyes. The <a href=\"https://skeptics.stackexchange.com/questions/16485/can-humans-functionally-move-their-eyeballs-independently-of-one-another\">Skeptics SE</a> seems to agree with this on a question about pilots using eyes independently.</p>\n","answer_id":114583,"answer_text":"The answer must be an unequivocal yes and you only need to focus on one object. However, it's not quite how you describe the problem, so not quite what you mean.\n\n\n\n\nIf you look at a single object off to one side of your face, but within the \"infinity\" distance of our eyes (about six meters/19.7 feet (https://biology.stackexchange.com/questions/15981/whats-the-minimum-distance-of-focus-for-the-lens-of-a-human-eye-to-reach-maximu)), the path lengths between the object and each eye must be different lengths, therefore they must have different focal distances. Obviously the difference isn't massive but the decision to focus on that object is intentional and therefore you have the ability to have different focus points for each eye in an intentional system.\n\n\n\n\nThe ability to focus on different objects with each eye is another matter. As far as I am aware, people with Amblyopia (https://en.wikipedia.org/wiki/Amblyopia) (AKA \"lazy eye\") are not able to focus or not able to focus well with the amblyopic eye and suffer loss of vision control in that eye if not treated. I don't know if anyone has looked at the abilities of people who can independently control their eyes. We have dominant eyes (just as we have dominant hands), so I suspect that we would ignore the input from one eye in a situation where you were looking at two separate objects with two eyes. The Skeptics SE (https://skeptics.stackexchange.com/questions/16485/can-humans-functionally-move-their-eyeballs-independently-of-one-another) seems to agree with this on a question about pilots using eyes independently.","answer_url":"https://biology.stackexchange.com/a/114583","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2024-04-28T01:29:47+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":114581,"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":"2024-04-28T01:29:47+00:00","raw_file":"raw/codex_api_v1/d310c9264de040c00738c99839c79b1aaf2778b649c466f104bf2aae5ea6c1ae_1790824079287810200_0.json","raw_sha256":"6e933306cc5429de28b498686eb7d6b004bc79b7012dd1a0f2d99766a5d1a3af","revision_guid":"65177D45-567C-4199-8DEC-0DF39562CD38","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/65177D45-567C-4199-8DEC-0DF39562CD38/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Astrovis","author_url":"https://biology.stackexchange.com/users/80701/astrovis","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Astrovis","profile_url":"https://biology.stackexchange.com/users/80701/astrovis","user_type":"registered"},"created_at":"2024-04-27T16:01:10+00:00","raw_file":"raw/codex_api_v1/d310c9264de040c00738c99839c79b1aaf2778b649c466f104bf2aae5ea6c1ae_1790824079287810200_0.json","raw_sha256":"6e933306cc5429de28b498686eb7d6b004bc79b7012dd1a0f2d99766a5d1a3af","revision_guid":"143FAE88-3C7A-4873-A8AC-BADF92F336E5","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/143FAE88-3C7A-4873-A8AC-BADF92F336E5/view-source"}],"url":"https://biology.stackexchange.com/questions/114581/can-both-lenses-of-different-eyes-intentionally-focus-at-different-amounts"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"114583","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":"2024-04-28T01:29:47+00:00","raw_file":"raw/codex_api_v1/d310c9264de040c00738c99839c79b1aaf2778b649c466f104bf2aae5ea6c1ae_1790824079287810200_0.json","raw_sha256":"6e933306cc5429de28b498686eb7d6b004bc79b7012dd1a0f2d99766a5d1a3af","revision_guid":"65177D45-567C-4199-8DEC-0DF39562CD38","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/65177D45-567C-4199-8DEC-0DF39562CD38/view-source"}],"url":"https://biology.stackexchange.com/a/114583"}],"contexts":[{"context_id":"question","html":"<p>Can each lens of both eyes have different accommodation rates, or have a different focal length to view objects of different distances. I understand that this can be a problem known as Anisometropia, but can this happen intentionally? For instance, if you place one finger close to the eye but one finger far away, can you focus both eyes in a way so that both appear in view? Assume that the fingers are not placed in the eye's area of visual overlap. I tried this, and I wasn't able to focus on both fingers. But why is this? It seems to be that the eyes would need to be able to individually focus since objects will be different distances from both lenses, like if we look out of the corner of our eye.</p>\n","text":"Can each lens of both eyes have different accommodation rates, or have a different focal length to view objects of different distances. I understand that this can be a problem known as Anisometropia, but can this happen intentionally? For instance, if you place one finger close to the eye but one finger far away, can you focus both eyes in a way so that both appear in view? Assume that the fingers are not placed in the eye's area of visual overlap. I tried this, and I wasn't able to focus on both fingers. But why is this? It seems to be that the eyes would need to be able to individually focus since objects will be different distances from both lenses, like if we look out of the corner of our eye."},{"context_id":"114583","html":"<p>The answer must be an unequivocal yes and you only need to focus on one object. However, it's not quite how you describe the problem, so not quite what you mean.</p>\n<p>If you look at a single object off to one side of your face, but within the &quot;infinity&quot; distance of our eyes (about <a href=\"https://biology.stackexchange.com/questions/15981/whats-the-minimum-distance-of-focus-for-the-lens-of-a-human-eye-to-reach-maximu\">six meters/19.7 feet</a>), the path lengths between the object and each eye must be different lengths, therefore they must have different focal distances. Obviously the difference isn't massive but the decision to focus on that object is intentional and therefore you have the ability to have different focus points for each eye in an intentional system.</p>\n<p>The ability to focus on different objects with each eye is another matter. As far as I am aware, people with <a href=\"https://en.wikipedia.org/wiki/Amblyopia\" rel=\"nofollow noreferrer\">Amblyopia</a> (AKA &quot;lazy eye&quot;) are not able to focus or not able to focus well with the amblyopic eye and suffer loss of vision control in that eye if not treated. I don't know if anyone has looked at the abilities of people who can independently control their eyes. We have dominant eyes (just as we have dominant hands), so I suspect that we would ignore the input from one eye in a situation where you were looking at two separate objects with two eyes. The <a href=\"https://skeptics.stackexchange.com/questions/16485/can-humans-functionally-move-their-eyeballs-independently-of-one-another\">Skeptics SE</a> seems to agree with this on a question about pilots using eyes independently.</p>\n","text":"The answer must be an unequivocal yes and you only need to focus on one object. However, it's not quite how you describe the problem, so not quite what you mean.\n\n\n\n\nIf you look at a single object off to one side of your face, but within the \"infinity\" distance of our eyes (about six meters/19.7 feet (https://biology.stackexchange.com/questions/15981/whats-the-minimum-distance-of-focus-for-the-lens-of-a-human-eye-to-reach-maximu)), the path lengths between the object and each eye must be different lengths, therefore they must have different focal distances. Obviously the difference isn't massive but the decision to focus on that object is intentional and therefore you have the ability to have different focus points for each eye in an intentional system.\n\n\n\n\nThe ability to focus on different objects with each eye is another matter. As far as I am aware, people with Amblyopia (https://en.wikipedia.org/wiki/Amblyopia) (AKA \"lazy eye\") are not able to focus or not able to focus well with the amblyopic eye and suffer loss of vision control in that eye if not treated. I don't know if anyone has looked at the abilities of people who can independently control their eyes. We have dominant eyes (just as we have dominant hands), so I suspect that we would ignore the input from one eye in a situation where you were looking at two separate objects with two eyes. The Skeptics SE (https://skeptics.stackexchange.com/questions/16485/can-humans-functionally-move-their-eyeballs-independently-of-one-another) seems to agree with this on a question about pilots using eyes independently."}],"domain":"biology","external_citations":["https://biology.stackexchange.com/questions/15981/whats-the-minimum-distance-of-focus-for-the-lens-of-a-human-eye-to-reach-maximu","https://en.wikipedia.org/wiki/Amblyopia","https://skeptics.stackexchange.com/questions/16485/can-humans-functionally-move-their-eyeballs-independently-of-one-another"],"ground_truth_type":"metadata_grounded","group_id":"bffc079d8c15dc7fe0f059c1e7ac1339fefee2e159cbdab83916d7e8f7f09850","hard_case_family":["multiple_sources"],"id":"RHM-b4d26d5ff3ff0cdb905685c0","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":"Astrovis","profile_url":"https://biology.stackexchange.com/users/80701/astrovis","user_type":"registered"},"created_at":"2024-04-27T16:01:10+00:00","raw_file":"raw/codex_api_v1/d310c9264de040c00738c99839c79b1aaf2778b649c466f104bf2aae5ea6c1ae_1790824079287810200_0.json","raw_sha256":"6e933306cc5429de28b498686eb7d6b004bc79b7012dd1a0f2d99766a5d1a3af","revision_guid":"143FAE88-3C7A-4873-A8AC-BADF92F336E5","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/143FAE88-3C7A-4873-A8AC-BADF92F336E5/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":"114581","source_record_sha256":"5fcef54061368b28510cb1fdb1a497802e39c6fb9834662e82db9bd50f93513b","source_url":"https://biology.stackexchange.com/questions/114581/can-both-lenses-of-different-eyes-intentionally-focus-at-different-amounts","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Can both lenses of different eyes intentionally focus at different amounts\nCan each lens of both eyes have different accommodation rates, or have a different focal length to view objects of different distances. I understand that this can be a problem known as Anisometropia, but can this happen intentionally? For instance, if you place one finger close to the eye but one finger far away, can you focus both eyes in a way so that both appear in view? Assume that the fingers are not placed in the eye's area of visual overlap. I tried this, and I wasn't able to focus on both fingers. But why is this? It seems to be that the eyes would need to be able to individually focus since objects will be different distances from both lenses, like if we look out of the corner of our eye.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114583,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":114789,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I will not comment on the particular author's views and answer the question in the title.</p>\n<p>There are five conceivable theories for neural memory (following Hebb (<a href=\"https://doi.org/10.4324/9781410612403\" rel=\"nofollow noreferrer\">1</a>)):</p>\n<ol>\n<li>Memory is sustained by reverberations of neural activity which persist after the stimulus disappears.</li>\n<li>Memory takes place through the creation and elimination of synaptic structures, which re-wire the neural circuits.</li>\n<li>Memory subsists by adjusting the size of existing synaptic structures, which re-wire the neural circuits.</li>\n<li>Memory is internalized by cells through homeostatic adjustments in their molecular machinery.</li>\n<li>Memory is simply a re-arrangement of the connections between cells through microscopic movements of the synaptic elements (such as axonal boutons and dendritic spines).</li>\n</ol>\n<p>An early proponent of 1 was Lashley. Today, 1 is widely thought largely incompatible with existing evidence, although it can arguably play a role in the <em>formation</em> stage of memory.\nTheory 2 consists of the formation and elimination of new synaptic contacts. In most cases studied, i.e. in the cortex and the hippocampus, it appears that this comes down to the formation and elimination of dendritic spines.\nLong-term potentiation (LTP) and long-term depression (LTD) come into play with theory 3.\nHomeostatic regulation can refer to many different processes, such as changes in synaptic or <em>non-synaptic</em> distribution of some resource such as mRNA or actin, or changes in the distribution and electrical properties of particular types of ion channels and receptors.\nTheory 5 is largely incompatible with the apparent mobility allowed in real brains as shown by microscopic evidence.</p>\n<p>Theories 2, 3, 4, and 5 are not incompatible with each other. Hebb suggested all four possibilities and only discarded theory 1.\nMuch earlier, Tanji and Cajal were fighting a similar fight, Tanzi claiming that connections between cells change because the cables change in size (synapses were not discovered yet), while Cajal claiming that new structures must form --later, he changed his mind on this issue.</p>\n<p>The association between LTP and memory is overwhelmingly the most popular theory currently in neuroscience and no one could reasonably discard its existence.\nHowever, there is evidence that spine formation and elimination can also play a more limited role in the re-wiring of neural circuits.\nIt is still an open question to what extent and with what temporal features such re-structuring is coordinated through active processes that could resemble LTP (<a href=\"https://biology.stackexchange.com/questions/8/under-what-conditions-do-dendritic-spines-form/65530#65530\">2</a>), although it is safe to say that activity --thus, likely LTP/LTD-- is involved at some stage (<a href=\"https://doi.org/10.1038/nature15257\" rel=\"nofollow noreferrer\">3</a>).\nOn top of all that, homeostatic plasticity (theory 4) is generally thought to constantly take place, driven by less specific conditions (<a href=\"https://biology.stackexchange.com/questions/96463/do-neurons-that-dont-fire-together-unwire/96464#96464\">4</a>).</p>\n<hr />\n<p><strong>References</strong><br />\n1: Hebb, D. O. (2002). The Organization of Behavior. Routledge. <a href=\"https://doi.org/10.4324/9781410612403\" rel=\"nofollow noreferrer\">https://doi.org/10.4324/9781410612403</a><br />\n2: <a href=\"https://biology.stackexchange.com/questions/8/under-what-conditions-do-dendritic-spines-form/65530#65530\">Under what conditions do dendritic spines form?</a><br />\n3: Hayashi-Takagi, A., Yagishita, S., Nakamura, M., et al. (2015). Labelling and optical erasure of synaptic memory traces in the motor cortex. Nature, 525(7569), Article 7569. <a href=\"https://doi.org/10.1038/nature15257\" rel=\"nofollow noreferrer\">https://doi.org/10.1038/nature15257</a><br />\n4: <a href=\"https://biology.stackexchange.com/questions/96463/do-neurons-that-dont-fire-together-unwire/96464#96464\">Do neurons that *don&#39;t* fire together unwire?</a></p>\n","answer_id":114789,"answer_text":"I will not comment on the particular author's views and answer the question in the title.\n\n\n\n\nThere are five conceivable theories for neural memory (following Hebb (1 (https://doi.org/10.4324/9781410612403))):\n\n\n\n\n\nMemory is sustained by reverberations of neural activity which persist after the stimulus disappears.\n\n\n\n\nMemory takes place through the creation and elimination of synaptic structures, which re-wire the neural circuits.\n\n\n\n\nMemory subsists by adjusting the size of existing synaptic structures, which re-wire the neural circuits.\n\n\n\n\nMemory is internalized by cells through homeostatic adjustments in their molecular machinery.\n\n\n\n\nMemory is simply a re-arrangement of the connections between cells through microscopic movements of the synaptic elements (such as axonal boutons and dendritic spines).\n\n\n\n\n\nAn early proponent of 1 was Lashley. Today, 1 is widely thought largely incompatible with existing evidence, although it can arguably play a role in the formation stage of memory.\nTheory 2 consists of the formation and elimination of new synaptic contacts. In most cases studied, i.e. in the cortex and the hippocampus, it appears that this comes down to the formation and elimination of dendritic spines.\nLong-term potentiation (LTP) and long-term depression (LTD) come into play with theory 3.\nHomeostatic regulation can refer to many different processes, such as changes in synaptic or non-synaptic distribution of some resource such as mRNA or actin, or changes in the distribution and electrical properties of particular types of ion channels and receptors.\nTheory 5 is largely incompatible with the apparent mobility allowed in real brains as shown by microscopic evidence.\n\n\n\n\nTheories 2, 3, 4, and 5 are not incompatible with each other. Hebb suggested all four possibilities and only discarded theory 1.\nMuch earlier, Tanji and Cajal were fighting a similar fight, Tanzi claiming that connections between cells change because the cables change in size (synapses were not discovered yet), while Cajal claiming that new structures must form --later, he changed his mind on this issue.\n\n\n\n\nThe association between LTP and memory is overwhelmingly the most popular theory currently in neuroscience and no one could reasonably discard its existence.\nHowever, there is evidence that spine formation and elimination can also play a more limited role in the re-wiring of neural circuits.\nIt is still an open question to what extent and with what temporal features such re-structuring is coordinated through active processes that could resemble LTP (2 (https://biology.stackexchange.com/questions/8/under-what-conditions-do-dendritic-spines-form/65530#65530)), although it is safe to say that activity --thus, likely LTP/LTD-- is involved at some stage (3 (https://doi.org/10.1038/nature15257)).\nOn top of all that, homeostatic plasticity (theory 4) is generally thought to constantly take place, driven by less specific conditions (4 (https://biology.stackexchange.com/questions/96463/do-neurons-that-dont-fire-together-unwire/96464#96464)).\n\n\n\n\n\n\n\nReferences\n\n1: Hebb, D. O. (2002). The Organization of Behavior. Routledge. https://doi.org/10.4324/9781410612403 (https://doi.org/10.4324/9781410612403)\n\n2: Under what conditions do dendritic spines form? (https://biology.stackexchange.com/questions/8/under-what-conditions-do-dendritic-spines-form/65530#65530)\n\n3: Hayashi-Takagi, A., Yagishita, S., Nakamura, M., et al. (2015). Labelling and optical erasure of synaptic memory traces in the motor cortex. Nature, 525(7569), Article 7569. https://doi.org/10.1038/nature15257 (https://doi.org/10.1038/nature15257)\n\n4: Do neurons that *don't* fire together unwire? (https://biology.stackexchange.com/questions/96463/do-neurons-that-dont-fire-together-unwire/96464#96464)","answer_url":"https://biology.stackexchange.com/a/114789","author":"vkehayas","author_url":"https://biology.stackexchange.com/users/36209/vkehayas","content_license":"CC BY-SA 4.0","created_at":"2024-05-30T10:56:17+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":114784,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"vkehayas","profile_url":"https://biology.stackexchange.com/users/36209/vkehayas","user_type":"registered"},"created_at":"2024-05-30T10:56:17+00:00","raw_file":"raw/codex_api_v1/41500cf35bca9ae31b7ea454bad8679af7e3276d71713db5d1815d84a971bb0e_1790824088925435600_0.json","raw_sha256":"a764902131a161e2a7978a1f607c4912689efa157d70c2752a5b31e3a042aacb","revision_guid":"8254D2D9-63A6-490C-B869-92983BEDF560","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8254D2D9-63A6-490C-B869-92983BEDF560/view-source"}],"score":4}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Hans-Peter Stricker","author_url":"https://biology.stackexchange.com/users/27928/hans-peter-stricker","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Hans-Peter Stricker","profile_url":"https://biology.stackexchange.com/users/27928/hans-peter-stricker","user_type":"registered"},"created_at":"2024-05-29T13:13:52+00:00","raw_file":"raw/codex_api_v1/41500cf35bca9ae31b7ea454bad8679af7e3276d71713db5d1815d84a971bb0e_1790824088925435600_0.json","raw_sha256":"a764902131a161e2a7978a1f607c4912689efa157d70c2752a5b31e3a042aacb","revision_guid":"77579459-54D8-49EE-A0F8-7244F871FFBA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/77579459-54D8-49EE-A0F8-7244F871FFBA/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":"2024-05-30T06:48:32+00:00","raw_file":"raw/codex_api_v1/41500cf35bca9ae31b7ea454bad8679af7e3276d71713db5d1815d84a971bb0e_1790824088925435600_0.json","raw_sha256":"a764902131a161e2a7978a1f607c4912689efa157d70c2752a5b31e3a042aacb","revision_guid":"30F687AC-73B0-490E-BD16-517F5A3AF800","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/30F687AC-73B0-490E-BD16-517F5A3AF800/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"vkehayas","profile_url":"https://biology.stackexchange.com/users/36209/vkehayas","user_type":"registered"},"created_at":"2024-05-30T10:32:13+00:00","raw_file":"raw/codex_api_v1/41500cf35bca9ae31b7ea454bad8679af7e3276d71713db5d1815d84a971bb0e_1790824088925435600_0.json","raw_sha256":"a764902131a161e2a7978a1f607c4912689efa157d70c2752a5b31e3a042aacb","revision_guid":"56A8BD22-439B-4A14-BC64-A4DDDD3218A8","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/56A8BD22-439B-4A14-BC64-A4DDDD3218A8/view-source"}],"url":"https://biology.stackexchange.com/questions/114784/how-could-memory-work-without-long-term-potentiation"},{"author":"vkehayas","author_url":"https://biology.stackexchange.com/users/36209/vkehayas","content_license":"CC BY-SA 4.0","context_id":"114789","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"vkehayas","profile_url":"https://biology.stackexchange.com/users/36209/vkehayas","user_type":"registered"},"created_at":"2024-05-30T10:56:17+00:00","raw_file":"raw/codex_api_v1/41500cf35bca9ae31b7ea454bad8679af7e3276d71713db5d1815d84a971bb0e_1790824088925435600_0.json","raw_sha256":"a764902131a161e2a7978a1f607c4912689efa157d70c2752a5b31e3a042aacb","revision_guid":"8254D2D9-63A6-490C-B869-92983BEDF560","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8254D2D9-63A6-490C-B869-92983BEDF560/view-source"}],"url":"https://biology.stackexchange.com/a/114789"}],"contexts":[{"context_id":"question","html":"<p>At the end of his review on <a href=\"https://pubmed.ncbi.nlm.nih.gov/34086051/\" rel=\"nofollow noreferrer\">the cell biology of synapse formation</a> (2021), Südhoff claims that</p>\n<blockquote>\n<p>there is scant evidence that long-term plasticity per se is\nphysiologically important for a behaviour.</p>\n</blockquote>\n<p>This lack of evidence - in the form of specific &quot;manipulations of some molecules with multifaceted roles that happen to affect LTP&quot; -, he continues,</p>\n<blockquote>\n<p>has not curtailed speculation that LTP is involved in memory, drug\naddiction, and scores of other human brain activities.</p>\n</blockquote>\n<p>I always considered it a dogma that LTP lies at the heart of memory etc. Does Südhoff's view have many other proponents? And how could the standard view (&quot;long-term memory = long-term potentiation&quot;) be so strong without evidence? What is it based on, then? Finally: What are alternatives to LTP to underlie memory?</p>\n","text":"At the end of his review on the cell biology of synapse formation (https://pubmed.ncbi.nlm.nih.gov/34086051/) (2021), Südhoff claims that\n\n\n\n\n\n\n\nthere is scant evidence that long-term plasticity per se is\nphysiologically important for a behaviour.\n\n\n\n\n\n\n\nThis lack of evidence - in the form of specific \"manipulations of some molecules with multifaceted roles that happen to affect LTP\" -, he continues,\n\n\n\n\n\n\n\nhas not curtailed speculation that LTP is involved in memory, drug\naddiction, and scores of other human brain activities.\n\n\n\n\n\n\n\nI always considered it a dogma that LTP lies at the heart of memory etc. Does Südhoff's view have many other proponents? And how could the standard view (\"long-term memory = long-term potentiation\") be so strong without evidence? What is it based on, then? Finally: What are alternatives to LTP to underlie memory?"},{"context_id":"114789","html":"<p>I will not comment on the particular author's views and answer the question in the title.</p>\n<p>There are five conceivable theories for neural memory (following Hebb (<a href=\"https://doi.org/10.4324/9781410612403\" rel=\"nofollow noreferrer\">1</a>)):</p>\n<ol>\n<li>Memory is sustained by reverberations of neural activity which persist after the stimulus disappears.</li>\n<li>Memory takes place through the creation and elimination of synaptic structures, which re-wire the neural circuits.</li>\n<li>Memory subsists by adjusting the size of existing synaptic structures, which re-wire the neural circuits.</li>\n<li>Memory is internalized by cells through homeostatic adjustments in their molecular machinery.</li>\n<li>Memory is simply a re-arrangement of the connections between cells through microscopic movements of the synaptic elements (such as axonal boutons and dendritic spines).</li>\n</ol>\n<p>An early proponent of 1 was Lashley. Today, 1 is widely thought largely incompatible with existing evidence, although it can arguably play a role in the <em>formation</em> stage of memory.\nTheory 2 consists of the formation and elimination of new synaptic contacts. In most cases studied, i.e. in the cortex and the hippocampus, it appears that this comes down to the formation and elimination of dendritic spines.\nLong-term potentiation (LTP) and long-term depression (LTD) come into play with theory 3.\nHomeostatic regulation can refer to many different processes, such as changes in synaptic or <em>non-synaptic</em> distribution of some resource such as mRNA or actin, or changes in the distribution and electrical properties of particular types of ion channels and receptors.\nTheory 5 is largely incompatible with the apparent mobility allowed in real brains as shown by microscopic evidence.</p>\n<p>Theories 2, 3, 4, and 5 are not incompatible with each other. Hebb suggested all four possibilities and only discarded theory 1.\nMuch earlier, Tanji and Cajal were fighting a similar fight, Tanzi claiming that connections between cells change because the cables change in size (synapses were not discovered yet), while Cajal claiming that new structures must form --later, he changed his mind on this issue.</p>\n<p>The association between LTP and memory is overwhelmingly the most popular theory currently in neuroscience and no one could reasonably discard its existence.\nHowever, there is evidence that spine formation and elimination can also play a more limited role in the re-wiring of neural circuits.\nIt is still an open question to what extent and with what temporal features such re-structuring is coordinated through active processes that could resemble LTP (<a href=\"https://biology.stackexchange.com/questions/8/under-what-conditions-do-dendritic-spines-form/65530#65530\">2</a>), although it is safe to say that activity --thus, likely LTP/LTD-- is involved at some stage (<a href=\"https://doi.org/10.1038/nature15257\" rel=\"nofollow noreferrer\">3</a>).\nOn top of all that, homeostatic plasticity (theory 4) is generally thought to constantly take place, driven by less specific conditions (<a href=\"https://biology.stackexchange.com/questions/96463/do-neurons-that-dont-fire-together-unwire/96464#96464\">4</a>).</p>\n<hr />\n<p><strong>References</strong><br />\n1: Hebb, D. O. (2002). The Organization of Behavior. Routledge. <a href=\"https://doi.org/10.4324/9781410612403\" rel=\"nofollow noreferrer\">https://doi.org/10.4324/9781410612403</a><br />\n2: <a href=\"https://biology.stackexchange.com/questions/8/under-what-conditions-do-dendritic-spines-form/65530#65530\">Under what conditions do dendritic spines form?</a><br />\n3: Hayashi-Takagi, A., Yagishita, S., Nakamura, M., et al. (2015). Labelling and optical erasure of synaptic memory traces in the motor cortex. Nature, 525(7569), Article 7569. <a href=\"https://doi.org/10.1038/nature15257\" rel=\"nofollow noreferrer\">https://doi.org/10.1038/nature15257</a><br />\n4: <a href=\"https://biology.stackexchange.com/questions/96463/do-neurons-that-dont-fire-together-unwire/96464#96464\">Do neurons that *don&#39;t* fire together unwire?</a></p>\n","text":"I will not comment on the particular author's views and answer the question in the title.\n\n\n\n\nThere are five conceivable theories for neural memory (following Hebb (1 (https://doi.org/10.4324/9781410612403))):\n\n\n\n\n\nMemory is sustained by reverberations of neural activity which persist after the stimulus disappears.\n\n\n\n\nMemory takes place through the creation and elimination of synaptic structures, which re-wire the neural circuits.\n\n\n\n\nMemory subsists by adjusting the size of existing synaptic structures, which re-wire the neural circuits.\n\n\n\n\nMemory is internalized by cells through homeostatic adjustments in their molecular machinery.\n\n\n\n\nMemory is simply a re-arrangement of the connections between cells through microscopic movements of the synaptic elements (such as axonal boutons and dendritic spines).\n\n\n\n\n\nAn early proponent of 1 was Lashley. Today, 1 is widely thought largely incompatible with existing evidence, although it can arguably play a role in the formation stage of memory.\nTheory 2 consists of the formation and elimination of new synaptic contacts. In most cases studied, i.e. in the cortex and the hippocampus, it appears that this comes down to the formation and elimination of dendritic spines.\nLong-term potentiation (LTP) and long-term depression (LTD) come into play with theory 3.\nHomeostatic regulation can refer to many different processes, such as changes in synaptic or non-synaptic distribution of some resource such as mRNA or actin, or changes in the distribution and electrical properties of particular types of ion channels and receptors.\nTheory 5 is largely incompatible with the apparent mobility allowed in real brains as shown by microscopic evidence.\n\n\n\n\nTheories 2, 3, 4, and 5 are not incompatible with each other. Hebb suggested all four possibilities and only discarded theory 1.\nMuch earlier, Tanji and Cajal were fighting a similar fight, Tanzi claiming that connections between cells change because the cables change in size (synapses were not discovered yet), while Cajal claiming that new structures must form --later, he changed his mind on this issue.\n\n\n\n\nThe association between LTP and memory is overwhelmingly the most popular theory currently in neuroscience and no one could reasonably discard its existence.\nHowever, there is evidence that spine formation and elimination can also play a more limited role in the re-wiring of neural circuits.\nIt is still an open question to what extent and with what temporal features such re-structuring is coordinated through active processes that could resemble LTP (2 (https://biology.stackexchange.com/questions/8/under-what-conditions-do-dendritic-spines-form/65530#65530)), although it is safe to say that activity --thus, likely LTP/LTD-- is involved at some stage (3 (https://doi.org/10.1038/nature15257)).\nOn top of all that, homeostatic plasticity (theory 4) is generally thought to constantly take place, driven by less specific conditions (4 (https://biology.stackexchange.com/questions/96463/do-neurons-that-dont-fire-together-unwire/96464#96464)).\n\n\n\n\n\n\n\nReferences\n\n1: Hebb, D. O. (2002). The Organization of Behavior. Routledge. https://doi.org/10.4324/9781410612403 (https://doi.org/10.4324/9781410612403)\n\n2: Under what conditions do dendritic spines form? (https://biology.stackexchange.com/questions/8/under-what-conditions-do-dendritic-spines-form/65530#65530)\n\n3: Hayashi-Takagi, A., Yagishita, S., Nakamura, M., et al. (2015). Labelling and optical erasure of synaptic memory traces in the motor cortex. Nature, 525(7569), Article 7569. https://doi.org/10.1038/nature15257 (https://doi.org/10.1038/nature15257)\n\n4: Do neurons that *don't* fire together unwire? (https://biology.stackexchange.com/questions/96463/do-neurons-that-dont-fire-together-unwire/96464#96464)"}],"domain":"biology","external_citations":["https://biology.stackexchange.com/questions/8/under-what-conditions-do-dendritic-spines-form/65530#65530","https://biology.stackexchange.com/questions/96463/do-neurons-that-dont-fire-together-unwire/96464#96464","https://doi.org/10.1038/nature15257","https://doi.org/10.4324/9781410612403","https://pubmed.ncbi.nlm.nih.gov/34086051/"],"ground_truth_type":"metadata_grounded","group_id":"87af80f52736cdb679afe58c891429082c1b566b864c7d7ff40566e9be4d5de4","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-62abb5e0c15d529c4a1832ad","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":"Hans-Peter Stricker","profile_url":"https://biology.stackexchange.com/users/27928/hans-peter-stricker","user_type":"registered"},"created_at":"2024-05-29T13:13:52+00:00","raw_file":"raw/codex_api_v1/41500cf35bca9ae31b7ea454bad8679af7e3276d71713db5d1815d84a971bb0e_1790824088925435600_0.json","raw_sha256":"a764902131a161e2a7978a1f607c4912689efa157d70c2752a5b31e3a042aacb","revision_guid":"77579459-54D8-49EE-A0F8-7244F871FFBA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/77579459-54D8-49EE-A0F8-7244F871FFBA/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":"2024-05-30T06:48:32+00:00","raw_file":"raw/codex_api_v1/41500cf35bca9ae31b7ea454bad8679af7e3276d71713db5d1815d84a971bb0e_1790824088925435600_0.json","raw_sha256":"a764902131a161e2a7978a1f607c4912689efa157d70c2752a5b31e3a042aacb","revision_guid":"30F687AC-73B0-490E-BD16-517F5A3AF800","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/30F687AC-73B0-490E-BD16-517F5A3AF800/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"vkehayas","profile_url":"https://biology.stackexchange.com/users/36209/vkehayas","user_type":"registered"},"created_at":"2024-05-30T10:32:13+00:00","raw_file":"raw/codex_api_v1/41500cf35bca9ae31b7ea454bad8679af7e3276d71713db5d1815d84a971bb0e_1790824088925435600_0.json","raw_sha256":"a764902131a161e2a7978a1f607c4912689efa157d70c2752a5b31e3a042aacb","revision_guid":"56A8BD22-439B-4A14-BC64-A4DDDD3218A8","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/56A8BD22-439B-4A14-BC64-A4DDDD3218A8/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":"114784","source_record_sha256":"31989a2c8f15ea4d532c81bd9f6998f9a002450aa7a3088b763164d49bfe702f","source_url":"https://biology.stackexchange.com/questions/114784/how-could-memory-work-without-long-term-potentiation","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How could memory work without long-term potentiation?\nAt the end of his review on the cell biology of synapse formation (https://pubmed.ncbi.nlm.nih.gov/34086051/) (2021), Südhoff claims that\n\n\n\n\n\n\n\nthere is scant evidence that long-term plasticity per se is\nphysiologically important for a behaviour.\n\n\n\n\n\n\n\nThis lack of evidence - in the form of specific \"manipulations of some molecules with multifaceted roles that happen to affect LTP\" -, he continues,\n\n\n\n\n\n\n\nhas not curtailed speculation that LTP is involved in memory, drug\naddiction, and scores of other human brain activities.\n\n\n\n\n\n\n\nI always considered it a dogma that LTP lies at the heart of memory etc. Does Südhoff's view have many other proponents? And how could the standard view (\"long-term memory = long-term potentiation\") be so strong without evidence? What is it based on, then? Finally: What are alternatives to LTP to underlie memory?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114789,"score":4}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I have been working on nonequilibrium thermodynamics related to life and its implications for Hegelian philosophy and this concept you describe is quite interesting. Imagining that there is a being, an agent, that takes advantage of a certain mass for its survival, the simplest term would be &quot;<strong>metabolize</strong>&quot;, from the Greek μεταβολή (change, transformation) with the suffix indicating transformation.</p>\n<p>While metabolizable is a generic term for using something, I have distinguished between two varieties of metabolization. On the one hand, simple <strong>catabolization</strong>, decomposition into smaller parts for structural reuse, from the Greek καταβολή. Literally, καταβολή means to throw down. This &quot;throw&quot; is somewhat strange, but as it is an established term, it is better to use it.</p>\n<p>On the other hand, the use as a mere energy resource, we should use &quot;trophic&quot;, from τροφή (trophē): &quot;feeding&quot; or &quot;nutrition,&quot; derived from the verb &quot;τρέφω&quot; (trépho), which means &quot;to feed&quot; or &quot;to nourish.&quot;, giving <strong>metatrophism</strong> to the mere feeding without integrating into the body structure.</p>\n<p>Finally, let's see how to adapt this nomenclature to describe the concepts of your research, of things that are beyond the reach of use as energy:</p>\n<ul>\n<li>Parathrophic (parathrophizable) - unsuited to use as food (such as sand).</li>\n<li>Parametabolic (parametabolizable) - unsuited to decompose to use as structural elements (such as meat for vegetarians).</li>\n<li>Paracatabolic (paracatabolizable) - unsuited to decompose (such as cellulose for humans).</li>\n</ul>\n<p>Hope this helps with the nomenclature in your research!</p>\n","answer_id":114897,"answer_text":"I have been working on nonequilibrium thermodynamics related to life and its implications for Hegelian philosophy and this concept you describe is quite interesting. Imagining that there is a being, an agent, that takes advantage of a certain mass for its survival, the simplest term would be \"metabolize\", from the Greek μεταβολή (change, transformation) with the suffix indicating transformation.\n\n\n\n\nWhile metabolizable is a generic term for using something, I have distinguished between two varieties of metabolization. On the one hand, simple catabolization, decomposition into smaller parts for structural reuse, from the Greek καταβολή. Literally, καταβολή means to throw down. This \"throw\" is somewhat strange, but as it is an established term, it is better to use it.\n\n\n\n\nOn the other hand, the use as a mere energy resource, we should use \"trophic\", from τροφή (trophē): \"feeding\" or \"nutrition,\" derived from the verb \"τρέφω\" (trépho), which means \"to feed\" or \"to nourish.\", giving metatrophism to the mere feeding without integrating into the body structure.\n\n\n\n\nFinally, let's see how to adapt this nomenclature to describe the concepts of your research, of things that are beyond the reach of use as energy:\n\n\n\n\n\nParathrophic (parathrophizable) - unsuited to use as food (such as sand).\n\n\n\n\nParametabolic (parametabolizable) - unsuited to decompose to use as structural elements (such as meat for vegetarians).\n\n\n\n\nParacatabolic (paracatabolizable) - unsuited to decompose (such as cellulose for humans).\n\n\n\n\n\nHope this helps with the nomenclature in your research!","answer_url":"https://biology.stackexchange.com/a/114897","author":"Alfredo Maranca","author_url":"https://biology.stackexchange.com/users/81801/alfredo-maranca","content_license":"CC BY-SA 4.0","created_at":"2024-06-21T13:16:43+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; mechanical HTML-to-text; no LLM rewriting"},"question_id":114888,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Alfredo Maranca","profile_url":"https://biology.stackexchange.com/users/81801/alfredo-maranca","user_type":"registered"},"created_at":"2024-06-21T13:16:43+00:00","raw_file":"raw/codex_api_v1/b71692d4db54b1fd919e08bbd0e4d956635bb827b0cfa306c28bd8ef9b9590f2_1790824086740368100_0.json","raw_sha256":"fa87ea0a08a62d73a8b2c94b9665153275b3cd424a985b194879915043e1dde4","revision_guid":"6C97A126-42F6-41FE-A14F-C6831ABFF963","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/6C97A126-42F6-41FE-A14F-C6831ABFF963/view-source"}],"score":2},{"answer_html":"<p>I assume that, as suggested by the original form of this question and the comments requesting clarification, that the interest is in the energy a carnivorous animal predator can obtain from its killed prey. In this case, the most appropriate terms to describe this would seem to be those employed by nutritionalists. From a perusal of this topic in various Wikipedia articles I find no internationally recognized phrase, but would suggest the following as consistent with the terminology in this field:</p>\n<blockquote>\n<p><strong>Dietary Energy Equivalent</strong></p>\n</blockquote>\n<p>The use of the word “dietary” (or something similar) is important as it makes it clear that one is not concerned with the energy reserves that the living animal deposits for its own use, although these obviously contribute to the ‘dietary energy equivalent’.</p>\n<p>(One of the Wikipedia articles that prompted this suggestion was: <a href=\"https://en.wikipedia.org/wiki/List_of_countries_by_food_energy_intake\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/List_of_countries_by_food_energy_intake</a> — a table heading therein.).</p>\n","answer_id":114902,"answer_text":"I assume that, as suggested by the original form of this question and the comments requesting clarification, that the interest is in the energy a carnivorous animal predator can obtain from its killed prey. In this case, the most appropriate terms to describe this would seem to be those employed by nutritionalists. From a perusal of this topic in various Wikipedia articles I find no internationally recognized phrase, but would suggest the following as consistent with the terminology in this field:\n\n\n\n\n\n\n\nDietary Energy Equivalent\n\n\n\n\n\n\n\nThe use of the word “dietary” (or something similar) is important as it makes it clear that one is not concerned with the energy reserves that the living animal deposits for its own use, although these obviously contribute to the ‘dietary energy equivalent’.\n\n\n\n\n(One of the Wikipedia articles that prompted this suggestion was: https://en.wikipedia.org/wiki/List_of_countries_by_food_energy_intake (https://en.wikipedia.org/wiki/List_of_countries_by_food_energy_intake) — a table heading therein.).","answer_url":"https://biology.stackexchange.com/a/114902","author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 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Milone","profile_url":"https://biology.stackexchange.com/users/81847/matthew-milone","user_type":"registered"},"created_at":"2024-06-21T03:03:03+00:00","raw_file":"raw/codex_api_v1/b71692d4db54b1fd919e08bbd0e4d956635bb827b0cfa306c28bd8ef9b9590f2_1790824086740368100_0.json","raw_sha256":"fa87ea0a08a62d73a8b2c94b9665153275b3cd424a985b194879915043e1dde4","revision_guid":"7B72602E-AB5D-44C0-A8FC-74C4C3ECA7E5","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7B72602E-AB5D-44C0-A8FC-74C4C3ECA7E5/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Matthew Milone","profile_url":"https://biology.stackexchange.com/users/81847/matthew-milone","user_type":"registered"},"created_at":"2024-06-21T03:11:08+00:00","raw_file":"raw/codex_api_v1/b71692d4db54b1fd919e08bbd0e4d956635bb827b0cfa306c28bd8ef9b9590f2_1790824086740368100_0.json","raw_sha256":"fa87ea0a08a62d73a8b2c94b9665153275b3cd424a985b194879915043e1dde4","revision_guid":"68BF3653-8916-4A56-8DF2-D78C84AB5DDA","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/68BF3653-8916-4A56-8DF2-D78C84AB5DDA/view-source"}],"url":"https://biology.stackexchange.com/questions/114888/whats-the-term-for-energy-that-is-isnt-usable-by-an-organism"},{"author":"Alfredo Maranca","author_url":"https://biology.stackexchange.com/users/81801/alfredo-maranca","content_license":"CC BY-SA 4.0","context_id":"114897","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Alfredo Maranca","profile_url":"https://biology.stackexchange.com/users/81801/alfredo-maranca","user_type":"registered"},"created_at":"2024-06-21T13:16:43+00:00","raw_file":"raw/codex_api_v1/b71692d4db54b1fd919e08bbd0e4d956635bb827b0cfa306c28bd8ef9b9590f2_1790824086740368100_0.json","raw_sha256":"fa87ea0a08a62d73a8b2c94b9665153275b3cd424a985b194879915043e1dde4","revision_guid":"6C97A126-42F6-41FE-A14F-C6831ABFF963","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/6C97A126-42F6-41FE-A14F-C6831ABFF963/view-source"}],"url":"https://biology.stackexchange.com/a/114897"},{"author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","context_id":"114902","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":"2024-06-21T20:29:17+00:00","raw_file":"raw/codex_api_v1/b71692d4db54b1fd919e08bbd0e4d956635bb827b0cfa306c28bd8ef9b9590f2_1790824086740368100_0.json","raw_sha256":"fa87ea0a08a62d73a8b2c94b9665153275b3cd424a985b194879915043e1dde4","revision_guid":"7C37ADD9-DDD9-4BAF-8251-F964FB123823","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7C37ADD9-DDD9-4BAF-8251-F964FB123823/view-source"}],"url":"https://biology.stackexchange.com/a/114902"}],"contexts":[{"context_id":"question","html":"<p>Every healthy organism stores some of its biochemical energy in reserves (e.g. adipose tissue, glycogen), but much of an organism's biochemical energy is bound in ways that aren't normally accessible to it (e.g. protein in muscles or vital organs).</p>\n<p>The latter quantity has some thermodynamic implications. For example, the inaccessible energy can be transferred to a predator if the organism is eaten, and a fetus's inaccessible energy must be obtained from its mother.</p>\n<p>To research these concepts, <strong>I'm looking for a term for <em>energy that's accessible by the organism</em> and a term for <em>energy that's not accessible by the organism</em>.</strong></p>\n<p>I've searched the web (and StackExchange specifically) for a variety of terms, (e.g. &quot;expendable&quot;, &quot;reserved&quot;, &quot;essential&quot;, &quot;innate&quot;, etc.) but none of them produced relevant results.</p>\n","text":"Every healthy organism stores some of its biochemical energy in reserves (e.g. adipose tissue, glycogen), but much of an organism's biochemical energy is bound in ways that aren't normally accessible to it (e.g. protein in muscles or vital organs).\n\n\n\n\nThe latter quantity has some thermodynamic implications. For example, the inaccessible energy can be transferred to a predator if the organism is eaten, and a fetus's inaccessible energy must be obtained from its mother.\n\n\n\n\nTo research these concepts, I'm looking for a term for energy that's accessible by the organism and a term for energy that's not accessible by the organism.\n\n\n\n\nI've searched the web (and StackExchange specifically) for a variety of terms, (e.g. \"expendable\", \"reserved\", \"essential\", \"innate\", etc.) but none of them produced relevant results."},{"context_id":"114897","html":"<p>I have been working on nonequilibrium thermodynamics related to life and its implications for Hegelian philosophy and this concept you describe is quite interesting. Imagining that there is a being, an agent, that takes advantage of a certain mass for its survival, the simplest term would be &quot;<strong>metabolize</strong>&quot;, from the Greek μεταβολή (change, transformation) with the suffix indicating transformation.</p>\n<p>While metabolizable is a generic term for using something, I have distinguished between two varieties of metabolization. On the one hand, simple <strong>catabolization</strong>, decomposition into smaller parts for structural reuse, from the Greek καταβολή. Literally, καταβολή means to throw down. This &quot;throw&quot; is somewhat strange, but as it is an established term, it is better to use it.</p>\n<p>On the other hand, the use as a mere energy resource, we should use &quot;trophic&quot;, from τροφή (trophē): &quot;feeding&quot; or &quot;nutrition,&quot; derived from the verb &quot;τρέφω&quot; (trépho), which means &quot;to feed&quot; or &quot;to nourish.&quot;, giving <strong>metatrophism</strong> to the mere feeding without integrating into the body structure.</p>\n<p>Finally, let's see how to adapt this nomenclature to describe the concepts of your research, of things that are beyond the reach of use as energy:</p>\n<ul>\n<li>Parathrophic (parathrophizable) - unsuited to use as food (such as sand).</li>\n<li>Parametabolic (parametabolizable) - unsuited to decompose to use as structural elements (such as meat for vegetarians).</li>\n<li>Paracatabolic (paracatabolizable) - unsuited to decompose (such as cellulose for humans).</li>\n</ul>\n<p>Hope this helps with the nomenclature in your research!</p>\n","text":"I have been working on nonequilibrium thermodynamics related to life and its implications for Hegelian philosophy and this concept you describe is quite interesting. Imagining that there is a being, an agent, that takes advantage of a certain mass for its survival, the simplest term would be \"metabolize\", from the Greek μεταβολή (change, transformation) with the suffix indicating transformation.\n\n\n\n\nWhile metabolizable is a generic term for using something, I have distinguished between two varieties of metabolization. On the one hand, simple catabolization, decomposition into smaller parts for structural reuse, from the Greek καταβολή. Literally, καταβολή means to throw down. This \"throw\" is somewhat strange, but as it is an established term, it is better to use it.\n\n\n\n\nOn the other hand, the use as a mere energy resource, we should use \"trophic\", from τροφή (trophē): \"feeding\" or \"nutrition,\" derived from the verb \"τρέφω\" (trépho), which means \"to feed\" or \"to nourish.\", giving metatrophism to the mere feeding without integrating into the body structure.\n\n\n\n\nFinally, let's see how to adapt this nomenclature to describe the concepts of your research, of things that are beyond the reach of use as energy:\n\n\n\n\n\nParathrophic (parathrophizable) - unsuited to use as food (such as sand).\n\n\n\n\nParametabolic (parametabolizable) - unsuited to decompose to use as structural elements (such as meat for vegetarians).\n\n\n\n\nParacatabolic (paracatabolizable) - unsuited to decompose (such as cellulose for humans).\n\n\n\n\n\nHope this helps with the nomenclature in your research!"},{"context_id":"114902","html":"<p>I assume that, as suggested by the original form of this question and the comments requesting clarification, that the interest is in the energy a carnivorous animal predator can obtain from its killed prey. In this case, the most appropriate terms to describe this would seem to be those employed by nutritionalists. From a perusal of this topic in various Wikipedia articles I find no internationally recognized phrase, but would suggest the following as consistent with the terminology in this field:</p>\n<blockquote>\n<p><strong>Dietary Energy Equivalent</strong></p>\n</blockquote>\n<p>The use of the word “dietary” (or something similar) is important as it makes it clear that one is not concerned with the energy reserves that the living animal deposits for its own use, although these obviously contribute to the ‘dietary energy equivalent’.</p>\n<p>(One of the Wikipedia articles that prompted this suggestion was: <a href=\"https://en.wikipedia.org/wiki/List_of_countries_by_food_energy_intake\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/List_of_countries_by_food_energy_intake</a> — a table heading therein.).</p>\n","text":"I assume that, as suggested by the original form of this question and the comments requesting clarification, that the interest is in the energy a carnivorous animal predator can obtain from its killed prey. In this case, the most appropriate terms to describe this would seem to be those employed by nutritionalists. From a perusal of this topic in various Wikipedia articles I find no internationally recognized phrase, but would suggest the following as consistent with the terminology in this field:\n\n\n\n\n\n\n\nDietary Energy Equivalent\n\n\n\n\n\n\n\nThe use of the word “dietary” (or something similar) is important as it makes it clear that one is not concerned with the energy reserves that the living animal deposits for its own use, although these obviously contribute to the ‘dietary energy equivalent’.\n\n\n\n\n(One of the Wikipedia articles that prompted this suggestion was: https://en.wikipedia.org/wiki/List_of_countries_by_food_energy_intake (https://en.wikipedia.org/wiki/List_of_countries_by_food_energy_intake) — a table heading therein.)."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/List_of_countries_by_food_energy_intake"],"ground_truth_type":"metadata_grounded","group_id":"ecbae1c76abbce9b34d05dc83d25b87f900e01a0980c900867575f0d630d2ea5","hard_case_family":["no_accepted_answer","multiple_answer_candidates"],"id":"RHM-7d2480f625bc563bcc1f5b2d","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":"What's the term for energy that is/isn't usable by an organism?\nEvery healthy organism stores some of its biochemical energy in reserves (e.g. adipose tissue, glycogen), but much of an organism's biochemical energy is bound in ways that aren't normally accessible to it (e.g. protein in muscles or vital organs).\n\n\n\n\nThe latter quantity has some thermodynamic implications. For example, the inaccessible energy can be transferred to a predator if the organism is eaten, and a fetus's inaccessible energy must be obtained from its mother.\n\n\n\n\nTo research these concepts, I'm looking for a term for energy that's accessible by the organism and a term for energy that's not accessible by the organism.\n\n\n\n\nI've searched the web (and StackExchange specifically) for a variety of terms, (e.g. \"expendable\", \"reserved\", \"essential\", \"innate\", etc.) but none of them produced relevant results.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":114897,"score":2},{"answer_id":114902,"score":2}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Blood becomes bright red immediately after the haemoglobin molecules within absorb oxygen from the air, and in air it will maintain this color indefinitely as there is a constant supply of oxygen from the atmosphere and no way to lose it again.</p>\n","answer_id":115043,"answer_text":"Blood becomes bright red immediately after the haemoglobin molecules within absorb oxygen from the air, and in air it will maintain this color indefinitely as there is a constant supply of oxygen from the atmosphere and no way to lose it again.","answer_url":"https://biology.stackexchange.com/a/115043","author":"Sir Thinksalot","author_url":"https://biology.stackexchange.com/users/77161/sir-thinksalot","content_license":"CC BY-SA 4.0","created_at":"2024-07-24T17:17:30+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":115019,"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":"2024-07-24T17:17:30+00:00","raw_file":"raw/codex_api_v1/d27b3e16c09e1430a099a72b8b6dd2aeca3c9f4116d2c57936f72acccbad600e_1790824094070868300_0.json","raw_sha256":"75ae5a3acd2d5ed1aadac056a0d6e41f6b40d63445afc68b8af4b71a0282b5d9","revision_guid":"C5C823C5-F1DD-4584-AEF2-5D534556DD72","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C5C823C5-F1DD-4584-AEF2-5D534556DD72/view-source"}],"score":-1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"DONNELLY BURNS","author_url":"https://biology.stackexchange.com/users/83930/donnelly-burns","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"DONNELLY BURNS","profile_url":"https://biology.stackexchange.com/users/83930/donnelly-burns","user_type":"registered"},"created_at":"2024-07-19T16:00:43+00:00","raw_file":"raw/codex_api_v1/b791c89400945e2056cb034a53d0e8f06f87fe6cbca4604878f1fbb196e52630_1790824084561721000_0.json","raw_sha256":"00e0c2f3f9bf340522a9a667da4c0320086ed2d8ffa96deda47042bc8afd545c","revision_guid":"ED3018B2-3C56-4143-AB53-7F88CB48139E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/ED3018B2-3C56-4143-AB53-7F88CB48139E/view-source"}],"url":"https://biology.stackexchange.com/questions/115019/how-long-does-blood-stay-bright-red-after-being-exposed-to-the-air"},{"author":"Sir Thinksalot","author_url":"https://biology.stackexchange.com/users/77161/sir-thinksalot","content_license":"CC BY-SA 4.0","context_id":"115043","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":"2024-07-24T17:17:30+00:00","raw_file":"raw/codex_api_v1/d27b3e16c09e1430a099a72b8b6dd2aeca3c9f4116d2c57936f72acccbad600e_1790824094070868300_0.json","raw_sha256":"75ae5a3acd2d5ed1aadac056a0d6e41f6b40d63445afc68b8af4b71a0282b5d9","revision_guid":"C5C823C5-F1DD-4584-AEF2-5D534556DD72","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C5C823C5-F1DD-4584-AEF2-5D534556DD72/view-source"}],"url":"https://biology.stackexchange.com/a/115043"}],"contexts":[{"context_id":"question","html":"<p>I am having a hard time finding the answer to this question. There should be a general time like x-minutes. Does it matter if it is in the sunlight? Maybe even an approximate time like between x-minutes and x-minutes.</p>\n","text":"I am having a hard time finding the answer to this question. There should be a general time like x-minutes. Does it matter if it is in the sunlight? Maybe even an approximate time like between x-minutes and x-minutes."},{"context_id":"115043","html":"<p>Blood becomes bright red immediately after the haemoglobin molecules within absorb oxygen from the air, and in air it will maintain this color indefinitely as there is a constant supply of oxygen from the atmosphere and no way to lose it again.</p>\n","text":"Blood becomes bright red immediately after the haemoglobin molecules within absorb oxygen from the air, and in air it will maintain this color indefinitely as there is a constant supply of oxygen from the atmosphere and no way to lose it again."}],"domain":"biology","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"a567ef8e9ab6f5b05458797c75c5b1ac3583270d63e53868fc0f088ac01b5fe0","hard_case_family":["no_accepted_answer"],"id":"RHM-43166138d4ffa6ba294156cb","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":"DONNELLY BURNS","profile_url":"https://biology.stackexchange.com/users/83930/donnelly-burns","user_type":"registered"},"created_at":"2024-07-19T16:00:43+00:00","raw_file":"raw/codex_api_v1/b791c89400945e2056cb034a53d0e8f06f87fe6cbca4604878f1fbb196e52630_1790824084561721000_0.json","raw_sha256":"00e0c2f3f9bf340522a9a667da4c0320086ed2d8ffa96deda47042bc8afd545c","revision_guid":"ED3018B2-3C56-4143-AB53-7F88CB48139E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/ED3018B2-3C56-4143-AB53-7F88CB48139E/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":"115019","source_record_sha256":"c23d1b6bfbb632ed29f90dfc685368023b96317a5967b702a539b8c89db4d68e","source_url":"https://biology.stackexchange.com/questions/115019/how-long-does-blood-stay-bright-red-after-being-exposed-to-the-air","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How long does blood stay bright red after being exposed to the air?\nI am having a hard time finding the answer to this question. There should be a general time like x-minutes. Does it matter if it is in the sunlight? Maybe even an approximate time like between x-minutes and x-minutes.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115043,"score":-1}],"split":"validation"}
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I’ve never seen anything like it! <a href=\"https://i.sstatic.net/ZLfcHFEm.jpg\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/ZLfcHFEm.jpg\" alt=\"large mosquito looking insect in North Carolina July 22, 2024\" /></a></p>\n","text":"This is on top of a refrigerator on my porch in North Carolina about 45 minutes from the coast. I’ve never seen anything like it! [image: large mosquito looking insect in North Carolina July 22, 2024; source: https://i.sstatic.net/ZLfcHFEm.jpg] (https://i.sstatic.net/ZLfcHFEm.jpg)"},{"context_id":"115032","html":"<p>Looks like a <em>Diogmites</em> robber fly, but I'm not great at robber flies so it could be a different species.</p>\n<p><a href=\"https://i.sstatic.net/mL2qKaRD.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/mL2qKaRD.png\" alt=\"Detailed side view of a robber fly\" /></a></p>\n<p>See more images at <a href=\"https://bugguide.net/node/view/4600/bgimage\" rel=\"nofollow noreferrer\">Genus <em>Diogmites</em> - Hanging Thieves</a></p>\n","text":"Looks like a Diogmites robber fly, but I'm not great at robber flies so it could be a different species.\n\n\n\n\n[image: Detailed side view of a robber fly; source: https://i.sstatic.net/mL2qKaRD.png] (https://i.sstatic.net/mL2qKaRD.png)\n\n\n\n\nSee more images at Genus Diogmites - Hanging Thieves (https://bugguide.net/node/view/4600/bgimage)"}],"domain":"biology","external_citations":["https://bugguide.net/node/view/4600/bgimage","https://i.sstatic.net/ZLfcHFEm.jpg","https://i.sstatic.net/mL2qKaRD.png"],"ground_truth_type":"metadata_grounded","group_id":"7e59c0c75bea46d347dec54c5a8264690d68b541f290ac755d49c227e612501c","hard_case_family":["multiple_sources"],"id":"RHM-eeb0b09682df2e430ebe208c","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":"Penny Welch","profile_url":"https://biology.stackexchange.com/users/84126/penny-welch","user_type":"registered"},"created_at":"2024-07-22T17:28:13+00:00","raw_file":"raw/codex_api_v1/d27b3e16c09e1430a099a72b8b6dd2aeca3c9f4116d2c57936f72acccbad600e_1790824094070868300_0.json","raw_sha256":"75ae5a3acd2d5ed1aadac056a0d6e41f6b40d63445afc68b8af4b71a0282b5d9","revision_guid":"EF8762FD-8708-4F92-96EB-5F6E4059B1DA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/EF8762FD-8708-4F92-96EB-5F6E4059B1DA/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-07-23T01:30:44+00:00","raw_file":"raw/codex_api_v1/d27b3e16c09e1430a099a72b8b6dd2aeca3c9f4116d2c57936f72acccbad600e_1790824094070868300_0.json","raw_sha256":"75ae5a3acd2d5ed1aadac056a0d6e41f6b40d63445afc68b8af4b71a0282b5d9","revision_guid":"F083DC52-B09D-4BF8-A6E6-E35F06847C9F","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/F083DC52-B09D-4BF8-A6E6-E35F06847C9F/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":"115030","source_record_sha256":"07bdd62ff7d865ca65c949e4e4e7b409388b6139d3ba10d5620c1251ffabbdf5","source_url":"https://biology.stackexchange.com/questions/115030/what-is-this-huge-mosquito-looking-insect","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What is this huge mosquito looking insect?\nThis is on top of a refrigerator on my porch in North Carolina about 45 minutes from the coast. I’ve never seen anything like it! [image: large mosquito looking insect in North Carolina July 22, 2024; source: https://i.sstatic.net/ZLfcHFEm.jpg] (https://i.sstatic.net/ZLfcHFEm.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115032,"score":24}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<h3>Point #2 is a bit easier to understand (at least to me):</h3>\n<p>Forget about &quot;stretches of DNA&quot;, and focus on individual base pairs. There are around 3 billion (3x10^9) base pairs in a human genome. Each base pair arrived from some ancestor. If we look 1,000 years back, around 40 generations ago (assuming a generation is 25 years), then you have 2^40 ~= 10^12 (1 trillion) ancestors. It's impossible that you inherit at least 1 base pair from each of 1 trillion ancestors, if you only have 3 billion base pairs.</p>\n<h3>About #1:</h3>\n<p>You can get an intuition for it by looking at the &quot;extreme case&quot;. If you assume that you have only 1 chromosome pair, and there are no recombinations whatsoever, only 2 individuals contributed to your genome: the DNA of only 1 grandmother and 1 grandfather would be present in your genome.</p>\n<p>If you allow 1 recombination per generation, then you can have some DNA of all of your grandparents, but you no matter how you recombine the chromosomes, DNA of at least 2 of your great-grandparents will not survive:</p>\n<pre><code>Hypothetical stretches of DNA of great-grandparents that end up in next generation. Each letter represents a &quot;DNA fragment&quot;:\n#1: aaaa\n#2: bbbb\n#3: cccc\n#4: dddd\n#5: eeee\n#6: ffff\n#7: gggg\n#8: ffff\n\nGrandparents:\n#1+#2: aabb\n#3+#4: ccdd\n#5+#6: eeff\n#7+#7: gghh\n\nParents:\n#1+#2+#3+#4: acdd (we're losing one great-grandparent's DNA here, since only 1 recombination is allowed)\n#5+#6+#7+#8: eefh\n\nYou:\nacdd &amp; eefh (but no traces of &quot;b&quot; and &quot;g&quot; left in your genome)\n</code></pre>\n<p>So by allowing 1 recombination per parent, we got 2 extra individuals possibly contributing to the genome with each generation:</p>\n<ul>\n<li>You: max 2 people (your parents)</li>\n<li>Including your parents (N = 1): 2 + 2 = 4</li>\n<li>Including your grandparents (N = 2): 2 + 2 * 2 = 6</li>\n</ul>\n<p>And so on, using 2 + 2*N formula. It works the same way for more recombinations, and more chromosome pairs, but it's a bit more difficult to get the intuition for.</p>\n<h2>About the &quot;guarantee&quot; that some ancestors didn't contribute to your genome:</h2>\n<p>The math works out nicely, but of course no one had 1 trillion distinct ancestors 40 generations ago, because there's some intermarrying going on. To say with certainty that:</p>\n<blockquote>\n<p>Yet even if the genealogies are accurate, Queen Elizabeth II of England almost certainly inherited no DNA from William of Normandy, who conquered England in 1066 and who is believed to be her ancestor twenty-four generations back in time.</p>\n</blockquote>\n<p>we would need to know how often royal families intermarry.</p>\n<p>If we use 1 recombination per generation, and 1 chromosome pair example, and assume that instead of having 4 distinct great-grandmothers, and 4 distinct great-grandfathers, one has in fact 4 distinct great-grandmothers, but only 2 distinct great-grandfathers, that's only 6 distinct ancestors at N=2. Even though 2 + 2*N &lt; 2^(N+1), one could still inherit some DNA from all ancestors in such a case.</p>\n","answer_id":115172,"answer_text":"Point #2 is a bit easier to understand (at least to me):\n\n\n\n\nForget about \"stretches of DNA\", and focus on individual base pairs. There are around 3 billion (3x10^9) base pairs in a human genome. Each base pair arrived from some ancestor. If we look 1,000 years back, around 40 generations ago (assuming a generation is 25 years), then you have 2^40 ~= 10^12 (1 trillion) ancestors. It's impossible that you inherit at least 1 base pair from each of 1 trillion ancestors, if you only have 3 billion base pairs.\n\n\n\n\nAbout #1:\n\n\n\n\nYou can get an intuition for it by looking at the \"extreme case\". If you assume that you have only 1 chromosome pair, and there are no recombinations whatsoever, only 2 individuals contributed to your genome: the DNA of only 1 grandmother and 1 grandfather would be present in your genome.\n\n\n\n\nIf you allow 1 recombination per generation, then you can have some DNA of all of your grandparents, but you no matter how you recombine the chromosomes, DNA of at least 2 of your great-grandparents will not survive:\n\n\n\n\nHypothetical stretches of DNA of great-grandparents that end up in next generation. Each letter represents a \"DNA fragment\":\n#1: aaaa\n#2: bbbb\n#3: cccc\n#4: dddd\n#5: eeee\n#6: ffff\n#7: gggg\n#8: ffff\n\nGrandparents:\n#1+#2: aabb\n#3+#4: ccdd\n#5+#6: eeff\n#7+#7: gghh\n\nParents:\n#1+#2+#3+#4: acdd (we're losing one great-grandparent's DNA here, since only 1 recombination is allowed)\n#5+#6+#7+#8: eefh\n\nYou:\nacdd & eefh (but no traces of \"b\" and \"g\" left in your genome)\n\n\n\n\n\nSo by allowing 1 recombination per parent, we got 2 extra individuals possibly contributing to the genome with each generation:\n\n\n\n\n\nYou: max 2 people (your parents)\n\n\n\n\nIncluding your parents (N = 1): 2 + 2 = 4\n\n\n\n\nIncluding your grandparents (N = 2): 2 + 2 * 2 = 6\n\n\n\n\n\nAnd so on, using 2 + 2*N formula. It works the same way for more recombinations, and more chromosome pairs, but it's a bit more difficult to get the intuition for.\n\n\n\n\nAbout the \"guarantee\" that some ancestors didn't contribute to your genome:\n\n\n\n\nThe math works out nicely, but of course no one had 1 trillion distinct ancestors 40 generations ago, because there's some intermarrying going on. To say with certainty that:\n\n\n\n\n\n\n\nYet even if the genealogies are accurate, Queen Elizabeth II of England almost certainly inherited no DNA from William of Normandy, who conquered England in 1066 and who is believed to be her ancestor twenty-four generations back in time.\n\n\n\n\n\n\n\nwe would need to know how often royal families intermarry.\n\n\n\n\nIf we use 1 recombination per generation, and 1 chromosome pair example, and assume that instead of having 4 distinct great-grandmothers, and 4 distinct great-grandfathers, one has in fact 4 distinct great-grandmothers, but only 2 distinct great-grandfathers, that's only 6 distinct ancestors at N=2. Even though 2 + 2*N < 2^(N+1), one could still inherit some DNA from all ancestors in such a case.","answer_url":"https://biology.stackexchange.com/a/115172","author":"Amade","author_url":"https://biology.stackexchange.com/users/46016/amade","content_license":"CC BY-SA 4.0","created_at":"2024-08-13T10:38:47+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":115164,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Amade","profile_url":"https://biology.stackexchange.com/users/46016/amade","user_type":"registered"},"created_at":"2024-08-13T10:38:47+00:00","raw_file":"raw/codex_api_v1/920b7e5633cbad837bacc37f0887fd883044a5fce63b6e0fa3cc1504390bec54_1790824091899465600_0.json","raw_sha256":"bac2cc1988c9b300f258cae319a9302dc73ac2617e76f7491908df2a0b939d11","revision_guid":"82E991B3-EEC7-4D4C-A30C-C9A5FE9D7983","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/82E991B3-EEC7-4D4C-A30C-C9A5FE9D7983/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"dyxcvi","author_url":"https://biology.stackexchange.com/users/85549/dyxcvi","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"dyxcvi","profile_url":"https://biology.stackexchange.com/users/85549/dyxcvi","user_type":"registered"},"created_at":"2024-08-11T18:21:12+00:00","raw_file":"raw/codex_api_v1/920b7e5633cbad837bacc37f0887fd883044a5fce63b6e0fa3cc1504390bec54_1790824091899465600_0.json","raw_sha256":"bac2cc1988c9b300f258cae319a9302dc73ac2617e76f7491908df2a0b939d11","revision_guid":"0CDBA2F2-566F-4CC5-826A-29AEDD2280FC","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0CDBA2F2-566F-4CC5-826A-29AEDD2280FC/view-source"}],"url":"https://biology.stackexchange.com/questions/115164/contribution-of-ancestors-in-a-persons-genome-david-reichs-who-we-are-and-ho"},{"author":"Amade","author_url":"https://biology.stackexchange.com/users/46016/amade","content_license":"CC BY-SA 4.0","context_id":"115172","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Amade","profile_url":"https://biology.stackexchange.com/users/46016/amade","user_type":"registered"},"created_at":"2024-08-13T10:38:47+00:00","raw_file":"raw/codex_api_v1/920b7e5633cbad837bacc37f0887fd883044a5fce63b6e0fa3cc1504390bec54_1790824091899465600_0.json","raw_sha256":"bac2cc1988c9b300f258cae319a9302dc73ac2617e76f7491908df2a0b939d11","revision_guid":"82E991B3-EEC7-4D4C-A30C-C9A5FE9D7983","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/82E991B3-EEC7-4D4C-A30C-C9A5FE9D7983/view-source"}],"url":"https://biology.stackexchange.com/a/115172"}],"contexts":[{"context_id":"question","html":"<p>I was reading the book &quot;Who we are and how we got here&quot;, written by David Reich. There it has the following explanation:</p>\n<blockquote>\n<p>Females create an average of about forty-five new splices when producing eggs, while males create about twenty-six splices when producing sperm, for a total of about seventy-one new splices per generation. So it is that as we trace each generation back further into the past, a person’s genome is derived from an ever-increasing number of spliced-together ancestral fragments.</p>\n</blockquote>\n<blockquote>\n<p>Any person’s genome is derived from 47 stretches of DNA corresponding to the chromosomes transmitted by mother and father plus mitochondrial DNA. One generation back, a person’s genome is derived from about 118 (47 plus 71) stretches of DNA transmitted by his or her parents. Two generations back, the number of ancestry stretches of DNA grows to around 189 (47 plus 71 plus another 71) transmitted by four grandparents. Look even further back in time, and the additional increase in ancestral stretches of DNA every generation is rapidly overtaken by the doubling of ancestors. Ten generations back, for example, the number of ancestral stretches of DNA is around 757 but the number of ancestors is 1,024, guaranteeing that each person has several hundred ancestors from whom he or she has received no DNA whatsoever. Twenty generations in the past, the number of ancestors is almost a thousand times greater than the number of ancestral stretches of DNA in a person’s genome, so it is a certainty that each person has not inherited any DNA from the great majority of his or her actual ancestors.</p>\n</blockquote>\n<blockquote>\n<p>These calculations mean that a person’s genealogy, as reconstructed from historical records, is not the same as his or her genetic inheritance… Yet even if the genealogies are accurate, Queen Elizabeth II of England almost certainly inherited no DNA from William of Normandy, who conquered England in 1066 and who is believed to be her ancestor twenty-four generations back in time.</p>\n</blockquote>\n<p>So, when he talks about how most of the ancestors of a person are not really genetic ancestors, he justifies that at each generation, 71 new splices are generated on average. I got that those splices are the crossovers between mother's and father's chromosomes in a germ cell. So he calculates that a person's genome is derived from the 47 stretches of DNA (46 chromosomes + mtDNA), plus 71 by generation.</p>\n<p>To be honest, I just didn't get the logic behind it. The 71 new splices are splices for specific chromosomes, or each splice is a different combination for each of the chromosomes present in the germ cells? And since the splices are combinations of the chromosomes, in any scenario, why would be guaranteed that after 10 generations (1024 ancestors and 757 splices), some ancestors don't contribute to a person's genome? I mean, I can get that the chance is reduced, but I don't get the guarantee, since the stretches are random and uneven, parts of the chromosome could still contain DNA from any ancestor (I think!).</p>\n<p>So, to resume:</p>\n<ol>\n<li>Considering N generation, why the calculation for where the genome derives would be 71*N + 47?</li>\n<li>Considering the point 1 is clarified, why would that be a guarantee that some ancestors don't contribute to a person's genome?</li>\n</ol>\n","text":"I was reading the book \"Who we are and how we got here\", written by David Reich. There it has the following explanation:\n\n\n\n\n\n\n\nFemales create an average of about forty-five new splices when producing eggs, while males create about twenty-six splices when producing sperm, for a total of about seventy-one new splices per generation. So it is that as we trace each generation back further into the past, a person’s genome is derived from an ever-increasing number of spliced-together ancestral fragments.\n\n\n\n\n\n\n\n\n\n\nAny person’s genome is derived from 47 stretches of DNA corresponding to the chromosomes transmitted by mother and father plus mitochondrial DNA. One generation back, a person’s genome is derived from about 118 (47 plus 71) stretches of DNA transmitted by his or her parents. Two generations back, the number of ancestry stretches of DNA grows to around 189 (47 plus 71 plus another 71) transmitted by four grandparents. Look even further back in time, and the additional increase in ancestral stretches of DNA every generation is rapidly overtaken by the doubling of ancestors. Ten generations back, for example, the number of ancestral stretches of DNA is around 757 but the number of ancestors is 1,024, guaranteeing that each person has several hundred ancestors from whom he or she has received no DNA whatsoever. Twenty generations in the past, the number of ancestors is almost a thousand times greater than the number of ancestral stretches of DNA in a person’s genome, so it is a certainty that each person has not inherited any DNA from the great majority of his or her actual ancestors.\n\n\n\n\n\n\n\n\n\n\nThese calculations mean that a person’s genealogy, as reconstructed from historical records, is not the same as his or her genetic inheritance… Yet even if the genealogies are accurate, Queen Elizabeth II of England almost certainly inherited no DNA from William of Normandy, who conquered England in 1066 and who is believed to be her ancestor twenty-four generations back in time.\n\n\n\n\n\n\n\nSo, when he talks about how most of the ancestors of a person are not really genetic ancestors, he justifies that at each generation, 71 new splices are generated on average. I got that those splices are the crossovers between mother's and father's chromosomes in a germ cell. So he calculates that a person's genome is derived from the 47 stretches of DNA (46 chromosomes + mtDNA), plus 71 by generation.\n\n\n\n\nTo be honest, I just didn't get the logic behind it. The 71 new splices are splices for specific chromosomes, or each splice is a different combination for each of the chromosomes present in the germ cells? And since the splices are combinations of the chromosomes, in any scenario, why would be guaranteed that after 10 generations (1024 ancestors and 757 splices), some ancestors don't contribute to a person's genome? I mean, I can get that the chance is reduced, but I don't get the guarantee, since the stretches are random and uneven, parts of the chromosome could still contain DNA from any ancestor (I think!).\n\n\n\n\nSo, to resume:\n\n\n\n\n\nConsidering N generation, why the calculation for where the genome derives would be 71*N + 47?\n\n\n\n\nConsidering the point 1 is clarified, why would that be a guarantee that some ancestors don't contribute to a person's genome?"},{"context_id":"115172","html":"<h3>Point #2 is a bit easier to understand (at least to me):</h3>\n<p>Forget about &quot;stretches of DNA&quot;, and focus on individual base pairs. There are around 3 billion (3x10^9) base pairs in a human genome. Each base pair arrived from some ancestor. If we look 1,000 years back, around 40 generations ago (assuming a generation is 25 years), then you have 2^40 ~= 10^12 (1 trillion) ancestors. It's impossible that you inherit at least 1 base pair from each of 1 trillion ancestors, if you only have 3 billion base pairs.</p>\n<h3>About #1:</h3>\n<p>You can get an intuition for it by looking at the &quot;extreme case&quot;. If you assume that you have only 1 chromosome pair, and there are no recombinations whatsoever, only 2 individuals contributed to your genome: the DNA of only 1 grandmother and 1 grandfather would be present in your genome.</p>\n<p>If you allow 1 recombination per generation, then you can have some DNA of all of your grandparents, but you no matter how you recombine the chromosomes, DNA of at least 2 of your great-grandparents will not survive:</p>\n<pre><code>Hypothetical stretches of DNA of great-grandparents that end up in next generation. Each letter represents a &quot;DNA fragment&quot;:\n#1: aaaa\n#2: bbbb\n#3: cccc\n#4: dddd\n#5: eeee\n#6: ffff\n#7: gggg\n#8: ffff\n\nGrandparents:\n#1+#2: aabb\n#3+#4: ccdd\n#5+#6: eeff\n#7+#7: gghh\n\nParents:\n#1+#2+#3+#4: acdd (we're losing one great-grandparent's DNA here, since only 1 recombination is allowed)\n#5+#6+#7+#8: eefh\n\nYou:\nacdd &amp; eefh (but no traces of &quot;b&quot; and &quot;g&quot; left in your genome)\n</code></pre>\n<p>So by allowing 1 recombination per parent, we got 2 extra individuals possibly contributing to the genome with each generation:</p>\n<ul>\n<li>You: max 2 people (your parents)</li>\n<li>Including your parents (N = 1): 2 + 2 = 4</li>\n<li>Including your grandparents (N = 2): 2 + 2 * 2 = 6</li>\n</ul>\n<p>And so on, using 2 + 2*N formula. It works the same way for more recombinations, and more chromosome pairs, but it's a bit more difficult to get the intuition for.</p>\n<h2>About the &quot;guarantee&quot; that some ancestors didn't contribute to your genome:</h2>\n<p>The math works out nicely, but of course no one had 1 trillion distinct ancestors 40 generations ago, because there's some intermarrying going on. To say with certainty that:</p>\n<blockquote>\n<p>Yet even if the genealogies are accurate, Queen Elizabeth II of England almost certainly inherited no DNA from William of Normandy, who conquered England in 1066 and who is believed to be her ancestor twenty-four generations back in time.</p>\n</blockquote>\n<p>we would need to know how often royal families intermarry.</p>\n<p>If we use 1 recombination per generation, and 1 chromosome pair example, and assume that instead of having 4 distinct great-grandmothers, and 4 distinct great-grandfathers, one has in fact 4 distinct great-grandmothers, but only 2 distinct great-grandfathers, that's only 6 distinct ancestors at N=2. Even though 2 + 2*N &lt; 2^(N+1), one could still inherit some DNA from all ancestors in such a case.</p>\n","text":"Point #2 is a bit easier to understand (at least to me):\n\n\n\n\nForget about \"stretches of DNA\", and focus on individual base pairs. There are around 3 billion (3x10^9) base pairs in a human genome. Each base pair arrived from some ancestor. If we look 1,000 years back, around 40 generations ago (assuming a generation is 25 years), then you have 2^40 ~= 10^12 (1 trillion) ancestors. It's impossible that you inherit at least 1 base pair from each of 1 trillion ancestors, if you only have 3 billion base pairs.\n\n\n\n\nAbout #1:\n\n\n\n\nYou can get an intuition for it by looking at the \"extreme case\". If you assume that you have only 1 chromosome pair, and there are no recombinations whatsoever, only 2 individuals contributed to your genome: the DNA of only 1 grandmother and 1 grandfather would be present in your genome.\n\n\n\n\nIf you allow 1 recombination per generation, then you can have some DNA of all of your grandparents, but you no matter how you recombine the chromosomes, DNA of at least 2 of your great-grandparents will not survive:\n\n\n\n\nHypothetical stretches of DNA of great-grandparents that end up in next generation. Each letter represents a \"DNA fragment\":\n#1: aaaa\n#2: bbbb\n#3: cccc\n#4: dddd\n#5: eeee\n#6: ffff\n#7: gggg\n#8: ffff\n\nGrandparents:\n#1+#2: aabb\n#3+#4: ccdd\n#5+#6: eeff\n#7+#7: gghh\n\nParents:\n#1+#2+#3+#4: acdd (we're losing one great-grandparent's DNA here, since only 1 recombination is allowed)\n#5+#6+#7+#8: eefh\n\nYou:\nacdd & eefh (but no traces of \"b\" and \"g\" left in your genome)\n\n\n\n\n\nSo by allowing 1 recombination per parent, we got 2 extra individuals possibly contributing to the genome with each generation:\n\n\n\n\n\nYou: max 2 people (your parents)\n\n\n\n\nIncluding your parents (N = 1): 2 + 2 = 4\n\n\n\n\nIncluding your grandparents (N = 2): 2 + 2 * 2 = 6\n\n\n\n\n\nAnd so on, using 2 + 2*N formula. It works the same way for more recombinations, and more chromosome pairs, but it's a bit more difficult to get the intuition for.\n\n\n\n\nAbout the \"guarantee\" that some ancestors didn't contribute to your genome:\n\n\n\n\nThe math works out nicely, but of course no one had 1 trillion distinct ancestors 40 generations ago, because there's some intermarrying going on. To say with certainty that:\n\n\n\n\n\n\n\nYet even if the genealogies are accurate, Queen Elizabeth II of England almost certainly inherited no DNA from William of Normandy, who conquered England in 1066 and who is believed to be her ancestor twenty-four generations back in time.\n\n\n\n\n\n\n\nwe would need to know how often royal families intermarry.\n\n\n\n\nIf we use 1 recombination per generation, and 1 chromosome pair example, and assume that instead of having 4 distinct great-grandmothers, and 4 distinct great-grandfathers, one has in fact 4 distinct great-grandmothers, but only 2 distinct great-grandfathers, that's only 6 distinct ancestors at N=2. Even though 2 + 2*N < 2^(N+1), one could still inherit some DNA from all ancestors in such a case."}],"domain":"biology","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"7375c683e704d7f6fd465e5591bb80d3a3bd9ee651094815e59413363fa6fa18","hard_case_family":["no_accepted_answer"],"id":"RHM-67ad7fe626871ff8797bc651","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":"dyxcvi","profile_url":"https://biology.stackexchange.com/users/85549/dyxcvi","user_type":"registered"},"created_at":"2024-08-11T18:21:12+00:00","raw_file":"raw/codex_api_v1/920b7e5633cbad837bacc37f0887fd883044a5fce63b6e0fa3cc1504390bec54_1790824091899465600_0.json","raw_sha256":"bac2cc1988c9b300f258cae319a9302dc73ac2617e76f7491908df2a0b939d11","revision_guid":"0CDBA2F2-566F-4CC5-826A-29AEDD2280FC","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0CDBA2F2-566F-4CC5-826A-29AEDD2280FC/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":"115164","source_record_sha256":"582335db136061f240dee1bfb03f692bd3110432b07724fa108d5b4c29b564c6","source_url":"https://biology.stackexchange.com/questions/115164/contribution-of-ancestors-in-a-persons-genome-david-reichs-who-we-are-and-ho","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Contribution of ancestors in a person's genome (David Reich's \"Who we are and how we got here\")\nI was reading the book \"Who we are and how we got here\", written by David Reich. There it has the following explanation:\n\n\n\n\n\n\n\nFemales create an average of about forty-five new splices when producing eggs, while males create about twenty-six splices when producing sperm, for a total of about seventy-one new splices per generation. So it is that as we trace each generation back further into the past, a person’s genome is derived from an ever-increasing number of spliced-together ancestral fragments.\n\n\n\n\n\n\n\n\n\n\nAny person’s genome is derived from 47 stretches of DNA corresponding to the chromosomes transmitted by mother and father plus mitochondrial DNA. One generation back, a person’s genome is derived from about 118 (47 plus 71) stretches of DNA transmitted by his or her parents. Two generations back, the number of ancestry stretches of DNA grows to around 189 (47 plus 71 plus another 71) transmitted by four grandparents. Look even further back in time, and the additional increase in ancestral stretches of DNA every generation is rapidly overtaken by the doubling of ancestors. Ten generations back, for example, the number of ancestral stretches of DNA is around 757 but the number of ancestors is 1,024, guaranteeing that each person has several hundred ancestors from whom he or she has received no DNA whatsoever. Twenty generations in the past, the number of ancestors is almost a thousand times greater than the number of ancestral stretches of DNA in a person’s genome, so it is a certainty that each person has not inherited any DNA from the great majority of his or her actual ancestors.\n\n\n\n\n\n\n\n\n\n\nThese calculations mean that a person’s genealogy, as reconstructed from historical records, is not the same as his or her genetic inheritance… Yet even if the genealogies are accurate, Queen Elizabeth II of England almost certainly inherited no DNA from William of Normandy, who conquered England in 1066 and who is believed to be her ancestor twenty-four generations back in time.\n\n\n\n\n\n\n\nSo, when he talks about how most of the ancestors of a person are not really genetic ancestors, he justifies that at each generation, 71 new splices are generated on average. I got that those splices are the crossovers between mother's and father's chromosomes in a germ cell. So he calculates that a person's genome is derived from the 47 stretches of DNA (46 chromosomes + mtDNA), plus 71 by generation.\n\n\n\n\nTo be honest, I just didn't get the logic behind it. The 71 new splices are splices for specific chromosomes, or each splice is a different combination for each of the chromosomes present in the germ cells? And since the splices are combinations of the chromosomes, in any scenario, why would be guaranteed that after 10 generations (1024 ancestors and 757 splices), some ancestors don't contribute to a person's genome? I mean, I can get that the chance is reduced, but I don't get the guarantee, since the stretches are random and uneven, parts of the chromosome could still contain DNA from any ancestor (I think!).\n\n\n\n\nSo, to resume:\n\n\n\n\n\nConsidering N generation, why the calculation for where the genome derives would be 71*N + 47?\n\n\n\n\nConsidering the point 1 is clarified, why would that be a guarantee that some ancestors don't contribute to a person's genome?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115172,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Any sex determination here would be speculation.</p>\n<p><a href=\"https://www.butterfliesandmoths.org/species/Pyrgus-albescens\" rel=\"nofollow noreferrer\">Butterflies and Moths of North America</a> has this to say about <em><a href=\"https://en.wikipedia.org/wiki/Burnsius_albezens\" rel=\"nofollow noreferrer\">Burnsius albezens</a></em>. Note the bolded last sentence:</p>\n<blockquote>\n<p>Identification: Paler than Pyrgus communis. Male often has complete black checks in wing fringes. Upperside of male is blue-gray; female is black. Both sexes have large white spots which form median bands across both wings. Male has a costal fold enclosing scent scales on the upperside of the forewing. Underside is dull white with dark gray bands. <strong>Positive identification can be made only by dissection and scrutiny of the male genitalia</strong>.</p>\n</blockquote>\n","answer_id":115178,"answer_text":"Any sex determination here would be speculation.\n\n\n\n\nButterflies and Moths of North America (https://www.butterfliesandmoths.org/species/Pyrgus-albescens) has this to say about Burnsius albezens (https://en.wikipedia.org/wiki/Burnsius_albezens). Note the bolded last sentence:\n\n\n\n\n\n\n\nIdentification: Paler than Pyrgus communis. Male often has complete black checks in wing fringes. Upperside of male is blue-gray; female is black. Both sexes have large white spots which form median bands across both wings. Male has a costal fold enclosing scent scales on the upperside of the forewing. Underside is dull white with dark gray bands. Positive identification can be made only by dissection and scrutiny of the male genitalia.","answer_url":"https://biology.stackexchange.com/a/115178","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2024-08-13T21:24:26+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":115177,"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":"2024-08-13T21:24:26+00:00","raw_file":"raw/codex_api_v1/920b7e5633cbad837bacc37f0887fd883044a5fce63b6e0fa3cc1504390bec54_1790824091899465600_0.json","raw_sha256":"bac2cc1988c9b300f258cae319a9302dc73ac2617e76f7491908df2a0b939d11","revision_guid":"E9314187-71B0-4207-9358-1D9435F4B5A5","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E9314187-71B0-4207-9358-1D9435F4B5A5/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Brandon","author_url":"https://biology.stackexchange.com/users/85706/brandon","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Brandon","profile_url":"https://biology.stackexchange.com/users/85706/brandon","user_type":"registered"},"created_at":"2024-08-13T21:07:59+00:00","raw_file":"raw/codex_api_v1/920b7e5633cbad837bacc37f0887fd883044a5fce63b6e0fa3cc1504390bec54_1790824091899465600_0.json","raw_sha256":"bac2cc1988c9b300f258cae319a9302dc73ac2617e76f7491908df2a0b939d11","revision_guid":"D16240F7-AD7D-4EE6-8061-69667482A965","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D16240F7-AD7D-4EE6-8061-69667482A965/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":"2024-08-14T13:03:22+00:00","raw_file":"raw/codex_api_v1/920b7e5633cbad837bacc37f0887fd883044a5fce63b6e0fa3cc1504390bec54_1790824091899465600_0.json","raw_sha256":"bac2cc1988c9b300f258cae319a9302dc73ac2617e76f7491908df2a0b939d11","revision_guid":"6C980D3D-F7ED-401F-B344-6359BA719591","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/6C980D3D-F7ED-401F-B344-6359BA719591/view-source"}],"url":"https://biology.stackexchange.com/questions/115177/sex-identification-of-two-white-checkered-skipper-butterflies"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"115178","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":"2024-08-13T21:24:26+00:00","raw_file":"raw/codex_api_v1/920b7e5633cbad837bacc37f0887fd883044a5fce63b6e0fa3cc1504390bec54_1790824091899465600_0.json","raw_sha256":"bac2cc1988c9b300f258cae319a9302dc73ac2617e76f7491908df2a0b939d11","revision_guid":"E9314187-71B0-4207-9358-1D9435F4B5A5","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E9314187-71B0-4207-9358-1D9435F4B5A5/view-source"}],"url":"https://biology.stackexchange.com/a/115178"}],"contexts":[{"context_id":"question","html":"<p>I have two white checkered skippers and ik for a fact one is a female(at least i think) but im not sure abt the other one? Can some one tell which is which or if there the same sex? One butterfly has a bulkier body with larger wings and wingspan with a smaller head which I believe that one's a female the other one has a smaller body smaller Wings in a bigger head which I believe to be a male but I'm not sure can somebody help me sorry about the picture quality my phone takes bad pictures<a href=\"https://i.sstatic.net/wjZnXEVY.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/wjZnXEVY.jpg\" alt=\"enter image description here\" /></a><a href=\"https://i.sstatic.net/2fawrthM.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/2fawrthM.jpg\" alt=\"enter image description here\" /></a></p>\n","text":"I have two white checkered skippers and ik for a fact one is a female(at least i think) but im not sure abt the other one? Can some one tell which is which or if there the same sex? One butterfly has a bulkier body with larger wings and wingspan with a smaller head which I believe that one's a female the other one has a smaller body smaller Wings in a bigger head which I believe to be a male but I'm not sure can somebody help me sorry about the picture quality my phone takes bad pictures[image: enter image description here; source: https://i.sstatic.net/wjZnXEVY.jpg] (https://i.sstatic.net/wjZnXEVY.jpg)[image: enter image description here; source: https://i.sstatic.net/2fawrthM.jpg] (https://i.sstatic.net/2fawrthM.jpg)"},{"context_id":"115178","html":"<p>Any sex determination here would be speculation.</p>\n<p><a href=\"https://www.butterfliesandmoths.org/species/Pyrgus-albescens\" rel=\"nofollow noreferrer\">Butterflies and Moths of North America</a> has this to say about <em><a href=\"https://en.wikipedia.org/wiki/Burnsius_albezens\" rel=\"nofollow noreferrer\">Burnsius albezens</a></em>. Note the bolded last sentence:</p>\n<blockquote>\n<p>Identification: Paler than Pyrgus communis. Male often has complete black checks in wing fringes. Upperside of male is blue-gray; female is black. Both sexes have large white spots which form median bands across both wings. Male has a costal fold enclosing scent scales on the upperside of the forewing. Underside is dull white with dark gray bands. <strong>Positive identification can be made only by dissection and scrutiny of the male genitalia</strong>.</p>\n</blockquote>\n","text":"Any sex determination here would be speculation.\n\n\n\n\nButterflies and Moths of North America (https://www.butterfliesandmoths.org/species/Pyrgus-albescens) has this to say about Burnsius albezens (https://en.wikipedia.org/wiki/Burnsius_albezens). Note the bolded last sentence:\n\n\n\n\n\n\n\nIdentification: Paler than Pyrgus communis. Male often has complete black checks in wing fringes. Upperside of male is blue-gray; female is black. Both sexes have large white spots which form median bands across both wings. Male has a costal fold enclosing scent scales on the upperside of the forewing. Underside is dull white with dark gray bands. Positive identification can be made only by dissection and scrutiny of the male genitalia."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Burnsius_albezens","https://i.sstatic.net/2fawrthM.jpg","https://i.sstatic.net/wjZnXEVY.jpg","https://www.butterfliesandmoths.org/species/Pyrgus-albescens"],"ground_truth_type":"metadata_grounded","group_id":"3c605f2748ab6c58cc0d3731fda657b3b271e50a6181d81871b2809d5f290dc7","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-46bce20f61104b4d2be5a483","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":"Brandon","profile_url":"https://biology.stackexchange.com/users/85706/brandon","user_type":"registered"},"created_at":"2024-08-13T21:07:59+00:00","raw_file":"raw/codex_api_v1/920b7e5633cbad837bacc37f0887fd883044a5fce63b6e0fa3cc1504390bec54_1790824091899465600_0.json","raw_sha256":"bac2cc1988c9b300f258cae319a9302dc73ac2617e76f7491908df2a0b939d11","revision_guid":"D16240F7-AD7D-4EE6-8061-69667482A965","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D16240F7-AD7D-4EE6-8061-69667482A965/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":"2024-08-14T13:03:22+00:00","raw_file":"raw/codex_api_v1/920b7e5633cbad837bacc37f0887fd883044a5fce63b6e0fa3cc1504390bec54_1790824091899465600_0.json","raw_sha256":"bac2cc1988c9b300f258cae319a9302dc73ac2617e76f7491908df2a0b939d11","revision_guid":"6C980D3D-F7ED-401F-B344-6359BA719591","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/6C980D3D-F7ED-401F-B344-6359BA719591/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":"115177","source_record_sha256":"96dc0d2cde3c9a64d3a4a9d0c8edd9729069af317f843549d4472a0adb455217","source_url":"https://biology.stackexchange.com/questions/115177/sex-identification-of-two-white-checkered-skipper-butterflies","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Sex identification of two white checkered Skipper butterflies\nI have two white checkered skippers and ik for a fact one is a female(at least i think) but im not sure abt the other one? Can some one tell which is which or if there the same sex? One butterfly has a bulkier body with larger wings and wingspan with a smaller head which I believe that one's a female the other one has a smaller body smaller Wings in a bigger head which I believe to be a male but I'm not sure can somebody help me sorry about the picture quality my phone takes bad pictures[image: enter image description here; source: https://i.sstatic.net/wjZnXEVY.jpg] (https://i.sstatic.net/wjZnXEVY.jpg)[image: enter image description here; source: https://i.sstatic.net/2fawrthM.jpg] (https://i.sstatic.net/2fawrthM.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115178,"score":3}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The insertions don't count towards the annealing temperature, at least for the first and most critical cycle of the PCR. After the first cycle, where the bases get incorporated into the product, for the second and subsequent cycles these bases should matter, but the primers should match the target 100% (because of the incorporated primer) and a lack of efficiency caused by the high Tm doesn't matter because of the binding specificity.</p>\n<p>Remove the non-annealing insertion bases before calculating the annealing temp.</p>\n","answer_id":115261,"answer_text":"The insertions don't count towards the annealing temperature, at least for the first and most critical cycle of the PCR. After the first cycle, where the bases get incorporated into the product, for the second and subsequent cycles these bases should matter, but the primers should match the target 100% (because of the incorporated primer) and a lack of efficiency caused by the high Tm doesn't matter because of the binding specificity.\n\n\n\n\nRemove the non-annealing insertion bases before calculating the annealing temp.","answer_url":"https://biology.stackexchange.com/a/115261","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2024-08-27T02:11:53+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":115260,"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":"2024-08-27T02:11:53+00:00","raw_file":"raw/codex_api_v1/4bbe364c2c0b55919fce726e178cdb32ab306e340604f39e109365ddf10bf33a_1790824101438704600_0.json","raw_sha256":"543547c61ef58ea6aa21585687a86f5656890613501e14bb9bcf2c66b6831fb2","revision_guid":"5E260EA5-94E1-456C-9C80-4A9CE3E11B6E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5E260EA5-94E1-456C-9C80-4A9CE3E11B6E/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"user48660","author_url":"https://biology.stackexchange.com/users/86633/user48660","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user48660","profile_url":"https://biology.stackexchange.com/users/86633/user48660","user_type":"registered"},"created_at":"2024-08-26T23:02:13+00:00","raw_file":"raw/codex_api_v1/4bbe364c2c0b55919fce726e178cdb32ab306e340604f39e109365ddf10bf33a_1790824101438704600_0.json","raw_sha256":"543547c61ef58ea6aa21585687a86f5656890613501e14bb9bcf2c66b6831fb2","revision_guid":"3B2B7085-0969-44CB-8B7A-B960C197DC43","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3B2B7085-0969-44CB-8B7A-B960C197DC43/view-source"}],"url":"https://biology.stackexchange.com/questions/115260/are-the-tm-and-ta-values-of-pcr-primers-based-on-entire-sequences-or-just-anneal"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"115261","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":"2024-08-27T02:11:53+00:00","raw_file":"raw/codex_api_v1/4bbe364c2c0b55919fce726e178cdb32ab306e340604f39e109365ddf10bf33a_1790824101438704600_0.json","raw_sha256":"543547c61ef58ea6aa21585687a86f5656890613501e14bb9bcf2c66b6831fb2","revision_guid":"5E260EA5-94E1-456C-9C80-4A9CE3E11B6E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5E260EA5-94E1-456C-9C80-4A9CE3E11B6E/view-source"}],"url":"https://biology.stackexchange.com/a/115261"}],"contexts":[{"context_id":"question","html":"<p>I am trying to use the Q5 mutagenesis kit to produce an indel mutation in my protein.</p>\n<p>I used the NEB BaseChanger interface to design my primers (<a href=\"https://nebasechanger.neb.com/\" rel=\"nofollow noreferrer\">https://nebasechanger.neb.com/</a>). However, I am confused about the way NEB BaseChanger calculates the Tm and Ta of these primers. When it generates the primers, it indicates the Tm and Ta are in the low 60s. However, when I put the same primers into the NEB Tm calculator, I found that their Tm is in the high 80s.</p>\n<p>I suspect this is because the NEB BaseChanger is not counting non-annealing bases (bases that encode the inserted amino acids). I am wondering which website to trust - I understand that if the Tm and Ta are what the NEB Tm calculator suggests they are, my PCR will likely not work. But if the Tm and Ta are what the BaseChanger suggests, the reaction should run.</p>\n<p>Thanks for any and all advice!</p>\n","text":"I am trying to use the Q5 mutagenesis kit to produce an indel mutation in my protein.\n\n\n\n\nI used the NEB BaseChanger interface to design my primers (https://nebasechanger.neb.com/ (https://nebasechanger.neb.com/)). However, I am confused about the way NEB BaseChanger calculates the Tm and Ta of these primers. When it generates the primers, it indicates the Tm and Ta are in the low 60s. However, when I put the same primers into the NEB Tm calculator, I found that their Tm is in the high 80s.\n\n\n\n\nI suspect this is because the NEB BaseChanger is not counting non-annealing bases (bases that encode the inserted amino acids). I am wondering which website to trust - I understand that if the Tm and Ta are what the NEB Tm calculator suggests they are, my PCR will likely not work. But if the Tm and Ta are what the BaseChanger suggests, the reaction should run.\n\n\n\n\nThanks for any and all advice!"},{"context_id":"115261","html":"<p>The insertions don't count towards the annealing temperature, at least for the first and most critical cycle of the PCR. After the first cycle, where the bases get incorporated into the product, for the second and subsequent cycles these bases should matter, but the primers should match the target 100% (because of the incorporated primer) and a lack of efficiency caused by the high Tm doesn't matter because of the binding specificity.</p>\n<p>Remove the non-annealing insertion bases before calculating the annealing temp.</p>\n","text":"The insertions don't count towards the annealing temperature, at least for the first and most critical cycle of the PCR. After the first cycle, where the bases get incorporated into the product, for the second and subsequent cycles these bases should matter, but the primers should match the target 100% (because of the incorporated primer) and a lack of efficiency caused by the high Tm doesn't matter because of the binding specificity.\n\n\n\n\nRemove the non-annealing insertion bases before calculating the annealing temp."}],"domain":"biology","external_citations":["https://nebasechanger.neb.com/"],"ground_truth_type":"metadata_grounded","group_id":"30af6fbcd4691d72fdb8932728509c1798ebebfb70e2aedb4ab91003fe92740f","hard_case_family":["no_accepted_answer"],"id":"RHM-d40a24d1059458f06b6a9f45","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":"user48660","profile_url":"https://biology.stackexchange.com/users/86633/user48660","user_type":"registered"},"created_at":"2024-08-26T23:02:13+00:00","raw_file":"raw/codex_api_v1/4bbe364c2c0b55919fce726e178cdb32ab306e340604f39e109365ddf10bf33a_1790824101438704600_0.json","raw_sha256":"543547c61ef58ea6aa21585687a86f5656890613501e14bb9bcf2c66b6831fb2","revision_guid":"3B2B7085-0969-44CB-8B7A-B960C197DC43","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3B2B7085-0969-44CB-8B7A-B960C197DC43/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":"115260","source_record_sha256":"efec53e9a6dcb945bb8777a921a0c1d12a6c7381900b4be50eed988d2eddebc7","source_url":"https://biology.stackexchange.com/questions/115260/are-the-tm-and-ta-values-of-pcr-primers-based-on-entire-sequences-or-just-anneal","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Are the Tm and Ta values of PCR primers based on entire sequences or just annealing portions?\nI am trying to use the Q5 mutagenesis kit to produce an indel mutation in my protein.\n\n\n\n\nI used the NEB BaseChanger interface to design my primers (https://nebasechanger.neb.com/ (https://nebasechanger.neb.com/)). However, I am confused about the way NEB BaseChanger calculates the Tm and Ta of these primers. When it generates the primers, it indicates the Tm and Ta are in the low 60s. However, when I put the same primers into the NEB Tm calculator, I found that their Tm is in the high 80s.\n\n\n\n\nI suspect this is because the NEB BaseChanger is not counting non-annealing bases (bases that encode the inserted amino acids). I am wondering which website to trust - I understand that if the Tm and Ta are what the NEB Tm calculator suggests they are, my PCR will likely not work. But if the Tm and Ta are what the BaseChanger suggests, the reaction should run.\n\n\n\n\nThanks for any and all advice!","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115261,"score":2}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":115268,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I've contacted <a href=\"https://en.butantan.gov.br/\" rel=\"nofollow noreferrer\">Instituto Butantan</a> (main producer of antivenoms and antitoxins in Brazil), inquired about this specimen and forwarded these photos.</p>\n<p>They have confirmed it is <em>Nesticodes rufipes</em>.</p>\n","answer_id":115268,"answer_text":"I've contacted Instituto Butantan (https://en.butantan.gov.br/) (main producer of antivenoms and antitoxins in Brazil), inquired about this specimen and forwarded these photos.\n\n\n\n\nThey have confirmed it is Nesticodes rufipes.","answer_url":"https://biology.stackexchange.com/a/115268","author":"André Carini","author_url":"https://biology.stackexchange.com/users/86723/andr%c3%a9-carini","content_license":"CC BY-SA 4.0","created_at":"2024-08-29T01:57:49+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":115264,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"André Carini","profile_url":"https://biology.stackexchange.com/users/86723/andr%c3%a9-carini","user_type":"registered"},"created_at":"2024-08-29T01:57:49+00:00","raw_file":"raw/codex_api_v1/cedb71cd945e8f995b79cadd8e6718011c2863cc935a3a1410ded32d454feeef_1790824099288070500_0.json","raw_sha256":"6569d2607abeaad3ebe6e725128dec16202338bf9cbd6c8013a07c01af6e0905","revision_guid":"DB2EFC2C-17FF-4DF2-BC07-548D367694AD","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DB2EFC2C-17FF-4DF2-BC07-548D367694AD/view-source"}],"score":2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"André Carini","author_url":"https://biology.stackexchange.com/users/86723/andr%c3%a9-carini","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"André Carini","profile_url":"https://biology.stackexchange.com/users/86723/andr%c3%a9-carini","user_type":"registered"},"created_at":"2024-08-28T01:13:32+00:00","raw_file":"raw/codex_api_v1/cedb71cd945e8f995b79cadd8e6718011c2863cc935a3a1410ded32d454feeef_1790824099288070500_0.json","raw_sha256":"6569d2607abeaad3ebe6e725128dec16202338bf9cbd6c8013a07c01af6e0905","revision_guid":"C8B4F29E-67A7-46DB-9402-D8680258CB9A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C8B4F29E-67A7-46DB-9402-D8680258CB9A/view-source"}],"url":"https://biology.stackexchange.com/questions/115264/spider-identification-nesticodes-rufipes-or-loxosceles-gaucho-south-of-brazil"},{"author":"André Carini","author_url":"https://biology.stackexchange.com/users/86723/andr%c3%a9-carini","content_license":"CC BY-SA 4.0","context_id":"115268","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"André Carini","profile_url":"https://biology.stackexchange.com/users/86723/andr%c3%a9-carini","user_type":"registered"},"created_at":"2024-08-29T01:57:49+00:00","raw_file":"raw/codex_api_v1/cedb71cd945e8f995b79cadd8e6718011c2863cc935a3a1410ded32d454feeef_1790824099288070500_0.json","raw_sha256":"6569d2607abeaad3ebe6e725128dec16202338bf9cbd6c8013a07c01af6e0905","revision_guid":"DB2EFC2C-17FF-4DF2-BC07-548D367694AD","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DB2EFC2C-17FF-4DF2-BC07-548D367694AD/view-source"}],"url":"https://biology.stackexchange.com/a/115268"}],"contexts":[{"context_id":"question","html":"<p>I need help identifying a spider species frequently encountered in my apartment in Porto Alegre, southern Brazil.</p>\n<ul>\n<li>Habitat: Found indoors on ceiling/wall corners, door frames, and behind paintings.</li>\n<li>Web pattern: No discernible regular web pattern observed.</li>\n<li>Size: Body length approximately 5mm, excluding legs.</li>\n<li>Geographic location: Porto Alegre, Rio Grande do Sul, Brazil.</li>\n<li>Behaviour and other notes: I've found them on any season, any time of day, and not hidden at all (ceiling/wall corners). They are usually standing still, and when prodded with a stick either curl up into a ball or very quickly draw a string of web and descend. I've seen much smaller ones (spiderlings?) whose body length is 1mm or less.</li>\n</ul>\n<p>I think might be either of these:</p>\n<ol>\n<li><em>Nesticodes rufipes</em></li>\n<li><em>Loxosceles gaucho</em></li>\n</ol>\n<p>I took some photos to the best of my ability/equipment, all of them are the same specimen but under different lighting and angles:</p>\n<p><a href=\"https://i.sstatic.net/JltcmY2C.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/JltcmY2C.jpg\" alt=\"Photo 1\" /></a></p>\n<p><a href=\"https://i.sstatic.net/3GE0aN5l.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/3GE0aN5l.jpg\" alt=\"Photo 2\" /></a></p>\n<p><a href=\"https://i.sstatic.net/B6aQK8zu.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/B6aQK8zu.jpg\" alt=\"Photo 3\" /></a></p>\n<p><a href=\"https://i.sstatic.net/1blaPl3L.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/1blaPl3L.jpg\" alt=\"Photo 4\" /></a></p>\n<p><a href=\"https://i.sstatic.net/T9ANM3Jj.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/T9ANM3Jj.jpg\" alt=\"Photo 5\" /></a></p>\n","text":"I need help identifying a spider species frequently encountered in my apartment in Porto Alegre, southern Brazil.\n\n\n\n\n\nHabitat: Found indoors on ceiling/wall corners, door frames, and behind paintings.\n\n\n\n\nWeb pattern: No discernible regular web pattern observed.\n\n\n\n\nSize: Body length approximately 5mm, excluding legs.\n\n\n\n\nGeographic location: Porto Alegre, Rio Grande do Sul, Brazil.\n\n\n\n\nBehaviour and other notes: I've found them on any season, any time of day, and not hidden at all (ceiling/wall corners). They are usually standing still, and when prodded with a stick either curl up into a ball or very quickly draw a string of web and descend. I've seen much smaller ones (spiderlings?) whose body length is 1mm or less.\n\n\n\n\n\nI think might be either of these:\n\n\n\n\n\nNesticodes rufipes\n\n\n\n\nLoxosceles gaucho\n\n\n\n\n\nI took some photos to the best of my ability/equipment, all of them are the same specimen but under different lighting and angles:\n\n\n\n\n[image: Photo 1; source: https://i.sstatic.net/JltcmY2C.jpg] (https://i.sstatic.net/JltcmY2C.jpg)\n\n\n\n\n[image: Photo 2; source: https://i.sstatic.net/3GE0aN5l.jpg] (https://i.sstatic.net/3GE0aN5l.jpg)\n\n\n\n\n[image: Photo 3; source: https://i.sstatic.net/B6aQK8zu.jpg] (https://i.sstatic.net/B6aQK8zu.jpg)\n\n\n\n\n[image: Photo 4; source: https://i.sstatic.net/1blaPl3L.jpg] (https://i.sstatic.net/1blaPl3L.jpg)\n\n\n\n\n[image: Photo 5; source: https://i.sstatic.net/T9ANM3Jj.jpg] (https://i.sstatic.net/T9ANM3Jj.jpg)"},{"context_id":"115268","html":"<p>I've contacted <a href=\"https://en.butantan.gov.br/\" rel=\"nofollow noreferrer\">Instituto Butantan</a> (main producer of antivenoms and antitoxins in Brazil), inquired about this specimen and forwarded these photos.</p>\n<p>They have confirmed it is <em>Nesticodes rufipes</em>.</p>\n","text":"I've contacted Instituto Butantan (https://en.butantan.gov.br/) (main producer of antivenoms and antitoxins in Brazil), inquired about this specimen and forwarded these photos.\n\n\n\n\nThey have confirmed it is Nesticodes rufipes."}],"domain":"biology","external_citations":["https://en.butantan.gov.br/","https://i.sstatic.net/1blaPl3L.jpg","https://i.sstatic.net/3GE0aN5l.jpg","https://i.sstatic.net/B6aQK8zu.jpg","https://i.sstatic.net/JltcmY2C.jpg","https://i.sstatic.net/T9ANM3Jj.jpg"],"ground_truth_type":"metadata_grounded","group_id":"34c22ace4dcac7a68e16f32483a1e8ded61da011244de3b5d40ae3f930b7236f","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-5993c2bb2eb8f6a30168c038","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":"André Carini","profile_url":"https://biology.stackexchange.com/users/86723/andr%c3%a9-carini","user_type":"registered"},"created_at":"2024-08-28T01:13:32+00:00","raw_file":"raw/codex_api_v1/cedb71cd945e8f995b79cadd8e6718011c2863cc935a3a1410ded32d454feeef_1790824099288070500_0.json","raw_sha256":"6569d2607abeaad3ebe6e725128dec16202338bf9cbd6c8013a07c01af6e0905","revision_guid":"C8B4F29E-67A7-46DB-9402-D8680258CB9A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C8B4F29E-67A7-46DB-9402-D8680258CB9A/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":"115264","source_record_sha256":"345dd6299f9e67841353c1822ed7a3479ca390a4efdea2f435231ab71721d7e0","source_url":"https://biology.stackexchange.com/questions/115264/spider-identification-nesticodes-rufipes-or-loxosceles-gaucho-south-of-brazil","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Spider identification: Nesticodes rufipes or Loxosceles gaucho? (South of Brazil)\nI need help identifying a spider species frequently encountered in my apartment in Porto Alegre, southern Brazil.\n\n\n\n\n\nHabitat: Found indoors on ceiling/wall corners, door frames, and behind paintings.\n\n\n\n\nWeb pattern: No discernible regular web pattern observed.\n\n\n\n\nSize: Body length approximately 5mm, excluding legs.\n\n\n\n\nGeographic location: Porto Alegre, Rio Grande do Sul, Brazil.\n\n\n\n\nBehaviour and other notes: I've found them on any season, any time of day, and not hidden at all (ceiling/wall corners). They are usually standing still, and when prodded with a stick either curl up into a ball or very quickly draw a string of web and descend. I've seen much smaller ones (spiderlings?) whose body length is 1mm or less.\n\n\n\n\n\nI think might be either of these:\n\n\n\n\n\nNesticodes rufipes\n\n\n\n\nLoxosceles gaucho\n\n\n\n\n\nI took some photos to the best of my ability/equipment, all of them are the same specimen but under different lighting and angles:\n\n\n\n\n[image: Photo 1; source: https://i.sstatic.net/JltcmY2C.jpg] (https://i.sstatic.net/JltcmY2C.jpg)\n\n\n\n\n[image: Photo 2; source: https://i.sstatic.net/3GE0aN5l.jpg] (https://i.sstatic.net/3GE0aN5l.jpg)\n\n\n\n\n[image: Photo 3; source: https://i.sstatic.net/B6aQK8zu.jpg] (https://i.sstatic.net/B6aQK8zu.jpg)\n\n\n\n\n[image: Photo 4; source: https://i.sstatic.net/1blaPl3L.jpg] (https://i.sstatic.net/1blaPl3L.jpg)\n\n\n\n\n[image: Photo 5; source: https://i.sstatic.net/T9ANM3Jj.jpg] (https://i.sstatic.net/T9ANM3Jj.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115268,"score":2}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Current consensus <a href=\"https://www.inaturalist.org/observations/246633978\" rel=\"nofollow noreferrer\">on iNaturalist</a> seems to be that it is some sort of whip scorpion. Cool!</p>\n<p>What to me looked like the head and &quot;eyes&quot; in the above photo are the pedilaps being held tightly together in front of the actual head. If you look closely at the rear end, you can also see the &quot;whip&quot; folded forward reaching towards its head. I am unable to determine which species it is exactly (this one is more long and skinny than anything I can find examples of), but here is an <a href=\"https://www.inaturalist.org/observations/179084058\" rel=\"nofollow noreferrer\">example of a whip scorpion holding its pedilaps together in a similar fashion</a>.</p>\n","answer_id":115561,"answer_text":"Current consensus on iNaturalist (https://www.inaturalist.org/observations/246633978) seems to be that it is some sort of whip scorpion. Cool!\n\n\n\n\nWhat to me looked like the head and \"eyes\" in the above photo are the pedilaps being held tightly together in front of the actual head. If you look closely at the rear end, you can also see the \"whip\" folded forward reaching towards its head. I am unable to determine which species it is exactly (this one is more long and skinny than anything I can find examples of), but here is an example of a whip scorpion holding its pedilaps together in a similar fashion (https://www.inaturalist.org/observations/179084058).","answer_url":"https://biology.stackexchange.com/a/115561","author":"Jay Paroline","author_url":"https://biology.stackexchange.com/users/91460/jay-paroline","content_license":"CC BY-SA 4.0","created_at":"2024-10-28T20:48:53+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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Paroline","profile_url":"https://biology.stackexchange.com/users/91460/jay-paroline","user_type":"registered"},"created_at":"2024-11-03T02:21:37+00:00","raw_file":"raw/codex_api_v1/fb80d81a1c70306a433c194be5c69283394737e480e8a1af86817861a93350f3_1790824106677381800_0.json","raw_sha256":"b7384c2681ecb308baf2a286966aa4a5b1b0bd51b1336b06545b82d1c7eda92a","revision_guid":"0B8B736B-B87C-4F16-85BD-30316AB19E0C","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0B8B736B-B87C-4F16-85BD-30316AB19E0C/view-source"},{"content_license":null,"contributor":{"display_name":"theforestecologist","profile_url":"https://biology.stackexchange.com/users/16866/theforestecologist","user_type":"registered"},"created_at":"2024-12-22T18:18:16+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"5C0D38C0-CC57-4970-9EC6-11F9FF4BEDE2","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/5C0D38C0-CC57-4970-9EC6-11F9FF4BEDE2/view-source"},{"content_license":null,"contributor":{"display_name":"theforestecologist","profile_url":"https://biology.stackexchange.com/users/16866/theforestecologist","user_type":"registered"},"created_at":"2024-12-22T18:18:30+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"2E20A7EB-2AEF-4C61-9261-5A9256E64059","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/2E20A7EB-2AEF-4C61-9261-5A9256E64059/view-source"}],"score":1},{"answer_html":"<p>looks like a house centipede a baby one def not whip scorpion the body is too thin doesn't have mandibles honeselty it might just be a house centipedege that just hatched or lost legs just a theory <a href=\"https://i.sstatic.net/2fKasGLM.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/2fKasGLM.png\" alt=\"enter image description here\" /></a></p>\n","answer_id":119657,"answer_text":"looks like a house centipede a baby one def not whip scorpion the body is too thin doesn't have mandibles honeselty it might just be a house centipedege that just hatched or lost legs just a theory [image: enter image description here; source: https://i.sstatic.net/2fKasGLM.png] (https://i.sstatic.net/2fKasGLM.png)","answer_url":"https://biology.stackexchange.com/a/119657","author":"macrophage","author_url":"https://biology.stackexchange.com/users/129757/macrophage","content_license":"CC BY-SA 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Google and iNaturalist are failing me. I think it's about 3 inches long not counting the antennae. It didn't have a strong reaction to the light but did sink further into the crevices. <a href=\"https://i.sstatic.net/H3SdFaQO.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/H3SdFaQO.jpg\" alt=\"long black cave imsect\" /></a></p>\n","text":"I encountered this strange insect in a cave in Thailand (Kaew in Sam Roi Yot, to be specific) a couple of weeks ago. Google and iNaturalist are failing me. I think it's about 3 inches long not counting the antennae. It didn't have a strong reaction to the light but did sink further into the crevices. [image: long black cave imsect; source: https://i.sstatic.net/H3SdFaQO.jpg] (https://i.sstatic.net/H3SdFaQO.jpg)"},{"context_id":"115561","html":"<p>Current consensus <a href=\"https://www.inaturalist.org/observations/246633978\" rel=\"nofollow noreferrer\">on iNaturalist</a> seems to be that it is some sort of whip scorpion. Cool!</p>\n<p>What to me looked like the head and &quot;eyes&quot; in the above photo are the pedilaps being held tightly together in front of the actual head. If you look closely at the rear end, you can also see the &quot;whip&quot; folded forward reaching towards its head. I am unable to determine which species it is exactly (this one is more long and skinny than anything I can find examples of), but here is an <a href=\"https://www.inaturalist.org/observations/179084058\" rel=\"nofollow noreferrer\">example of a whip scorpion holding its pedilaps together in a similar fashion</a>.</p>\n","text":"Current consensus on iNaturalist (https://www.inaturalist.org/observations/246633978) seems to be that it is some sort of whip scorpion. Cool!\n\n\n\n\nWhat to me looked like the head and \"eyes\" in the above photo are the pedilaps being held tightly together in front of the actual head. If you look closely at the rear end, you can also see the \"whip\" folded forward reaching towards its head. I am unable to determine which species it is exactly (this one is more long and skinny than anything I can find examples of), but here is an example of a whip scorpion holding its pedilaps together in a similar fashion (https://www.inaturalist.org/observations/179084058)."},{"context_id":"119657","html":"<p>looks like a house centipede a baby one def not whip scorpion the body is too thin doesn't have mandibles honeselty it might just be a house centipedege that just hatched or lost legs just a theory <a href=\"https://i.sstatic.net/2fKasGLM.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/2fKasGLM.png\" alt=\"enter image description here\" /></a></p>\n","text":"looks like a house centipede a baby one def not whip scorpion the body is too thin doesn't have mandibles honeselty it might just be a house centipedege that just hatched or lost legs just a theory [image: enter image description here; source: https://i.sstatic.net/2fKasGLM.png] 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Google and iNaturalist are failing me. I think it's about 3 inches long not counting the antennae. It didn't have a strong reaction to the light but did sink further into the crevices. [image: long black cave imsect; source: https://i.sstatic.net/H3SdFaQO.jpg] (https://i.sstatic.net/H3SdFaQO.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115561,"score":1},{"answer_id":119657,"score":-1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":115563,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Without the proper tests to identify the bacteria you have no method of identifying which species you have isolated and there is a chance that some of them are pathogens, especially as you have isolated from somewhere that is used for sanitation. There's a goodish chance that you haven't just isolated bacteria, but also yeast and other fungi.</p>\n<p>Feces contains quite a range of bacteria, many species of which are opportunistic pathogens such as <em><a href=\"https://en.wikipedia.org/wiki/Escherichia_coli\" rel=\"nofollow noreferrer\">Escherichia coli</a></em> (the famous &quot;E. coli&quot;), some strains of which are quite pathogenic. There are also species from genera like <em><a href=\"https://en.wikipedia.org/wiki/Shigella\" rel=\"nofollow noreferrer\">Shigella</a></em>, <em><a href=\"https://en.wikipedia.org/wiki/Salmonella\" rel=\"nofollow noreferrer\">Salmonella</a></em>, <em><a href=\"https://en.wikipedia.org/wiki/Klebsiella\" rel=\"nofollow noreferrer\">Klebsiella</a></em>, <em><a href=\"https://en.wikipedia.org/wiki/Clostridium\" rel=\"nofollow noreferrer\">Clostridium</a></em> and <a href=\"https://microbenotes.com/pathogenic-bacteria-stool/\" rel=\"nofollow noreferrer\">many others</a> which are very common pathogens.</p>\n<p>Handling these sorts of things is not necessarily dangerous with appropriate training and proper precautions (e.g. gloves, washing and sanitizing hands properly). If you decide to go ahead, make sure that you don't open the plate(s), to ensure that you can't spread the isolates around. If you do not have someone to advise on techniques and train you, you should not handle the samples!</p>\n<p>You should discard the plate(s) in a biohazardous waste stream, do not just throw in the rubbish. Your school may be able to help with this.</p>\n","answer_id":115563,"answer_text":"Without the proper tests to identify the bacteria you have no method of identifying which species you have isolated and there is a chance that some of them are pathogens, especially as you have isolated from somewhere that is used for sanitation. There's a goodish chance that you haven't just isolated bacteria, but also yeast and other fungi.\n\n\n\n\nFeces contains quite a range of bacteria, many species of which are opportunistic pathogens such as Escherichia coli (https://en.wikipedia.org/wiki/Escherichia_coli) (the famous \"E. coli\"), some strains of which are quite pathogenic. There are also species from genera like Shigella (https://en.wikipedia.org/wiki/Shigella), Salmonella (https://en.wikipedia.org/wiki/Salmonella), Klebsiella (https://en.wikipedia.org/wiki/Klebsiella), Clostridium (https://en.wikipedia.org/wiki/Clostridium) and many others (https://microbenotes.com/pathogenic-bacteria-stool/) which are very common pathogens.\n\n\n\n\nHandling these sorts of things is not necessarily dangerous with appropriate training and proper precautions (e.g. gloves, washing and sanitizing hands properly). If you decide to go ahead, make sure that you don't open the plate(s), to ensure that you can't spread the isolates around. If you do not have someone to advise on techniques and train you, you should not handle the samples!\n\n\n\n\nYou should discard the plate(s) in a biohazardous waste stream, do not just throw in the rubbish. Your school may be able to help with this.","answer_url":"https://biology.stackexchange.com/a/115563","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2024-10-29T06:00:04+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; 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After 3 days, it now has a number of colonies and smells really bad. This was originally for my school science fair(next week) Now I am really scared that the culture may contain pathogenic bacteria. Is it safe to continue the culture or should I dispose it off?? Please help</p>\n","text":"I had taken a sample of bacteria from my toilet bowl and allowed it to grow on an agar plate. After 3 days, it now has a number of colonies and smells really bad. This was originally for my school science fair(next week) Now I am really scared that the culture may contain pathogenic bacteria. Is it safe to continue the culture or should I dispose it off?? Please help"},{"context_id":"115563","html":"<p>Without the proper tests to identify the bacteria you have no method of identifying which species you have isolated and there is a chance that some of them are pathogens, especially as you have isolated from somewhere that is used for sanitation. There's a goodish chance that you haven't just isolated bacteria, but also yeast and other fungi.</p>\n<p>Feces contains quite a range of bacteria, many species of which are opportunistic pathogens such as <em><a href=\"https://en.wikipedia.org/wiki/Escherichia_coli\" rel=\"nofollow noreferrer\">Escherichia coli</a></em> (the famous &quot;E. coli&quot;), some strains of which are quite pathogenic. There are also species from genera like <em><a href=\"https://en.wikipedia.org/wiki/Shigella\" rel=\"nofollow noreferrer\">Shigella</a></em>, <em><a href=\"https://en.wikipedia.org/wiki/Salmonella\" rel=\"nofollow noreferrer\">Salmonella</a></em>, <em><a href=\"https://en.wikipedia.org/wiki/Klebsiella\" rel=\"nofollow noreferrer\">Klebsiella</a></em>, <em><a href=\"https://en.wikipedia.org/wiki/Clostridium\" rel=\"nofollow noreferrer\">Clostridium</a></em> and <a href=\"https://microbenotes.com/pathogenic-bacteria-stool/\" rel=\"nofollow noreferrer\">many others</a> which are very common pathogens.</p>\n<p>Handling these sorts of things is not necessarily dangerous with appropriate training and proper precautions (e.g. gloves, washing and sanitizing hands properly). If you decide to go ahead, make sure that you don't open the plate(s), to ensure that you can't spread the isolates around. If you do not have someone to advise on techniques and train you, you should not handle the samples!</p>\n<p>You should discard the plate(s) in a biohazardous waste stream, do not just throw in the rubbish. Your school may be able to help with this.</p>\n","text":"Without the proper tests to identify the bacteria you have no method of identifying which species you have isolated and there is a chance that some of them are pathogens, especially as you have isolated from somewhere that is used for sanitation. There's a goodish chance that you haven't just isolated bacteria, but also yeast and other fungi.\n\n\n\n\nFeces contains quite a range of bacteria, many species of which are opportunistic pathogens such as Escherichia coli (https://en.wikipedia.org/wiki/Escherichia_coli) (the famous \"E. coli\"), some strains of which are quite pathogenic. There are also species from genera like Shigella (https://en.wikipedia.org/wiki/Shigella), Salmonella (https://en.wikipedia.org/wiki/Salmonella), Klebsiella (https://en.wikipedia.org/wiki/Klebsiella), Clostridium (https://en.wikipedia.org/wiki/Clostridium) and many others (https://microbenotes.com/pathogenic-bacteria-stool/) which are very common pathogens.\n\n\n\n\nHandling these sorts of things is not necessarily dangerous with appropriate training and proper precautions (e.g. gloves, washing and sanitizing hands properly). If you decide to go ahead, make sure that you don't open the plate(s), to ensure that you can't spread the isolates around. If you do not have someone to advise on techniques and train you, you should not handle the samples!\n\n\n\n\nYou should discard the plate(s) in a biohazardous waste stream, do not just throw in the rubbish. Your school may be able to help with this."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Clostridium","https://en.wikipedia.org/wiki/Escherichia_coli","https://en.wikipedia.org/wiki/Klebsiella","https://en.wikipedia.org/wiki/Salmonella","https://en.wikipedia.org/wiki/Shigella","https://microbenotes.com/pathogenic-bacteria-stool/"],"ground_truth_type":"metadata_grounded","group_id":"ad876e5adc4d7b02d2ede5ff6959177116bacc1b523626fc10887cdd441f95db","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-f988e3246d434fcaa8692d4e","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":"Padma Barik","profile_url":"https://biology.stackexchange.com/users/92218/padma-barik","user_type":"registered"},"created_at":"2024-10-29T05:12:11+00:00","raw_file":"raw/codex_api_v1/fb80d81a1c70306a433c194be5c69283394737e480e8a1af86817861a93350f3_1790824106677381800_0.json","raw_sha256":"b7384c2681ecb308baf2a286966aa4a5b1b0bd51b1336b06545b82d1c7eda92a","revision_guid":"228F5DF2-85CD-4B68-95C0-5438C4196E2A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/228F5DF2-85CD-4B68-95C0-5438C4196E2A/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-10-29T13:12:20+00:00","raw_file":"raw/codex_api_v1/fb80d81a1c70306a433c194be5c69283394737e480e8a1af86817861a93350f3_1790824106677381800_0.json","raw_sha256":"b7384c2681ecb308baf2a286966aa4a5b1b0bd51b1336b06545b82d1c7eda92a","revision_guid":"A96BA91D-1B4F-48AA-A0EF-6F3A44EE0C13","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/A96BA91D-1B4F-48AA-A0EF-6F3A44EE0C13/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-10-29T13:12:22+00:00","raw_file":"raw/codex_api_v1/fb80d81a1c70306a433c194be5c69283394737e480e8a1af86817861a93350f3_1790824106677381800_0.json","raw_sha256":"b7384c2681ecb308baf2a286966aa4a5b1b0bd51b1336b06545b82d1c7eda92a","revision_guid":"5F69ABD9-D441-4C57-9241-D537F8492B86","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/5F69ABD9-D441-4C57-9241-D537F8492B86/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":"115562","source_record_sha256":"a4bd0fdb6bb73c67bb26df2d856e9896f2885d097128770165629726d5a62933","source_url":"https://biology.stackexchange.com/questions/115562/unknown-bacterial-culture","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Unknown bacterial culture\nI had taken a sample of bacteria from my toilet bowl and allowed it to grow on an agar plate. After 3 days, it now has a number of colonies and smells really bad. This was originally for my school science fair(next week) Now I am really scared that the culture may contain pathogenic bacteria. Is it safe to continue the culture or should I dispose it off?? Please help","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115563,"score":4}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":115593,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>There is extensive work attempting to decompose phenotypic variance into genetic, epigenetic etc. terms. Here are just three random examples from the last 10 years that I got by googling this:</p>\n<ul>\n<li><a href=\"https://www.nature.com/articles/s41437-019-0261-8\" rel=\"nofollow noreferrer\">https://www.nature.com/articles/s41437-019-0261-8</a></li>\n<li><a href=\"https://www.nature.com/articles/s41467-020-16520-1\" rel=\"nofollow noreferrer\">https://www.nature.com/articles/s41467-020-16520-1</a> (focuses specifically on DNA methylation, which is possibly dubious from a classic interpretation of epigenetics)</li>\n<li><a href=\"https://www.nature.com/articles/s41437-018-0114-x.pdf\" rel=\"nofollow noreferrer\">https://www.nature.com/articles/s41437-018-0114-x.pdf</a> (theoretical review)</li>\n</ul>\n<p>In some cases phenotypes show &gt;50% of variance could be explained by epigenetic causes (see review). In other cases it is much less.</p>\n<p>However, as always when considering these variance decomposition approaches, <a href=\"https://academic.oup.com/ije/article/35/3/520/735787\" rel=\"nofollow noreferrer\">variance decomposition does not substitute for a causal analysis</a>. Heritability is far too unstable of an estimator to be informative except in very well designed cases- that are more or less impossible to find for humans, because we can't breed humans for ethical reasons.</p>\n<p>Epigenetic analysis only complicates this ambiguous approach, given its intimate relationship to both genetic and environmental contributors to phenotype.</p>\n","answer_id":115593,"answer_text":"There is extensive work attempting to decompose phenotypic variance into genetic, epigenetic etc. terms. Here are just three random examples from the last 10 years that I got by googling this:\n\n\n\n\n\nhttps://www.nature.com/articles/s41437-019-0261-8 (https://www.nature.com/articles/s41437-019-0261-8)\n\n\n\n\nhttps://www.nature.com/articles/s41467-020-16520-1 (https://www.nature.com/articles/s41467-020-16520-1) (focuses specifically on DNA methylation, which is possibly dubious from a classic interpretation of epigenetics)\n\n\n\n\nhttps://www.nature.com/articles/s41437-018-0114-x.pdf (https://www.nature.com/articles/s41437-018-0114-x.pdf) (theoretical review)\n\n\n\n\n\nIn some cases phenotypes show >50% of variance could be explained by epigenetic causes (see review). In other cases it is much less.\n\n\n\n\nHowever, as always when considering these variance decomposition approaches, variance decomposition does not substitute for a causal analysis (https://academic.oup.com/ije/article/35/3/520/735787). Heritability is far too unstable of an estimator to be informative except in very well designed cases- that are more or less impossible to find for humans, because we can't breed humans for ethical reasons.\n\n\n\n\nEpigenetic analysis only complicates this ambiguous approach, given its intimate relationship to both genetic and environmental contributors to phenotype.","answer_url":"https://biology.stackexchange.com/a/115593","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2024-11-04T17:40:42+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":115592,"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":"2024-11-04T17:40:42+00:00","raw_file":"raw/codex_api_v1/fb80d81a1c70306a433c194be5c69283394737e480e8a1af86817861a93350f3_1790824106677381800_0.json","raw_sha256":"b7384c2681ecb308baf2a286966aa4a5b1b0bd51b1336b06545b82d1c7eda92a","revision_guid":"90AEB86C-6A6C-4129-95B8-0008DD506709","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/90AEB86C-6A6C-4129-95B8-0008DD506709/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"High GPA","author_url":"https://biology.stackexchange.com/users/61410/high-gpa","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"High GPA","profile_url":"https://biology.stackexchange.com/users/61410/high-gpa","user_type":"registered"},"created_at":"2024-11-04T15:54:24+00:00","raw_file":"raw/codex_api_v1/fb80d81a1c70306a433c194be5c69283394737e480e8a1af86817861a93350f3_1790824106677381800_0.json","raw_sha256":"b7384c2681ecb308baf2a286966aa4a5b1b0bd51b1336b06545b82d1c7eda92a","revision_guid":"D33B2290-9E7D-4D8F-90D0-1F7DD1BDDBC8","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D33B2290-9E7D-4D8F-90D0-1F7DD1BDDBC8/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"High GPA","profile_url":"https://biology.stackexchange.com/users/61410/high-gpa","user_type":"registered"},"created_at":"2024-11-04T16:46:05+00:00","raw_file":"raw/codex_api_v1/fb80d81a1c70306a433c194be5c69283394737e480e8a1af86817861a93350f3_1790824106677381800_0.json","raw_sha256":"b7384c2681ecb308baf2a286966aa4a5b1b0bd51b1336b06545b82d1c7eda92a","revision_guid":"941ED629-164C-4069-9B64-F59F17332030","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/941ED629-164C-4069-9B64-F59F17332030/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"High GPA","profile_url":"https://biology.stackexchange.com/users/61410/high-gpa","user_type":"registered"},"created_at":"2024-11-04T17:40:28+00:00","raw_file":"raw/codex_api_v1/fb80d81a1c70306a433c194be5c69283394737e480e8a1af86817861a93350f3_1790824106677381800_0.json","raw_sha256":"b7384c2681ecb308baf2a286966aa4a5b1b0bd51b1336b06545b82d1c7eda92a","revision_guid":"32E0ECB9-D876-484B-9BC9-BF6454CB2F6F","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/32E0ECB9-D876-484B-9BC9-BF6454CB2F6F/view-source"}],"url":"https://biology.stackexchange.com/questions/115592/quantitatively-measure-the-impact-of-dna-vs-epigenetics"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"115593","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":"2024-11-04T17:40:42+00:00","raw_file":"raw/codex_api_v1/fb80d81a1c70306a433c194be5c69283394737e480e8a1af86817861a93350f3_1790824106677381800_0.json","raw_sha256":"b7384c2681ecb308baf2a286966aa4a5b1b0bd51b1336b06545b82d1c7eda92a","revision_guid":"90AEB86C-6A6C-4129-95B8-0008DD506709","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/90AEB86C-6A6C-4129-95B8-0008DD506709/view-source"}],"url":"https://biology.stackexchange.com/a/115593"}],"contexts":[{"context_id":"question","html":"<p><em><strong>Background:</strong></em> While classical genetics deals with how DNA sequences directly code for traits, epigenetics involves chemical modifications to DNA and associated proteins that can switch genes on or off without changing the underlying DNA sequence (including DNA methylation, histone modifications, and chromatin accessibility, etc).</p>\n<p><em><strong>Question:</strong></em> Is it possible to quantitatively measure and compare the impact of DNA and epigenetics on expression? Which one is more important and by how much? If so,</p>\n<blockquote>\n<p>What is the proportional contribution of epigenetic modifications\nversus DNA sequence variation to gene expression variance in human\nsomatic cells, expressed as percentages of total phenotypic variance?</p>\n</blockquote>\n<p><em><strong>Example equation:</strong></em></p>\n<p><span class=\"math-container\">$\\text{Total Phenotypic Variance} = \\sigma^2_G + \\sigma^2_E + \\sigma^2_{G \\times E} + \\sigma^2_{\\text{error}}$</span></p>\n<p>Here, G means genetics, E means epigenetics, and the third term is covariance.</p>\n<p><em><strong>Example result:</strong></em> I wonder if there are already results like this: Genetic sequence variation explains about 25-40% of expression variance in a sample. Epigenetic variation accounts for approximately 10-30% of expression variance. The remaining variance is attributed to environmental factors, measurement noise, and gene-environment interactions</p>\n<p>There are surely a lot of loopholes and drawbacks in this approach, so I wonder if there are better approaches. I think this quantitative analysis would be very important, because it can guide us in many areas. For example, in genetic engineering, we need to know if it is more efficient to edit the gene or to deal with the epigenetics.</p>\n","text":"Background: While classical genetics deals with how DNA sequences directly code for traits, epigenetics involves chemical modifications to DNA and associated proteins that can switch genes on or off without changing the underlying DNA sequence (including DNA methylation, histone modifications, and chromatin accessibility, etc).\n\n\n\n\nQuestion: Is it possible to quantitatively measure and compare the impact of DNA and epigenetics on expression? Which one is more important and by how much? If so,\n\n\n\n\n\n\n\nWhat is the proportional contribution of epigenetic modifications\nversus DNA sequence variation to gene expression variance in human\nsomatic cells, expressed as percentages of total phenotypic variance?\n\n\n\n\n\n\n\nExample equation:\n\n\n\n\n$\\text{Total Phenotypic Variance} = \\sigma^2_G + \\sigma^2_E + \\sigma^2_{G \\times E} + \\sigma^2_{\\text{error}}$\n\n\n\n\nHere, G means genetics, E means epigenetics, and the third term is covariance.\n\n\n\n\nExample result: I wonder if there are already results like this: Genetic sequence variation explains about 25-40% of expression variance in a sample. Epigenetic variation accounts for approximately 10-30% of expression variance. The remaining variance is attributed to environmental factors, measurement noise, and gene-environment interactions\n\n\n\n\nThere are surely a lot of loopholes and drawbacks in this approach, so I wonder if there are better approaches. I think this quantitative analysis would be very important, because it can guide us in many areas. For example, in genetic engineering, we need to know if it is more efficient to edit the gene or to deal with the epigenetics."},{"context_id":"115593","html":"<p>There is extensive work attempting to decompose phenotypic variance into genetic, epigenetic etc. terms. Here are just three random examples from the last 10 years that I got by googling this:</p>\n<ul>\n<li><a href=\"https://www.nature.com/articles/s41437-019-0261-8\" rel=\"nofollow noreferrer\">https://www.nature.com/articles/s41437-019-0261-8</a></li>\n<li><a href=\"https://www.nature.com/articles/s41467-020-16520-1\" rel=\"nofollow noreferrer\">https://www.nature.com/articles/s41467-020-16520-1</a> (focuses specifically on DNA methylation, which is possibly dubious from a classic interpretation of epigenetics)</li>\n<li><a href=\"https://www.nature.com/articles/s41437-018-0114-x.pdf\" rel=\"nofollow noreferrer\">https://www.nature.com/articles/s41437-018-0114-x.pdf</a> (theoretical review)</li>\n</ul>\n<p>In some cases phenotypes show &gt;50% of variance could be explained by epigenetic causes (see review). In other cases it is much less.</p>\n<p>However, as always when considering these variance decomposition approaches, <a href=\"https://academic.oup.com/ije/article/35/3/520/735787\" rel=\"nofollow noreferrer\">variance decomposition does not substitute for a causal analysis</a>. Heritability is far too unstable of an estimator to be informative except in very well designed cases- that are more or less impossible to find for humans, because we can't breed humans for ethical reasons.</p>\n<p>Epigenetic analysis only complicates this ambiguous approach, given its intimate relationship to both genetic and environmental contributors to phenotype.</p>\n","text":"There is extensive work attempting to decompose phenotypic variance into genetic, epigenetic etc. terms. Here are just three random examples from the last 10 years that I got by googling this:\n\n\n\n\n\nhttps://www.nature.com/articles/s41437-019-0261-8 (https://www.nature.com/articles/s41437-019-0261-8)\n\n\n\n\nhttps://www.nature.com/articles/s41467-020-16520-1 (https://www.nature.com/articles/s41467-020-16520-1) (focuses specifically on DNA methylation, which is possibly dubious from a classic interpretation of epigenetics)\n\n\n\n\nhttps://www.nature.com/articles/s41437-018-0114-x.pdf (https://www.nature.com/articles/s41437-018-0114-x.pdf) (theoretical review)\n\n\n\n\n\nIn some cases phenotypes show >50% of variance could be explained by epigenetic causes (see review). In other cases it is much less.\n\n\n\n\nHowever, as always when considering these variance decomposition approaches, variance decomposition does not substitute for a causal analysis (https://academic.oup.com/ije/article/35/3/520/735787). Heritability is far too unstable of an estimator to be informative except in very well designed cases- that are more or less impossible to find for humans, because we can't breed humans for ethical reasons.\n\n\n\n\nEpigenetic analysis only complicates this ambiguous approach, given its intimate relationship to both genetic and environmental contributors to phenotype."}],"domain":"biology","external_citations":["https://academic.oup.com/ije/article/35/3/520/735787","https://www.nature.com/articles/s41437-018-0114-x.pdf","https://www.nature.com/articles/s41437-019-0261-8","https://www.nature.com/articles/s41467-020-16520-1"],"ground_truth_type":"metadata_grounded","group_id":"ab118997bedf89d72535beb6005e4c91ec790f28aa3e2fd140400d0dfc188840","hard_case_family":["multiple_sources"],"id":"RHM-48be7fa32f0afa99907e88d5","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":"High GPA","profile_url":"https://biology.stackexchange.com/users/61410/high-gpa","user_type":"registered"},"created_at":"2024-11-04T15:54:24+00:00","raw_file":"raw/codex_api_v1/fb80d81a1c70306a433c194be5c69283394737e480e8a1af86817861a93350f3_1790824106677381800_0.json","raw_sha256":"b7384c2681ecb308baf2a286966aa4a5b1b0bd51b1336b06545b82d1c7eda92a","revision_guid":"D33B2290-9E7D-4D8F-90D0-1F7DD1BDDBC8","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D33B2290-9E7D-4D8F-90D0-1F7DD1BDDBC8/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"High GPA","profile_url":"https://biology.stackexchange.com/users/61410/high-gpa","user_type":"registered"},"created_at":"2024-11-04T16:46:05+00:00","raw_file":"raw/codex_api_v1/fb80d81a1c70306a433c194be5c69283394737e480e8a1af86817861a93350f3_1790824106677381800_0.json","raw_sha256":"b7384c2681ecb308baf2a286966aa4a5b1b0bd51b1336b06545b82d1c7eda92a","revision_guid":"941ED629-164C-4069-9B64-F59F17332030","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/941ED629-164C-4069-9B64-F59F17332030/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"High GPA","profile_url":"https://biology.stackexchange.com/users/61410/high-gpa","user_type":"registered"},"created_at":"2024-11-04T17:40:28+00:00","raw_file":"raw/codex_api_v1/fb80d81a1c70306a433c194be5c69283394737e480e8a1af86817861a93350f3_1790824106677381800_0.json","raw_sha256":"b7384c2681ecb308baf2a286966aa4a5b1b0bd51b1336b06545b82d1c7eda92a","revision_guid":"32E0ECB9-D876-484B-9BC9-BF6454CB2F6F","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/32E0ECB9-D876-484B-9BC9-BF6454CB2F6F/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":"115592","source_record_sha256":"0275fde3733a06c6582920c99c9cb66d63a22c9597e873292e459e51b14f6866","source_url":"https://biology.stackexchange.com/questions/115592/quantitatively-measure-the-impact-of-dna-vs-epigenetics","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Quantitatively measure the impact of DNA vs epigenetics?\nBackground: While classical genetics deals with how DNA sequences directly code for traits, epigenetics involves chemical modifications to DNA and associated proteins that can switch genes on or off without changing the underlying DNA sequence (including DNA methylation, histone modifications, and chromatin accessibility, etc).\n\n\n\n\nQuestion: Is it possible to quantitatively measure and compare the impact of DNA and epigenetics on expression? Which one is more important and by how much? If so,\n\n\n\n\n\n\n\nWhat is the proportional contribution of epigenetic modifications\nversus DNA sequence variation to gene expression variance in human\nsomatic cells, expressed as percentages of total phenotypic variance?\n\n\n\n\n\n\n\nExample equation:\n\n\n\n\n$\\text{Total Phenotypic Variance} = \\sigma^2_G + \\sigma^2_E + \\sigma^2_{G \\times E} + \\sigma^2_{\\text{error}}$\n\n\n\n\nHere, G means genetics, E means epigenetics, and the third term is covariance.\n\n\n\n\nExample result: I wonder if there are already results like this: Genetic sequence variation explains about 25-40% of expression variance in a sample. Epigenetic variation accounts for approximately 10-30% of expression variance. The remaining variance is attributed to environmental factors, measurement noise, and gene-environment interactions\n\n\n\n\nThere are surely a lot of loopholes and drawbacks in this approach, so I wonder if there are better approaches. I think this quantitative analysis would be very important, because it can guide us in many areas. For example, in genetic engineering, we need to know if it is more efficient to edit the gene or to deal with the epigenetics.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115593,"score":3}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":115737,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Harder to find the answer than you might think, and I'm still not sure that I have the full answer to this.</p>\n<p>However, there are quite a few species within the <a href=\"https://en.wikipedia.org/wiki/Macropodidae\" rel=\"noreferrer\">Macropodidae</a>, of which only 4 are commonly called Kangaroo. These are the larger species within the Macropodidae; namely the Red Kangaroo (<em><a href=\"https://en.wikipedia.org/wiki/Red_kangaroo\" rel=\"noreferrer\">Osphranter rufus</a></em>), the Eastern Grey Kangaroo (<em><a href=\"https://en.wikipedia.org/wiki/Eastern_grey_kangaroo\" rel=\"noreferrer\">Macropus giganteus</a></em>), the Western Grey Kangaroo (<em><a href=\"https://en.wikipedia.org/wiki/Western_grey_kangaroo\" rel=\"noreferrer\">Macropus fuliginosus</a></em>) and the Antilopine Kangaroo (<em><a href=\"https://en.wikipedia.org/wiki/Antilopine_kangaroo\" rel=\"noreferrer\">Osphrantus antilopinus</a></em>).</p>\n<p>The studies I found all look at the reproductive biology of the Western and/or Eastern Grey Kangaroo. Fortunately mostly by CSIRO scientists (Australian Government funding), and as such the results are free to read (as far as I can tell). <a href=\"https://www.publish.csiro.au/zo/ZO9750333\" rel=\"noreferrer\">Poole (1975)</a><sup>1</sup> (abstract; full text PDF link on right hand side of page) found that the age of last exit from the pouch in Eastern and Western Grey Kangaroos was about 320 days. <a href=\"https://www.publish.csiro.au/WR/WR9910561\" rel=\"noreferrer\">Arnold <em>et al</em> (1991)</a><sup>2</sup> provided growth curves from estimated age after leaving pouch permanently with equations to suit:</p>\n<p>For females:</p>\n<p><span class=\"math-container\">$$Y = 33.85(1-exp^{-0.00104age})$$</span></p>\n<p>And males:</p>\n<p><span class=\"math-container\">$$ Y= 121.43(1-exp^{0.00028age}) $$</span></p>\n<p>Figure 3 in Arnold <em>et al</em> indicates a weight of about 5 - 7 kg for both males and females at age ~1 year (or roughly the age at which they leave the pouch), and that females have a maximum weight of about 35 kg, so a maximum of abut 20% of maternal weight.</p>\n<p><a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC3025672/\" rel=\"noreferrer\">Hamilton <em>et al</em> (2010)</a><sup>3</sup> found that log of weight of weaning scales across mammalian groups, so you can probably apply these measures across the different species.</p>\n<p>Refs:</p>\n<ol>\n<li><p>Poole W. E. 1975. Reproduction in the two species of grey kangaroos, Macropus Giganteus (Shaw) and M. Fuliginosus (Desmarest). II. Gestation, parturition and pouch life. Aust. J. Zool. 23, 333–353 10.1071/ZO9750333</p>\n</li>\n<li><p>Arnold, G.W., Grassia, A., Steven, D.E., &amp; Weeldenburg, J.R. (1991). Population ecology of western grey kangaroos in a remnant of wandoo woodland at Baker's Hill, southern Western Australia. Wildlife Research, 18, 561-575.</p>\n</li>\n<li><p>Hamilton MJ, Davidson AD, Sibly RM, Brown JH. Universal scaling of production rates across mammalian lineages. Proc Biol Sci. 2011 Feb 22;278(1705):560-6. doi: 10.1098/rspb.2010.1056. Epub 2010 Aug 26. PMID: 20798111; PMCID: PMC3025672</p>\n</li>\n</ol>\n","answer_id":115737,"answer_text":"Harder to find the answer than you might think, and I'm still not sure that I have the full answer to this.\n\n\n\n\nHowever, there are quite a few species within the Macropodidae (https://en.wikipedia.org/wiki/Macropodidae), of which only 4 are commonly called Kangaroo. These are the larger species within the Macropodidae; namely the Red Kangaroo (Osphranter rufus (https://en.wikipedia.org/wiki/Red_kangaroo)), the Eastern Grey Kangaroo (Macropus giganteus (https://en.wikipedia.org/wiki/Eastern_grey_kangaroo)), the Western Grey Kangaroo (Macropus fuliginosus (https://en.wikipedia.org/wiki/Western_grey_kangaroo)) and the Antilopine Kangaroo (Osphrantus antilopinus (https://en.wikipedia.org/wiki/Antilopine_kangaroo)).\n\n\n\n\nThe studies I found all look at the reproductive biology of the Western and/or Eastern Grey Kangaroo. Fortunately mostly by CSIRO scientists (Australian Government funding), and as such the results are free to read (as far as I can tell). Poole (1975) (https://www.publish.csiro.au/zo/ZO9750333)1 (abstract; full text PDF link on right hand side of page) found that the age of last exit from the pouch in Eastern and Western Grey Kangaroos was about 320 days. Arnold et al (1991) (https://www.publish.csiro.au/WR/WR9910561)2 provided growth curves from estimated age after leaving pouch permanently with equations to suit:\n\n\n\n\nFor females:\n\n\n\n\n$$Y = 33.85(1-exp^{-0.00104age})$$\n\n\n\n\nAnd males:\n\n\n\n\n$$ Y= 121.43(1-exp^{0.00028age}) $$\n\n\n\n\nFigure 3 in Arnold et al indicates a weight of about 5 - 7 kg for both males and females at age ~1 year (or roughly the age at which they leave the pouch), and that females have a maximum weight of about 35 kg, so a maximum of abut 20% of maternal weight.\n\n\n\n\nHamilton et al (2010) (https://pmc.ncbi.nlm.nih.gov/articles/PMC3025672/)3 found that log of weight of weaning scales across mammalian groups, so you can probably apply these measures across the different species.\n\n\n\n\nRefs:\n\n\n\n\n\n\n\nPoole W. E. 1975. Reproduction in the two species of grey kangaroos, Macropus Giganteus (Shaw) and M. Fuliginosus (Desmarest). II. Gestation, parturition and pouch life. Aust. J. Zool. 23, 333–353 10.1071/ZO9750333\n\n\n\n\n\n\n\n\n\nArnold, G.W., Grassia, A., Steven, D.E., & Weeldenburg, J.R. (1991). Population ecology of western grey kangaroos in a remnant of wandoo woodland at Baker's Hill, southern Western Australia. Wildlife Research, 18, 561-575.\n\n\n\n\n\n\n\n\n\nHamilton MJ, Davidson AD, Sibly RM, Brown JH. Universal scaling of production rates across mammalian lineages. Proc Biol Sci. 2011 Feb 22;278(1705):560-6. doi: 10.1098/rspb.2010.1056. Epub 2010 Aug 26. PMID: 20798111; PMCID: PMC3025672","answer_url":"https://biology.stackexchange.com/a/115737","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2024-12-05T23:13:16+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":115736,"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":"2024-12-05T23:13:16+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"780F5E25-CE4E-49D0-948F-F97FBC10028E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/780F5E25-CE4E-49D0-948F-F97FBC10028E/view-source"}],"score":6}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"E Tam","author_url":"https://biology.stackexchange.com/users/5149/e-tam","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"E Tam","profile_url":"https://biology.stackexchange.com/users/5149/e-tam","user_type":"registered"},"created_at":"2024-12-05T21:38:21+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"D712507F-D644-43F5-9132-5FE9C5620B71","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D712507F-D644-43F5-9132-5FE9C5620B71/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":"2024-12-05T22:47:44+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"CF756389-A471-4E08-89AC-18FA52198248","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CF756389-A471-4E08-89AC-18FA52198248/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-12-06T05:44:33+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"92E8C81D-0142-443F-ABE7-99819A8A626E","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/92E8C81D-0142-443F-ABE7-99819A8A626E/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"E Tam","profile_url":"https://biology.stackexchange.com/users/5149/e-tam","user_type":"registered"},"created_at":"2024-12-11T14:57:35+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"3100C6F3-D31E-4224-A2CD-02EA5623C70F","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3100C6F3-D31E-4224-A2CD-02EA5623C70F/view-source"}],"url":"https://biology.stackexchange.com/questions/115736/how-large-are-joeys-when-they-leave-the-mother-kangaroos-pouch"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"115737","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":"2024-12-05T23:13:16+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"780F5E25-CE4E-49D0-948F-F97FBC10028E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/780F5E25-CE4E-49D0-948F-F97FBC10028E/view-source"}],"url":"https://biology.stackexchange.com/a/115737"}],"contexts":[{"context_id":"question","html":"<p>It makes sense to me that the mother stops letting the joey back in when it gets too large to carry. I didn't want to just accept this without proof, so I went looking for information online. I found two okay sources that say the joey is not allowed back into the pouch when it is ~20% of the mother’s weight <a href=\"https://luckykangaroos.com/en/how-long-do-kangaroos-stay-in-the-pouch/\" rel=\"nofollow noreferrer\"> [1</a>, <a href=\"http://artserve.anu.edu.au/raid1/student_projects/kangaroos/p-emerg.html\" rel=\"nofollow noreferrer\">2]</a>. Does anyone know where that number comes from, or have a better source for it?</p>\n<p>EDIT: I found that the second source I gave is word-for-word copied from the book Kangaroos by Terence Dawson, available on the <a href=\"https://archive.org/details/kangaroosbiology00daws/mode/2up\" rel=\"nofollow noreferrer\">Internet Archive</a>. The original also includes some interesting graphs showing young's development in terms of both mass and time. Unfortunately, he does not provide a source for the 20% claim.</p>\n","text":"It makes sense to me that the mother stops letting the joey back in when it gets too large to carry. I didn't want to just accept this without proof, so I went looking for information online. I found two okay sources that say the joey is not allowed back into the pouch when it is ~20% of the mother’s weight  [1 (https://luckykangaroos.com/en/how-long-do-kangaroos-stay-in-the-pouch/), 2] (http://artserve.anu.edu.au/raid1/student_projects/kangaroos/p-emerg.html). Does anyone know where that number comes from, or have a better source for it?\n\n\n\n\nEDIT: I found that the second source I gave is word-for-word copied from the book Kangaroos by Terence Dawson, available on the Internet Archive (https://archive.org/details/kangaroosbiology00daws/mode/2up). The original also includes some interesting graphs showing young's development in terms of both mass and time. Unfortunately, he does not provide a source for the 20% claim."},{"context_id":"115737","html":"<p>Harder to find the answer than you might think, and I'm still not sure that I have the full answer to this.</p>\n<p>However, there are quite a few species within the <a href=\"https://en.wikipedia.org/wiki/Macropodidae\" rel=\"noreferrer\">Macropodidae</a>, of which only 4 are commonly called Kangaroo. These are the larger species within the Macropodidae; namely the Red Kangaroo (<em><a href=\"https://en.wikipedia.org/wiki/Red_kangaroo\" rel=\"noreferrer\">Osphranter rufus</a></em>), the Eastern Grey Kangaroo (<em><a href=\"https://en.wikipedia.org/wiki/Eastern_grey_kangaroo\" rel=\"noreferrer\">Macropus giganteus</a></em>), the Western Grey Kangaroo (<em><a href=\"https://en.wikipedia.org/wiki/Western_grey_kangaroo\" rel=\"noreferrer\">Macropus fuliginosus</a></em>) and the Antilopine Kangaroo (<em><a href=\"https://en.wikipedia.org/wiki/Antilopine_kangaroo\" rel=\"noreferrer\">Osphrantus antilopinus</a></em>).</p>\n<p>The studies I found all look at the reproductive biology of the Western and/or Eastern Grey Kangaroo. Fortunately mostly by CSIRO scientists (Australian Government funding), and as such the results are free to read (as far as I can tell). <a href=\"https://www.publish.csiro.au/zo/ZO9750333\" rel=\"noreferrer\">Poole (1975)</a><sup>1</sup> (abstract; full text PDF link on right hand side of page) found that the age of last exit from the pouch in Eastern and Western Grey Kangaroos was about 320 days. <a href=\"https://www.publish.csiro.au/WR/WR9910561\" rel=\"noreferrer\">Arnold <em>et al</em> (1991)</a><sup>2</sup> provided growth curves from estimated age after leaving pouch permanently with equations to suit:</p>\n<p>For females:</p>\n<p><span class=\"math-container\">$$Y = 33.85(1-exp^{-0.00104age})$$</span></p>\n<p>And males:</p>\n<p><span class=\"math-container\">$$ Y= 121.43(1-exp^{0.00028age}) $$</span></p>\n<p>Figure 3 in Arnold <em>et al</em> indicates a weight of about 5 - 7 kg for both males and females at age ~1 year (or roughly the age at which they leave the pouch), and that females have a maximum weight of about 35 kg, so a maximum of abut 20% of maternal weight.</p>\n<p><a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC3025672/\" rel=\"noreferrer\">Hamilton <em>et al</em> (2010)</a><sup>3</sup> found that log of weight of weaning scales across mammalian groups, so you can probably apply these measures across the different species.</p>\n<p>Refs:</p>\n<ol>\n<li><p>Poole W. E. 1975. Reproduction in the two species of grey kangaroos, Macropus Giganteus (Shaw) and M. Fuliginosus (Desmarest). II. Gestation, parturition and pouch life. Aust. J. Zool. 23, 333–353 10.1071/ZO9750333</p>\n</li>\n<li><p>Arnold, G.W., Grassia, A., Steven, D.E., &amp; Weeldenburg, J.R. (1991). Population ecology of western grey kangaroos in a remnant of wandoo woodland at Baker's Hill, southern Western Australia. Wildlife Research, 18, 561-575.</p>\n</li>\n<li><p>Hamilton MJ, Davidson AD, Sibly RM, Brown JH. Universal scaling of production rates across mammalian lineages. Proc Biol Sci. 2011 Feb 22;278(1705):560-6. doi: 10.1098/rspb.2010.1056. Epub 2010 Aug 26. PMID: 20798111; PMCID: PMC3025672</p>\n</li>\n</ol>\n","text":"Harder to find the answer than you might think, and I'm still not sure that I have the full answer to this.\n\n\n\n\nHowever, there are quite a few species within the Macropodidae (https://en.wikipedia.org/wiki/Macropodidae), of which only 4 are commonly called Kangaroo. These are the larger species within the Macropodidae; namely the Red Kangaroo (Osphranter rufus (https://en.wikipedia.org/wiki/Red_kangaroo)), the Eastern Grey Kangaroo (Macropus giganteus (https://en.wikipedia.org/wiki/Eastern_grey_kangaroo)), the Western Grey Kangaroo (Macropus fuliginosus (https://en.wikipedia.org/wiki/Western_grey_kangaroo)) and the Antilopine Kangaroo (Osphrantus antilopinus (https://en.wikipedia.org/wiki/Antilopine_kangaroo)).\n\n\n\n\nThe studies I found all look at the reproductive biology of the Western and/or Eastern Grey Kangaroo. Fortunately mostly by CSIRO scientists (Australian Government funding), and as such the results are free to read (as far as I can tell). Poole (1975) (https://www.publish.csiro.au/zo/ZO9750333)1 (abstract; full text PDF link on right hand side of page) found that the age of last exit from the pouch in Eastern and Western Grey Kangaroos was about 320 days. Arnold et al (1991) (https://www.publish.csiro.au/WR/WR9910561)2 provided growth curves from estimated age after leaving pouch permanently with equations to suit:\n\n\n\n\nFor females:\n\n\n\n\n$$Y = 33.85(1-exp^{-0.00104age})$$\n\n\n\n\nAnd males:\n\n\n\n\n$$ Y= 121.43(1-exp^{0.00028age}) $$\n\n\n\n\nFigure 3 in Arnold et al indicates a weight of about 5 - 7 kg for both males and females at age ~1 year (or roughly the age at which they leave the pouch), and that females have a maximum weight of about 35 kg, so a maximum of abut 20% of maternal weight.\n\n\n\n\nHamilton et al (2010) (https://pmc.ncbi.nlm.nih.gov/articles/PMC3025672/)3 found that log of weight of weaning scales across mammalian groups, so you can probably apply these measures across the different species.\n\n\n\n\nRefs:\n\n\n\n\n\n\n\nPoole W. E. 1975. Reproduction in the two species of grey kangaroos, Macropus Giganteus (Shaw) and M. Fuliginosus (Desmarest). II. Gestation, parturition and pouch life. Aust. J. Zool. 23, 333–353 10.1071/ZO9750333\n\n\n\n\n\n\n\n\n\nArnold, G.W., Grassia, A., Steven, D.E., & Weeldenburg, J.R. (1991). Population ecology of western grey kangaroos in a remnant of wandoo woodland at Baker's Hill, southern Western Australia. Wildlife Research, 18, 561-575.\n\n\n\n\n\n\n\n\n\nHamilton MJ, Davidson AD, Sibly RM, Brown JH. Universal scaling of production rates across mammalian lineages. Proc Biol Sci. 2011 Feb 22;278(1705):560-6. doi: 10.1098/rspb.2010.1056. Epub 2010 Aug 26. PMID: 20798111; PMCID: PMC3025672"}],"domain":"biology","external_citations":["http://artserve.anu.edu.au/raid1/student_projects/kangaroos/p-emerg.html","https://archive.org/details/kangaroosbiology00daws/mode/2up","https://en.wikipedia.org/wiki/Antilopine_kangaroo","https://en.wikipedia.org/wiki/Eastern_grey_kangaroo","https://en.wikipedia.org/wiki/Macropodidae","https://en.wikipedia.org/wiki/Red_kangaroo","https://en.wikipedia.org/wiki/Western_grey_kangaroo","https://luckykangaroos.com/en/how-long-do-kangaroos-stay-in-the-pouch/","https://pmc.ncbi.nlm.nih.gov/articles/PMC3025672/","https://www.publish.csiro.au/WR/WR9910561","https://www.publish.csiro.au/zo/ZO9750333"],"ground_truth_type":"metadata_grounded","group_id":"2ce3af6628b0e1aa95e24b1653895a229802f4d59bf5b97f60a557bdbf023313","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-6c32afa89302c805081c63a8","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":"E Tam","profile_url":"https://biology.stackexchange.com/users/5149/e-tam","user_type":"registered"},"created_at":"2024-12-05T21:38:21+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"D712507F-D644-43F5-9132-5FE9C5620B71","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D712507F-D644-43F5-9132-5FE9C5620B71/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":"2024-12-05T22:47:44+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"CF756389-A471-4E08-89AC-18FA52198248","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CF756389-A471-4E08-89AC-18FA52198248/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2024-12-06T05:44:33+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"92E8C81D-0142-443F-ABE7-99819A8A626E","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/92E8C81D-0142-443F-ABE7-99819A8A626E/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"E Tam","profile_url":"https://biology.stackexchange.com/users/5149/e-tam","user_type":"registered"},"created_at":"2024-12-11T14:57:35+00:00","raw_file":"raw/codex_api_v1/e9f8d53002b67c70a1e0faa4e07e18311daa0dd2e2a655222036d0cc60803d5a_1790824104499255500_0.json","raw_sha256":"7675135c0936bb0999aeac9143b12cafaa9f0b2130abeca1b246467c5d0b26d5","revision_guid":"3100C6F3-D31E-4224-A2CD-02EA5623C70F","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3100C6F3-D31E-4224-A2CD-02EA5623C70F/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":"115736","source_record_sha256":"6afcdc5e982b656501ef6d4494eae17cbd332482816742085d022e0aecd11760","source_url":"https://biology.stackexchange.com/questions/115736/how-large-are-joeys-when-they-leave-the-mother-kangaroos-pouch","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How large are joeys when they leave the mother kangaroo's pouch?\nIt makes sense to me that the mother stops letting the joey back in when it gets too large to carry. I didn't want to just accept this without proof, so I went looking for information online. I found two okay sources that say the joey is not allowed back into the pouch when it is ~20% of the mother’s weight  [1 (https://luckykangaroos.com/en/how-long-do-kangaroos-stay-in-the-pouch/), 2] (http://artserve.anu.edu.au/raid1/student_projects/kangaroos/p-emerg.html). Does anyone know where that number comes from, or have a better source for it?\n\n\n\n\nEDIT: I found that the second source I gave is word-for-word copied from the book Kangaroos by Terence Dawson, available on the Internet Archive (https://archive.org/details/kangaroosbiology00daws/mode/2up). The original also includes some interesting graphs showing young's development in terms of both mass and time. Unfortunately, he does not provide a source for the 20% claim.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115737,"score":6}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Plants need to both capture carbon, and capture light energy to store it in carbon bonds. Since plants use CO<sub>2</sub> as their carbon source, but can't store CO<sub>2</sub> directly, carbon capture and photosynthesis are intimately linked. In my opinion, it doesn't really make sense to distinguish between photosynthesis or carbon capture specialization.</p>\n<p>That said, plants have many adaptations around gas exchange. Although water is used directly in the photosynthesis reaction, the main loss of water is in the gas exchange itself. Essentially, whenever the <a href=\"https://en.wikipedia.org/wiki/Stoma\" rel=\"noreferrer\">stomata</a> (the structures on a leaf surface that open/close to allow gas exchange) are open to accept CO<sub>2</sub>, the plant is also losing water through transpiration. Despite OP's assertion that water is abundant within a plant, most plants need to tightly control their water budget, as they will generally face water scarcity at some point in their lives.</p>\n<p>Off the top of my head, an adaptation for increasing the gas exchange is the structure of the spongy <a href=\"https://en.wikipedia.org/wiki/Leaf#Mesophyll\" rel=\"noreferrer\">mesophyll</a>, which has space between the cells allowing for air exchange through the stomata. Plants have many adaptations to increase <a href=\"https://en.wikipedia.org/wiki/Water-use_efficiency\" rel=\"noreferrer\">water use efficiency</a>. Two of the primary ones are <a href=\"https://en.wikipedia.org/wiki/C4_carbon_fixation\" rel=\"noreferrer\">C<sub>4</sub></a> and <a href=\"https://en.wikipedia.org/wiki/Crassulacean_acid_metabolism\" rel=\"noreferrer\">CAM</a> photosynthesis, which separate carbon fixation from the photosynthesis reactions either physically (C<sub>4</sub>) or temporally (CAM).</p>\n<p>Alternatively, low-light plants do have adaptations to improve light gathering, especially for light that has been filtered through leaves of an upper canopy. Plants adapted to low light may adjust the <a href=\"https://doi.org/10.1073/pnas.87.19.7502\" rel=\"noreferrer\">stoichiometry</a> between <a href=\"https://doi.org/10.1023/A:1005870301868\" rel=\"noreferrer\">photosystems</a> I and II to better take advantage of far-red wavelengths passing through other leaves.</p>\n<p>Because of the interplay between light, water, and carbon in photosynthesis—and the extremely varied environments that plants inhabit—I'd say that declaring that leaves are &quot;specialized for photosynthesis&quot; naturally encompasses a specialization for each of these resources, tailored to the habitat (and micro-habitat) of the species.</p>\n","answer_id":115774,"answer_text":"Plants need to both capture carbon, and capture light energy to store it in carbon bonds. Since plants use CO2 as their carbon source, but can't store CO2 directly, carbon capture and photosynthesis are intimately linked. In my opinion, it doesn't really make sense to distinguish between photosynthesis or carbon capture specialization.\n\n\n\n\nThat said, plants have many adaptations around gas exchange. Although water is used directly in the photosynthesis reaction, the main loss of water is in the gas exchange itself. Essentially, whenever the stomata (https://en.wikipedia.org/wiki/Stoma) (the structures on a leaf surface that open/close to allow gas exchange) are open to accept CO2, the plant is also losing water through transpiration. Despite OP's assertion that water is abundant within a plant, most plants need to tightly control their water budget, as they will generally face water scarcity at some point in their lives.\n\n\n\n\nOff the top of my head, an adaptation for increasing the gas exchange is the structure of the spongy mesophyll (https://en.wikipedia.org/wiki/Leaf#Mesophyll), which has space between the cells allowing for air exchange through the stomata. Plants have many adaptations to increase water use efficiency (https://en.wikipedia.org/wiki/Water-use_efficiency). Two of the primary ones are C4 (https://en.wikipedia.org/wiki/C4_carbon_fixation) and CAM (https://en.wikipedia.org/wiki/Crassulacean_acid_metabolism) photosynthesis, which separate carbon fixation from the photosynthesis reactions either physically (C4) or temporally (CAM).\n\n\n\n\nAlternatively, low-light plants do have adaptations to improve light gathering, especially for light that has been filtered through leaves of an upper canopy. Plants adapted to low light may adjust the stoichiometry (https://doi.org/10.1073/pnas.87.19.7502) between photosystems (https://doi.org/10.1023/A:1005870301868) I and II to better take advantage of far-red wavelengths passing through other leaves.\n\n\n\n\nBecause of the interplay between light, water, and carbon in photosynthesis—and the extremely varied environments that plants inhabit—I'd say that declaring that leaves are \"specialized for photosynthesis\" naturally encompasses a specialization for each of these resources, tailored to the habitat (and micro-habitat) of the species.","answer_url":"https://biology.stackexchange.com/a/115774","author":"Darlingtonia","author_url":"https://biology.stackexchange.com/users/1197/darlingtonia","content_license":"CC BY-SA 4.0","created_at":"2024-12-10T21:58:40+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":115764,"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":"2024-12-10T21:58:40+00:00","raw_file":"raw/codex_api_v1/5ced1a9f1ef6cec4e5ea414f5920558abe1f2afe671db804d768d0c0886f0b02_1790824127343029500_0.json","raw_sha256":"9b7f4987291adc582d9a7ae47056606e7a91fc10c512e504e60da3797727c346","revision_guid":"99448EF5-07CA-47F9-8763-DC1841D112EE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/99448EF5-07CA-47F9-8763-DC1841D112EE/view-source"}],"score":5},{"answer_html":"<blockquote>\n<p>the energy efficiency of photosynthesis is only about 0.1-4.3%</p>\n</blockquote>\n<p>A lot of that is due to non-photochemical quenching.</p>\n<blockquote>\n<p>increasing chloroplast density</p>\n</blockquote>\n<p>Nutrient limitation. Chlorophyll requires magnesium and rubisco requires a huge amount of nitrogen. Iron is also an important cofactor in a lot of metabolic enzymes. Also, rubisco is slow and oxygen is a competitive inhibitor of RuBP carboxylation, so you need a lot of it. It's the most abundant enzyme on the planet already (<a href=\"https://doi.org/10.1016/0968-0004(79)90212-3\" rel=\"nofollow noreferrer\">Ellis 1979, Trends in biochemical sciences</a>; <a href=\"https://doi.org/10.1073/pnas.1816654116\" rel=\"nofollow noreferrer\">Bar-On &amp; Milo, 2019, <em>PNAS</em></a>).</p>\n<blockquote>\n<p>recruiting different pigments</p>\n</blockquote>\n<p>Chlorophyll (Chl) c is present in some algae. Chl b can absorb light in plants as well. But the light-harvesting antennae of photosystems I and II evolved to use Chl a as the final electron donor to the reaction core of the photosystems.</p>\n<blockquote>\n<p>the limiting factor would seem to be rate at which carbon dioxide can be extracted from air</p>\n</blockquote>\n<p>Depends. Photosynthesis can be limited by rubisco, RuBP regeneration, or triose phosphate use. A key concept put forward by <a href=\"https://link.springer.com/article/10.1007/Bf00386231#citeas\" rel=\"nofollow noreferrer\">Farquhar, von Caemmerer and Berry 1980 <em>Planta</em></a> is that photosynthesis occurs as fast as the slowest sub-process.</p>\n<p>Triose phosphate use tends to be a limitation at high CO2 or low temperature.</p>\n<p>RuBP regeneration is limited at moderate CO2 or temperature by ATP and reductant produced from the light reactions, which occurs when stress inhibits Photosystem II repair. Being the strongest oxidizing agent, it hands the brunt of the excitation energy from Chl a, and its reaction core protein D1 is known to require high rates of protein repair.</p>\n<p>At current ambient CO2 concentrations it can vary between rubisco or RuBP. For example, at high temperatures or low CO2 rubisco can limit photosynthesis because of photorespiration and heat deactivation of rubisco activase.</p>\n<p>Lots of work has been done on this, but nice work has been done by <a href=\"https://doi.org/10.1111/nph.14258\" rel=\"nofollow noreferrer\">Busch &amp; Sage 2016 New Phyt</a>.</p>\n<blockquote>\n<p>Could it be instead that leaves are structurally optimized mainly for carbon dioxide extraction, with light harvesting secondary, only just enough to process the resulting carbon? Is there any evidence for this?</p>\n</blockquote>\n<p>They're optimized for the slowest process. More light doesn't help when you're rubisco-limited, and making more rubisco doesn't help when you're light limited. If you're not turning triose phosphates into glucose and starch fast enough, increasing the rates of light reactions and CO2 assimilation doesn't help. Thus, your statement is partially true.</p>\n","answer_id":116115,"answer_text":"the energy efficiency of photosynthesis is only about 0.1-4.3%\n\n\n\n\n\n\n\nA lot of that is due to non-photochemical quenching.\n\n\n\n\n\n\n\nincreasing chloroplast density\n\n\n\n\n\n\n\nNutrient limitation. Chlorophyll requires magnesium and rubisco requires a huge amount of nitrogen. Iron is also an important cofactor in a lot of metabolic enzymes. Also, rubisco is slow and oxygen is a competitive inhibitor of RuBP carboxylation, so you need a lot of it. It's the most abundant enzyme on the planet already (Ellis 1979, Trends in biochemical sciences (https://doi.org/10.1016/0968-0004(79)90212-3); Bar-On & Milo, 2019, PNAS (https://doi.org/10.1073/pnas.1816654116)).\n\n\n\n\n\n\n\nrecruiting different pigments\n\n\n\n\n\n\n\nChlorophyll (Chl) c is present in some algae. Chl b can absorb light in plants as well. But the light-harvesting antennae of photosystems I and II evolved to use Chl a as the final electron donor to the reaction core of the photosystems.\n\n\n\n\n\n\n\nthe limiting factor would seem to be rate at which carbon dioxide can be extracted from air\n\n\n\n\n\n\n\nDepends. Photosynthesis can be limited by rubisco, RuBP regeneration, or triose phosphate use. A key concept put forward by Farquhar, von Caemmerer and Berry 1980 Planta (https://link.springer.com/article/10.1007/Bf00386231#citeas) is that photosynthesis occurs as fast as the slowest sub-process.\n\n\n\n\nTriose phosphate use tends to be a limitation at high CO2 or low temperature.\n\n\n\n\nRuBP regeneration is limited at moderate CO2 or temperature by ATP and reductant produced from the light reactions, which occurs when stress inhibits Photosystem II repair. Being the strongest oxidizing agent, it hands the brunt of the excitation energy from Chl a, and its reaction core protein D1 is known to require high rates of protein repair.\n\n\n\n\nAt current ambient CO2 concentrations it can vary between rubisco or RuBP. For example, at high temperatures or low CO2 rubisco can limit photosynthesis because of photorespiration and heat deactivation of rubisco activase.\n\n\n\n\nLots of work has been done on this, but nice work has been done by Busch & Sage 2016 New Phyt (https://doi.org/10.1111/nph.14258).\n\n\n\n\n\n\n\nCould it be instead that leaves are structurally optimized mainly for carbon dioxide extraction, with light harvesting secondary, only just enough to process the resulting carbon? Is there any evidence for this?\n\n\n\n\n\n\n\nThey're optimized for the slowest process. More light doesn't help when you're rubisco-limited, and making more rubisco doesn't help when you're light limited. If you're not turning triose phosphates into glucose and starch fast enough, increasing the rates of light reactions and CO2 assimilation doesn't help. Thus, your statement is partially true.","answer_url":"https://biology.stackexchange.com/a/116115","author":"aleungplants","author_url":"https://biology.stackexchange.com/users/101099/aleungplants","content_license":"CC BY-SA 4.0","created_at":"2025-02-17T04:31:24+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":115764,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"aleungplants","profile_url":"https://biology.stackexchange.com/users/101099/aleungplants","user_type":"registered"},"created_at":"2025-02-17T04:31:24+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"3DE39FB4-204A-450C-BBDE-70883177C8A8","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3DE39FB4-204A-450C-BBDE-70883177C8A8/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Henry Tarpal","author_url":"https://biology.stackexchange.com/users/82923/henry-tarpal","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Henry Tarpal","profile_url":"https://biology.stackexchange.com/users/82923/henry-tarpal","user_type":"registered"},"created_at":"2024-12-10T01:45:35+00:00","raw_file":"raw/codex_api_v1/5ced1a9f1ef6cec4e5ea414f5920558abe1f2afe671db804d768d0c0886f0b02_1790824127343029500_0.json","raw_sha256":"9b7f4987291adc582d9a7ae47056606e7a91fc10c512e504e60da3797727c346","revision_guid":"B09FA35D-4D7D-40DA-A94A-D9ABBC746764","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B09FA35D-4D7D-40DA-A94A-D9ABBC746764/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"kmm","profile_url":"https://biology.stackexchange.com/users/107/kmm","user_type":"registered"},"created_at":"2024-12-10T14:02:13+00:00","raw_file":"raw/codex_api_v1/5ced1a9f1ef6cec4e5ea414f5920558abe1f2afe671db804d768d0c0886f0b02_1790824127343029500_0.json","raw_sha256":"9b7f4987291adc582d9a7ae47056606e7a91fc10c512e504e60da3797727c346","revision_guid":"899845B4-3C01-4E7A-AEB9-9EBC2849C509","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/899845B4-3C01-4E7A-AEB9-9EBC2849C509/view-source"}],"url":"https://biology.stackexchange.com/questions/115764/what-is-the-primary-function-of-a-leaf"},{"author":"Darlingtonia","author_url":"https://biology.stackexchange.com/users/1197/darlingtonia","content_license":"CC BY-SA 4.0","context_id":"115774","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":"2024-12-10T21:58:40+00:00","raw_file":"raw/codex_api_v1/5ced1a9f1ef6cec4e5ea414f5920558abe1f2afe671db804d768d0c0886f0b02_1790824127343029500_0.json","raw_sha256":"9b7f4987291adc582d9a7ae47056606e7a91fc10c512e504e60da3797727c346","revision_guid":"99448EF5-07CA-47F9-8763-DC1841D112EE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/99448EF5-07CA-47F9-8763-DC1841D112EE/view-source"}],"url":"https://biology.stackexchange.com/a/115774"},{"author":"aleungplants","author_url":"https://biology.stackexchange.com/users/101099/aleungplants","content_license":"CC BY-SA 4.0","context_id":"116115","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"aleungplants","profile_url":"https://biology.stackexchange.com/users/101099/aleungplants","user_type":"registered"},"created_at":"2025-02-17T04:31:24+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"3DE39FB4-204A-450C-BBDE-70883177C8A8","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3DE39FB4-204A-450C-BBDE-70883177C8A8/view-source"}],"url":"https://biology.stackexchange.com/a/116115"}],"contexts":[{"context_id":"question","html":"<p>The Wikipedia article (<a href=\"https://en.wikipedia.org/wiki/Leaf\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/Leaf</a>) gives the usual view:</p>\n<p><em>'A leaf (pl.: leaves) is a principal appendage of the stem of a vascular plant,[1] usually borne laterally above ground and specialized for photosynthesis.'</em>,</p>\n<p>with the article on photosynthesis (<a href=\"https://en.wikipedia.org/wiki/Photosynthesis\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/Photosynthesis</a>) launching into an explanation of the capture and conversion of light energy into chemical energy stored as simple carbohydrates. In this view, light harvesting and energy conversion is primary.</p>\n<p>However, the energy efficiency of photosynthesis is only about 0.1-4.3% (<a href=\"https://en.wikipedia.org/wiki/Photosynthetic_efficiency\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/Photosynthetic_efficiency</a>). If light energy capture and conversion is primary, why is the efficiency so low, especially since there seem to be some obvious ways to improve efficiency, such as increasing chloroplast density or recruiting different pigments to increase the number of usable frequencies of incoming light?</p>\n<p>But photosynthesis requires water and carbon dioxide as well as energy to function. From the Wikipedia article:</p>\n<p><span class=\"math-container\">$$\n6~H_2O + 6~CO_2 + Energy \\rightarrow C_6H_{12}O_6 + 6~O_2\n$$</span></p>\n<p>With water relatively abundant within the plant, the limiting factor would seem to be rate at which carbon dioxide can be extracted from air. Its concentration there is currently only about 430 ppm, and it was considerably lower in the recent past.</p>\n<p>Could it be instead that leaves are structurally optimized mainly for carbon dioxide extraction, with light harvesting secondary, only just enough to process the resulting carbon? Is there any evidence for this?</p>\n","text":"The Wikipedia article (https://en.wikipedia.org/wiki/Leaf (https://en.wikipedia.org/wiki/Leaf)) gives the usual view:\n\n\n\n\n'A leaf (pl.: leaves) is a principal appendage of the stem of a vascular plant,[1] usually borne laterally above ground and specialized for photosynthesis.',\n\n\n\n\nwith the article on photosynthesis (https://en.wikipedia.org/wiki/Photosynthesis (https://en.wikipedia.org/wiki/Photosynthesis)) launching into an explanation of the capture and conversion of light energy into chemical energy stored as simple carbohydrates. In this view, light harvesting and energy conversion is primary.\n\n\n\n\nHowever, the energy efficiency of photosynthesis is only about 0.1-4.3% (https://en.wikipedia.org/wiki/Photosynthetic_efficiency (https://en.wikipedia.org/wiki/Photosynthetic_efficiency)). If light energy capture and conversion is primary, why is the efficiency so low, especially since there seem to be some obvious ways to improve efficiency, such as increasing chloroplast density or recruiting different pigments to increase the number of usable frequencies of incoming light?\n\n\n\n\nBut photosynthesis requires water and carbon dioxide as well as energy to function. From the Wikipedia article:\n\n\n\n\n$$\n6~H_2O + 6~CO_2 + Energy \\rightarrow C_6H_{12}O_6 + 6~O_2\n$$\n\n\n\n\nWith water relatively abundant within the plant, the limiting factor would seem to be rate at which carbon dioxide can be extracted from air. Its concentration there is currently only about 430 ppm, and it was considerably lower in the recent past.\n\n\n\n\nCould it be instead that leaves are structurally optimized mainly for carbon dioxide extraction, with light harvesting secondary, only just enough to process the resulting carbon? Is there any evidence for this?"},{"context_id":"115774","html":"<p>Plants need to both capture carbon, and capture light energy to store it in carbon bonds. Since plants use CO<sub>2</sub> as their carbon source, but can't store CO<sub>2</sub> directly, carbon capture and photosynthesis are intimately linked. In my opinion, it doesn't really make sense to distinguish between photosynthesis or carbon capture specialization.</p>\n<p>That said, plants have many adaptations around gas exchange. Although water is used directly in the photosynthesis reaction, the main loss of water is in the gas exchange itself. Essentially, whenever the <a href=\"https://en.wikipedia.org/wiki/Stoma\" rel=\"noreferrer\">stomata</a> (the structures on a leaf surface that open/close to allow gas exchange) are open to accept CO<sub>2</sub>, the plant is also losing water through transpiration. Despite OP's assertion that water is abundant within a plant, most plants need to tightly control their water budget, as they will generally face water scarcity at some point in their lives.</p>\n<p>Off the top of my head, an adaptation for increasing the gas exchange is the structure of the spongy <a href=\"https://en.wikipedia.org/wiki/Leaf#Mesophyll\" rel=\"noreferrer\">mesophyll</a>, which has space between the cells allowing for air exchange through the stomata. Plants have many adaptations to increase <a href=\"https://en.wikipedia.org/wiki/Water-use_efficiency\" rel=\"noreferrer\">water use efficiency</a>. Two of the primary ones are <a href=\"https://en.wikipedia.org/wiki/C4_carbon_fixation\" rel=\"noreferrer\">C<sub>4</sub></a> and <a href=\"https://en.wikipedia.org/wiki/Crassulacean_acid_metabolism\" rel=\"noreferrer\">CAM</a> photosynthesis, which separate carbon fixation from the photosynthesis reactions either physically (C<sub>4</sub>) or temporally (CAM).</p>\n<p>Alternatively, low-light plants do have adaptations to improve light gathering, especially for light that has been filtered through leaves of an upper canopy. Plants adapted to low light may adjust the <a href=\"https://doi.org/10.1073/pnas.87.19.7502\" rel=\"noreferrer\">stoichiometry</a> between <a href=\"https://doi.org/10.1023/A:1005870301868\" rel=\"noreferrer\">photosystems</a> I and II to better take advantage of far-red wavelengths passing through other leaves.</p>\n<p>Because of the interplay between light, water, and carbon in photosynthesis—and the extremely varied environments that plants inhabit—I'd say that declaring that leaves are &quot;specialized for photosynthesis&quot; naturally encompasses a specialization for each of these resources, tailored to the habitat (and micro-habitat) of the species.</p>\n","text":"Plants need to both capture carbon, and capture light energy to store it in carbon bonds. Since plants use CO2 as their carbon source, but can't store CO2 directly, carbon capture and photosynthesis are intimately linked. In my opinion, it doesn't really make sense to distinguish between photosynthesis or carbon capture specialization.\n\n\n\n\nThat said, plants have many adaptations around gas exchange. Although water is used directly in the photosynthesis reaction, the main loss of water is in the gas exchange itself. Essentially, whenever the stomata (https://en.wikipedia.org/wiki/Stoma) (the structures on a leaf surface that open/close to allow gas exchange) are open to accept CO2, the plant is also losing water through transpiration. Despite OP's assertion that water is abundant within a plant, most plants need to tightly control their water budget, as they will generally face water scarcity at some point in their lives.\n\n\n\n\nOff the top of my head, an adaptation for increasing the gas exchange is the structure of the spongy mesophyll (https://en.wikipedia.org/wiki/Leaf#Mesophyll), which has space between the cells allowing for air exchange through the stomata. Plants have many adaptations to increase water use efficiency (https://en.wikipedia.org/wiki/Water-use_efficiency). Two of the primary ones are C4 (https://en.wikipedia.org/wiki/C4_carbon_fixation) and CAM (https://en.wikipedia.org/wiki/Crassulacean_acid_metabolism) photosynthesis, which separate carbon fixation from the photosynthesis reactions either physically (C4) or temporally (CAM).\n\n\n\n\nAlternatively, low-light plants do have adaptations to improve light gathering, especially for light that has been filtered through leaves of an upper canopy. Plants adapted to low light may adjust the stoichiometry (https://doi.org/10.1073/pnas.87.19.7502) between photosystems (https://doi.org/10.1023/A:1005870301868) I and II to better take advantage of far-red wavelengths passing through other leaves.\n\n\n\n\nBecause of the interplay between light, water, and carbon in photosynthesis—and the extremely varied environments that plants inhabit—I'd say that declaring that leaves are \"specialized for photosynthesis\" naturally encompasses a specialization for each of these resources, tailored to the habitat (and micro-habitat) of the species."},{"context_id":"116115","html":"<blockquote>\n<p>the energy efficiency of photosynthesis is only about 0.1-4.3%</p>\n</blockquote>\n<p>A lot of that is due to non-photochemical quenching.</p>\n<blockquote>\n<p>increasing chloroplast density</p>\n</blockquote>\n<p>Nutrient limitation. Chlorophyll requires magnesium and rubisco requires a huge amount of nitrogen. Iron is also an important cofactor in a lot of metabolic enzymes. Also, rubisco is slow and oxygen is a competitive inhibitor of RuBP carboxylation, so you need a lot of it. It's the most abundant enzyme on the planet already (<a href=\"https://doi.org/10.1016/0968-0004(79)90212-3\" rel=\"nofollow noreferrer\">Ellis 1979, Trends in biochemical sciences</a>; <a href=\"https://doi.org/10.1073/pnas.1816654116\" rel=\"nofollow noreferrer\">Bar-On &amp; Milo, 2019, <em>PNAS</em></a>).</p>\n<blockquote>\n<p>recruiting different pigments</p>\n</blockquote>\n<p>Chlorophyll (Chl) c is present in some algae. Chl b can absorb light in plants as well. But the light-harvesting antennae of photosystems I and II evolved to use Chl a as the final electron donor to the reaction core of the photosystems.</p>\n<blockquote>\n<p>the limiting factor would seem to be rate at which carbon dioxide can be extracted from air</p>\n</blockquote>\n<p>Depends. Photosynthesis can be limited by rubisco, RuBP regeneration, or triose phosphate use. A key concept put forward by <a href=\"https://link.springer.com/article/10.1007/Bf00386231#citeas\" rel=\"nofollow noreferrer\">Farquhar, von Caemmerer and Berry 1980 <em>Planta</em></a> is that photosynthesis occurs as fast as the slowest sub-process.</p>\n<p>Triose phosphate use tends to be a limitation at high CO2 or low temperature.</p>\n<p>RuBP regeneration is limited at moderate CO2 or temperature by ATP and reductant produced from the light reactions, which occurs when stress inhibits Photosystem II repair. Being the strongest oxidizing agent, it hands the brunt of the excitation energy from Chl a, and its reaction core protein D1 is known to require high rates of protein repair.</p>\n<p>At current ambient CO2 concentrations it can vary between rubisco or RuBP. For example, at high temperatures or low CO2 rubisco can limit photosynthesis because of photorespiration and heat deactivation of rubisco activase.</p>\n<p>Lots of work has been done on this, but nice work has been done by <a href=\"https://doi.org/10.1111/nph.14258\" rel=\"nofollow noreferrer\">Busch &amp; Sage 2016 New Phyt</a>.</p>\n<blockquote>\n<p>Could it be instead that leaves are structurally optimized mainly for carbon dioxide extraction, with light harvesting secondary, only just enough to process the resulting carbon? Is there any evidence for this?</p>\n</blockquote>\n<p>They're optimized for the slowest process. More light doesn't help when you're rubisco-limited, and making more rubisco doesn't help when you're light limited. If you're not turning triose phosphates into glucose and starch fast enough, increasing the rates of light reactions and CO2 assimilation doesn't help. Thus, your statement is partially true.</p>\n","text":"the energy efficiency of photosynthesis is only about 0.1-4.3%\n\n\n\n\n\n\n\nA lot of that is due to non-photochemical quenching.\n\n\n\n\n\n\n\nincreasing chloroplast density\n\n\n\n\n\n\n\nNutrient limitation. Chlorophyll requires magnesium and rubisco requires a huge amount of nitrogen. Iron is also an important cofactor in a lot of metabolic enzymes. Also, rubisco is slow and oxygen is a competitive inhibitor of RuBP carboxylation, so you need a lot of it. It's the most abundant enzyme on the planet already (Ellis 1979, Trends in biochemical sciences (https://doi.org/10.1016/0968-0004(79)90212-3); Bar-On & Milo, 2019, PNAS (https://doi.org/10.1073/pnas.1816654116)).\n\n\n\n\n\n\n\nrecruiting different pigments\n\n\n\n\n\n\n\nChlorophyll (Chl) c is present in some algae. Chl b can absorb light in plants as well. But the light-harvesting antennae of photosystems I and II evolved to use Chl a as the final electron donor to the reaction core of the photosystems.\n\n\n\n\n\n\n\nthe limiting factor would seem to be rate at which carbon dioxide can be extracted from air\n\n\n\n\n\n\n\nDepends. Photosynthesis can be limited by rubisco, RuBP regeneration, or triose phosphate use. A key concept put forward by Farquhar, von Caemmerer and Berry 1980 Planta (https://link.springer.com/article/10.1007/Bf00386231#citeas) is that photosynthesis occurs as fast as the slowest sub-process.\n\n\n\n\nTriose phosphate use tends to be a limitation at high CO2 or low temperature.\n\n\n\n\nRuBP regeneration is limited at moderate CO2 or temperature by ATP and reductant produced from the light reactions, which occurs when stress inhibits Photosystem II repair. Being the strongest oxidizing agent, it hands the brunt of the excitation energy from Chl a, and its reaction core protein D1 is known to require high rates of protein repair.\n\n\n\n\nAt current ambient CO2 concentrations it can vary between rubisco or RuBP. For example, at high temperatures or low CO2 rubisco can limit photosynthesis because of photorespiration and heat deactivation of rubisco activase.\n\n\n\n\nLots of work has been done on this, but nice work has been done by Busch & Sage 2016 New Phyt (https://doi.org/10.1111/nph.14258).\n\n\n\n\n\n\n\nCould it be instead that leaves are structurally optimized mainly for carbon dioxide extraction, with light harvesting secondary, only just enough to process the resulting carbon? Is there any evidence for this?\n\n\n\n\n\n\n\nThey're optimized for the slowest process. More light doesn't help when you're rubisco-limited, and making more rubisco doesn't help when you're light limited. If you're not turning triose phosphates into glucose and starch fast enough, increasing the rates of light reactions and CO2 assimilation doesn't help. Thus, your statement is partially true."}],"domain":"biology","external_citations":["https://doi.org/10.1016/0968-0004(79)90212-3","https://doi.org/10.1023/A:1005870301868","https://doi.org/10.1073/pnas.1816654116","https://doi.org/10.1073/pnas.87.19.7502","https://doi.org/10.1111/nph.14258","https://en.wikipedia.org/wiki/C4_carbon_fixation","https://en.wikipedia.org/wiki/Crassulacean_acid_metabolism","https://en.wikipedia.org/wiki/Leaf","https://en.wikipedia.org/wiki/Leaf#Mesophyll","https://en.wikipedia.org/wiki/Photosynthesis","https://en.wikipedia.org/wiki/Photosynthetic_efficiency","https://en.wikipedia.org/wiki/Stoma","https://en.wikipedia.org/wiki/Water-use_efficiency","https://link.springer.com/article/10.1007/Bf00386231#citeas"],"ground_truth_type":"metadata_grounded","group_id":"8a6ae454496d3f0ba49957f43a784b359336fc7b8627317adaabc4a3be1515d7","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-b423cbdb4d16c5ce2e8e4949","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":"Henry Tarpal","profile_url":"https://biology.stackexchange.com/users/82923/henry-tarpal","user_type":"registered"},"created_at":"2024-12-10T01:45:35+00:00","raw_file":"raw/codex_api_v1/5ced1a9f1ef6cec4e5ea414f5920558abe1f2afe671db804d768d0c0886f0b02_1790824127343029500_0.json","raw_sha256":"9b7f4987291adc582d9a7ae47056606e7a91fc10c512e504e60da3797727c346","revision_guid":"B09FA35D-4D7D-40DA-A94A-D9ABBC746764","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B09FA35D-4D7D-40DA-A94A-D9ABBC746764/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"kmm","profile_url":"https://biology.stackexchange.com/users/107/kmm","user_type":"registered"},"created_at":"2024-12-10T14:02:13+00:00","raw_file":"raw/codex_api_v1/5ced1a9f1ef6cec4e5ea414f5920558abe1f2afe671db804d768d0c0886f0b02_1790824127343029500_0.json","raw_sha256":"9b7f4987291adc582d9a7ae47056606e7a91fc10c512e504e60da3797727c346","revision_guid":"899845B4-3C01-4E7A-AEB9-9EBC2849C509","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/899845B4-3C01-4E7A-AEB9-9EBC2849C509/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":"115764","source_record_sha256":"a00668c04dd79b7112a1c4839a3c0ecb1a9e2ac74e8edbe5b61ea98ed8e13a16","source_url":"https://biology.stackexchange.com/questions/115764/what-is-the-primary-function-of-a-leaf","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What is the primary function of a leaf?\nThe Wikipedia article (https://en.wikipedia.org/wiki/Leaf (https://en.wikipedia.org/wiki/Leaf)) gives the usual view:\n\n\n\n\n'A leaf (pl.: leaves) is a principal appendage of the stem of a vascular plant,[1] usually borne laterally above ground and specialized for photosynthesis.',\n\n\n\n\nwith the article on photosynthesis (https://en.wikipedia.org/wiki/Photosynthesis (https://en.wikipedia.org/wiki/Photosynthesis)) launching into an explanation of the capture and conversion of light energy into chemical energy stored as simple carbohydrates. In this view, light harvesting and energy conversion is primary.\n\n\n\n\nHowever, the energy efficiency of photosynthesis is only about 0.1-4.3% (https://en.wikipedia.org/wiki/Photosynthetic_efficiency (https://en.wikipedia.org/wiki/Photosynthetic_efficiency)). If light energy capture and conversion is primary, why is the efficiency so low, especially since there seem to be some obvious ways to improve efficiency, such as increasing chloroplast density or recruiting different pigments to increase the number of usable frequencies of incoming light?\n\n\n\n\nBut photosynthesis requires water and carbon dioxide as well as energy to function. From the Wikipedia article:\n\n\n\n\n$$\n6~H_2O + 6~CO_2 + Energy \\rightarrow C_6H_{12}O_6 + 6~O_2\n$$\n\n\n\n\nWith water relatively abundant within the plant, the limiting factor would seem to be rate at which carbon dioxide can be extracted from air. Its concentration there is currently only about 430 ppm, and it was considerably lower in the recent past.\n\n\n\n\nCould it be instead that leaves are structurally optimized mainly for carbon dioxide extraction, with light harvesting secondary, only just enough to process the resulting carbon? Is there any evidence for this?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115774,"score":5},{"answer_id":116115,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Both members of Liliaceae (<em>sensu stricto</em>) and <em>Allium</em> can have imbricate aestivation.</p>\n<p>I unfortunately couldn't find good images with shareable permissions. But if you look <a href=\"https://www.sciencephoto.com/media/1095498/view/onion-flower-buds-light-micrograph\" rel=\"nofollow noreferrer\">here</a> you can see a photo showing buds where an inner tepal is overlapped on both sides by other inner tepals.</p>\n<p><a href=\"https://www.triarchincorporated.com/product/allium-cepa-flower-bud-cs-prepared-microscope-slide-17-252-1/\" rel=\"nofollow noreferrer\">This image</a> is a bit more ambiguous, since some of the key areas are cropped out, but it could be showing valvate aestivation.</p>\n<p>If you google &quot;Lilium bud cross section&quot; you'll find several images, most of which nicely show imbricate aestivation. I also found a reference that <a href=\"https://www.researchgate.net/profile/Jones-Napaldet/publication/332963271_Morpho-Anatomical_Characterization_of_Benguet_Lily_Lilium_philippinense_Baker/links/5cd3f851458515712e9be092/Morpho-Anatomical-Characterization-of-Benguet-Lily-Lilium-philippinense-Baker.pdf\" rel=\"nofollow noreferrer\"><em>Lilium philippinense</em></a> has imbricate aestivation.</p>\n<p>However, it's commonly recognized now that <em>Allium</em> is not a part of family Liliaceae or even order Liliales, but a separate order, <a href=\"https://en.wikipedia.org/wiki/Asparagales\" rel=\"nofollow noreferrer\">Asparagales</a>. So, it's not entirely surprising that these groups might have different aestivations.</p>\n","answer_id":115869,"answer_text":"Both members of Liliaceae (sensu stricto) and Allium can have imbricate aestivation.\n\n\n\n\nI unfortunately couldn't find good images with shareable permissions. But if you look here (https://www.sciencephoto.com/media/1095498/view/onion-flower-buds-light-micrograph) you can see a photo showing buds where an inner tepal is overlapped on both sides by other inner tepals.\n\n\n\n\nThis image (https://www.triarchincorporated.com/product/allium-cepa-flower-bud-cs-prepared-microscope-slide-17-252-1/) is a bit more ambiguous, since some of the key areas are cropped out, but it could be showing valvate aestivation.\n\n\n\n\nIf you google \"Lilium bud cross section\" you'll find several images, most of which nicely show imbricate aestivation. I also found a reference that Lilium philippinense (https://www.researchgate.net/profile/Jones-Napaldet/publication/332963271_Morpho-Anatomical_Characterization_of_Benguet_Lily_Lilium_philippinense_Baker/links/5cd3f851458515712e9be092/Morpho-Anatomical-Characterization-of-Benguet-Lily-Lilium-philippinense-Baker.pdf) has imbricate aestivation.\n\n\n\n\nHowever, it's commonly recognized now that Allium is not a part of family Liliaceae or even order Liliales, but a separate order, Asparagales (https://en.wikipedia.org/wiki/Asparagales). So, it's not entirely surprising that these groups might have different aestivations.","answer_url":"https://biology.stackexchange.com/a/115869","author":"Darlingtonia","author_url":"https://biology.stackexchange.com/users/1197/darlingtonia","content_license":"CC BY-SA 4.0","created_at":"2024-12-26T22:55:19+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":115857,"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":"2024-12-26T22:55:19+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"2EF7D9DD-66AE-49F9-A8CB-7D05ACF1A179","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2EF7D9DD-66AE-49F9-A8CB-7D05ACF1A179/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Jayjeet Dhal","author_url":"https://biology.stackexchange.com/users/96888/jayjeet-dhal","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Jayjeet Dhal","profile_url":"https://biology.stackexchange.com/users/96888/jayjeet-dhal","user_type":"registered"},"created_at":"2024-12-24T12:26:11+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"A6A427BF-3F2A-487F-924A-E8AAB1D3EF1A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A6A427BF-3F2A-487F-924A-E8AAB1D3EF1A/view-source"}],"url":"https://biology.stackexchange.com/questions/115857/whats-the-aestivation-in-onion-allium-cepa-is-it-valvate-or-imbricate"},{"author":"Darlingtonia","author_url":"https://biology.stackexchange.com/users/1197/darlingtonia","content_license":"CC BY-SA 4.0","context_id":"115869","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":"2024-12-26T22:55:19+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"2EF7D9DD-66AE-49F9-A8CB-7D05ACF1A179","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2EF7D9DD-66AE-49F9-A8CB-7D05ACF1A179/view-source"}],"url":"https://biology.stackexchange.com/a/115869"}],"contexts":[{"context_id":"question","html":"<p>In my textbook it's written Liliaceae has valvate aestivation but in a question asked in a popular entrance exam (NEET UG), onion is mentioned to have imbricate aestivation...I am confused.</p>\n","text":"In my textbook it's written Liliaceae has valvate aestivation but in a question asked in a popular entrance exam (NEET UG), onion is mentioned to have imbricate aestivation...I am confused."},{"context_id":"115869","html":"<p>Both members of Liliaceae (<em>sensu stricto</em>) and <em>Allium</em> can have imbricate aestivation.</p>\n<p>I unfortunately couldn't find good images with shareable permissions. But if you look <a href=\"https://www.sciencephoto.com/media/1095498/view/onion-flower-buds-light-micrograph\" rel=\"nofollow noreferrer\">here</a> you can see a photo showing buds where an inner tepal is overlapped on both sides by other inner tepals.</p>\n<p><a href=\"https://www.triarchincorporated.com/product/allium-cepa-flower-bud-cs-prepared-microscope-slide-17-252-1/\" rel=\"nofollow noreferrer\">This image</a> is a bit more ambiguous, since some of the key areas are cropped out, but it could be showing valvate aestivation.</p>\n<p>If you google &quot;Lilium bud cross section&quot; you'll find several images, most of which nicely show imbricate aestivation. I also found a reference that <a href=\"https://www.researchgate.net/profile/Jones-Napaldet/publication/332963271_Morpho-Anatomical_Characterization_of_Benguet_Lily_Lilium_philippinense_Baker/links/5cd3f851458515712e9be092/Morpho-Anatomical-Characterization-of-Benguet-Lily-Lilium-philippinense-Baker.pdf\" rel=\"nofollow noreferrer\"><em>Lilium philippinense</em></a> has imbricate aestivation.</p>\n<p>However, it's commonly recognized now that <em>Allium</em> is not a part of family Liliaceae or even order Liliales, but a separate order, <a href=\"https://en.wikipedia.org/wiki/Asparagales\" rel=\"nofollow noreferrer\">Asparagales</a>. So, it's not entirely surprising that these groups might have different aestivations.</p>\n","text":"Both members of Liliaceae (sensu stricto) and Allium can have imbricate aestivation.\n\n\n\n\nI unfortunately couldn't find good images with shareable permissions. But if you look here (https://www.sciencephoto.com/media/1095498/view/onion-flower-buds-light-micrograph) you can see a photo showing buds where an inner tepal is overlapped on both sides by other inner tepals.\n\n\n\n\nThis image (https://www.triarchincorporated.com/product/allium-cepa-flower-bud-cs-prepared-microscope-slide-17-252-1/) is a bit more ambiguous, since some of the key areas are cropped out, but it could be showing valvate aestivation.\n\n\n\n\nIf you google \"Lilium bud cross section\" you'll find several images, most of which nicely show imbricate aestivation. I also found a reference that Lilium philippinense (https://www.researchgate.net/profile/Jones-Napaldet/publication/332963271_Morpho-Anatomical_Characterization_of_Benguet_Lily_Lilium_philippinense_Baker/links/5cd3f851458515712e9be092/Morpho-Anatomical-Characterization-of-Benguet-Lily-Lilium-philippinense-Baker.pdf) has imbricate aestivation.\n\n\n\n\nHowever, it's commonly recognized now that Allium is not a part of family Liliaceae or even order Liliales, but a separate order, Asparagales (https://en.wikipedia.org/wiki/Asparagales). So, it's not entirely surprising that these groups might have different aestivations."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Asparagales","https://www.researchgate.net/profile/Jones-Napaldet/publication/332963271_Morpho-Anatomical_Characterization_of_Benguet_Lily_Lilium_philippinense_Baker/links/5cd3f851458515712e9be092/Morpho-Anatomical-Characterization-of-Benguet-Lily-Lilium-philippinense-Baker.pdf","https://www.sciencephoto.com/media/1095498/view/onion-flower-buds-light-micrograph","https://www.triarchincorporated.com/product/allium-cepa-flower-bud-cs-prepared-microscope-slide-17-252-1/"],"ground_truth_type":"metadata_grounded","group_id":"5b168e4798856a44d2e8c72c2057196595451bef0662283569ac6267f1369e0c","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-dd681ee36c7e9d839f2ec2b1","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":"Jayjeet Dhal","profile_url":"https://biology.stackexchange.com/users/96888/jayjeet-dhal","user_type":"registered"},"created_at":"2024-12-24T12:26:11+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"A6A427BF-3F2A-487F-924A-E8AAB1D3EF1A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A6A427BF-3F2A-487F-924A-E8AAB1D3EF1A/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":"115857","source_record_sha256":"5e2973ca94d6fa943f9b53d80b23e93af81cdfcd71e5e6c504e0f8a71790dc2b","source_url":"https://biology.stackexchange.com/questions/115857/whats-the-aestivation-in-onion-allium-cepa-is-it-valvate-or-imbricate","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"What's the aestivation in Onion (Allium cepa)? Is it valvate or imbricate?\nIn my textbook it's written Liliaceae has valvate aestivation but in a question asked in a popular entrance exam (NEET UG), onion is mentioned to have imbricate aestivation...I am confused.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115869,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Its a spider belonging to the family of Pholcidae also known as cellar spider or daddy long-legs spider. They are often mistaken for species of the family Opiliones.\nAn Urban legend claims that they are the most venomous spiders, this is incorrect and their venom is medically insignificant to humans (apart from not being able to penetrate skin.)\nDead spiders can often be found infected by a parasitic fungus Engyodontium aranearum which gives it this white fluffy appearance.</p>\n<p>For species identification</p>\n<p><a href=\"https://www.inaturalist.org/observations\" rel=\"nofollow noreferrer\">https://www.inaturalist.org/observations</a></p>\n<p>Pholcidae</p>\n<p><a href=\"https://en.wikipedia.org/wiki/Pholcidae\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/Pholcidae</a></p>\n<p>Fungus\n<a href=\"https://en.wikipedia.org/wiki/Engyodontium_aranearum\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/Engyodontium_aranearum</a></p>\n","answer_id":115893,"answer_text":"Its a spider belonging to the family of Pholcidae also known as cellar spider or daddy long-legs spider. They are often mistaken for species of the family Opiliones.\nAn Urban legend claims that they are the most venomous spiders, this is incorrect and their venom is medically insignificant to humans (apart from not being able to penetrate skin.)\nDead spiders can often be found infected by a parasitic fungus Engyodontium aranearum which gives it this white fluffy appearance.\n\n\n\n\nFor species identification\n\n\n\n\nhttps://www.inaturalist.org/observations (https://www.inaturalist.org/observations)\n\n\n\n\nPholcidae\n\n\n\n\nhttps://en.wikipedia.org/wiki/Pholcidae (https://en.wikipedia.org/wiki/Pholcidae)\n\n\n\n\nFungus\nhttps://en.wikipedia.org/wiki/Engyodontium_aranearum (https://en.wikipedia.org/wiki/Engyodontium_aranearum)","answer_url":"https://biology.stackexchange.com/a/115893","author":"Lukas4235","author_url":"https://biology.stackexchange.com/users/83315/lukas4235","content_license":"CC BY-SA 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BY-SA 4.0","context_id":"115893","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":"2025-01-02T08:48:40+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"A9EA0943-675B-429B-BD7E-4D0C34DF5AE8","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A9EA0943-675B-429B-BD7E-4D0C34DF5AE8/view-source"},{"content_license":"CC BY-SA 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spider?\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/I2tOD6Wk.png] (https://i.sstatic.net/I2tOD6Wk.png)"},{"context_id":"115893","html":"<p>Its a spider belonging to the family of Pholcidae also known as cellar spider or daddy long-legs spider. They are often mistaken for species of the family Opiliones.\nAn Urban legend claims that they are the most venomous spiders, this is incorrect and their venom is medically insignificant to humans (apart from not being able to penetrate skin.)\nDead spiders can often be found infected by a parasitic fungus Engyodontium aranearum which gives it this white fluffy appearance.</p>\n<p>For species identification</p>\n<p><a href=\"https://www.inaturalist.org/observations\" rel=\"nofollow noreferrer\">https://www.inaturalist.org/observations</a></p>\n<p>Pholcidae</p>\n<p><a href=\"https://en.wikipedia.org/wiki/Pholcidae\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/Pholcidae</a></p>\n<p>Fungus\n<a href=\"https://en.wikipedia.org/wiki/Engyodontium_aranearum\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/Engyodontium_aranearum</a></p>\n","text":"Its a spider belonging to the family of Pholcidae also known as cellar spider or daddy long-legs spider. They are often mistaken for species of the family Opiliones.\nAn Urban legend claims that they are the most venomous spiders, this is incorrect and their venom is medically insignificant to humans (apart from not being able to penetrate skin.)\nDead spiders can often be found infected by a parasitic fungus Engyodontium aranearum which gives it this white fluffy appearance.\n\n\n\n\nFor species identification\n\n\n\n\nhttps://www.inaturalist.org/observations (https://www.inaturalist.org/observations)\n\n\n\n\nPholcidae\n\n\n\n\nhttps://en.wikipedia.org/wiki/Pholcidae (https://en.wikipedia.org/wiki/Pholcidae)\n\n\n\n\nFungus\nhttps://en.wikipedia.org/wiki/Engyodontium_aranearum (https://en.wikipedia.org/wiki/Engyodontium_aranearum)"}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Engyodontium_aranearum","https://en.wikipedia.org/wiki/Pholcidae","https://i.sstatic.net/I2tOD6Wk.png","https://www.inaturalist.org/observations"],"ground_truth_type":"metadata_grounded","group_id":"7cade5869397db5ae21d9298f85faf0cebcc57ea2f1464a6b91cdcdbb52b0eae","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-52885e4d64d7efb3d74cedf9","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":"user366312","profile_url":"https://biology.stackexchange.com/users/71661/user366312","user_type":"registered"},"created_at":"2024-12-31T11:38:52+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"117C9D3A-5591-4C7E-ACF5-4E3713179930","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/117C9D3A-5591-4C7E-ACF5-4E3713179930/view-source"},{"content_license":null,"contributor":{"display_name":"theforestecologist","profile_url":"https://biology.stackexchange.com/users/16866/theforestecologist","user_type":"registered"},"created_at":"2025-01-01T16:53:48+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"FD862283-5B80-4CF6-921C-45945C74E86C","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FD862283-5B80-4CF6-921C-45945C74E86C/view-source"},{"content_license":null,"contributor":{"display_name":"Chris","profile_url":"https://biology.stackexchange.com/users/5144/chris","user_type":"moderator"},"created_at":"2025-01-06T07:54:03+00:00","raw_file":"raw/codex_api_v1/6498de963750b51efbda1119ed6af944d93448730fd638915c3f01fbcab0c1ec_1790824125196761600_0.json","raw_sha256":"6bc4a347798a1508410269e30549f130720c68f4c848e3ea1eb2f60991f67851","revision_guid":"14FA90EA-9C1A-4AF6-A894-7AD57F910745","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/14FA90EA-9C1A-4AF6-A894-7AD57F910745/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":"115886","source_record_sha256":"af4fe030bcc51bf66b6c52094ccf5823ec577699af11e3d7f4fd78b49be81c78","source_url":"https://biology.stackexchange.com/questions/115886/can-you-identify-this-animal","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"can you identify this animal?\nWhat kind of animal is this?\n\n\n\n\nis this a spider?\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/I2tOD6Wk.png] (https://i.sstatic.net/I2tOD6Wk.png)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":115893,"score":3}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":116098,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Someone appears to have made a tool specifically for this: <a href=\"https://github.com/pughlab/bamgineer\" rel=\"nofollow noreferrer\">Bamgineer</a>.</p>\n<p>This does not seem to me to be a good idea (see my comment), but nonetheless the tool does exist.</p>\n<p>There are some papers on this topic, e.g. <a href=\"https://www.sciencedirect.com/science/article/pii/S2949774424009646\" rel=\"nofollow noreferrer\">here</a>. I'd suggest searching PubMed.</p>\n","answer_id":116098,"answer_text":"Someone appears to have made a tool specifically for this: Bamgineer (https://github.com/pughlab/bamgineer).\n\n\n\n\nThis does not seem to me to be a good idea (see my comment), but nonetheless the tool does exist.\n\n\n\n\nThere are some papers on this topic, e.g. here (https://www.sciencedirect.com/science/article/pii/S2949774424009646). I'd suggest searching PubMed.","answer_url":"https://biology.stackexchange.com/a/116098","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2025-02-12T17:55:31+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":116097,"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":"2025-02-12T17:55:31+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"E4B59483-951D-4710-874B-B9AF164F6737","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E4B59483-951D-4710-874B-B9AF164F6737/view-source"}],"score":0}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Yonatan Wolberg","author_url":"https://biology.stackexchange.com/users/100747/yonatan-wolberg","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Yonatan Wolberg","profile_url":"https://biology.stackexchange.com/users/100747/yonatan-wolberg","user_type":"registered"},"created_at":"2025-02-12T14:07:31+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"D390822C-D2C5-4C39-A567-7946DDCCC608","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D390822C-D2C5-4C39-A567-7946DDCCC608/view-source"}],"url":"https://biology.stackexchange.com/questions/116097/generating-cnvs-del-dup-for-exome-sequencing-data-bam-and-inserting-them-int"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"116098","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":"2025-02-12T17:55:31+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"E4B59483-951D-4710-874B-B9AF164F6737","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E4B59483-951D-4710-874B-B9AF164F6737/view-source"}],"url":"https://biology.stackexchange.com/a/116098"}],"contexts":[{"context_id":"question","html":"<p>I'm looking at a way of simulating CNVs in exome sequencing data. The CNVs should be random, but cover any region in the exome and there can be several of them per individual. The CNVs must be of varying sizes, preferably at least 50 - 100 kb in size. Preferably, I would want to generate both deletions and duplications, of equal proportions and of variable copy number, although the limit is 6.</p>\n<p>I'm looking at using one tool to generate the CNVs and another to insert them into the exome sequencing BAM files. I understand that generating duplications and inserting them into the BAM file is tricky, but I would appreciate any advice about what tools to use for generating the CNVs and for inserting them into the BAM files.</p>\n<p>I'm not the most experienced with bioinformatics and so tools with a gentler learning curves would be preferable, although that must not come at the cost of effectiveness of the tool.</p>\n<p>The CNVs should be generated randomly but still be accessible to me in the form of a list file.</p>\n<p>Kind regards</p>\n","text":"I'm looking at a way of simulating CNVs in exome sequencing data. The CNVs should be random, but cover any region in the exome and there can be several of them per individual. The CNVs must be of varying sizes, preferably at least 50 - 100 kb in size. Preferably, I would want to generate both deletions and duplications, of equal proportions and of variable copy number, although the limit is 6.\n\n\n\n\nI'm looking at using one tool to generate the CNVs and another to insert them into the exome sequencing BAM files. I understand that generating duplications and inserting them into the BAM file is tricky, but I would appreciate any advice about what tools to use for generating the CNVs and for inserting them into the BAM files.\n\n\n\n\nI'm not the most experienced with bioinformatics and so tools with a gentler learning curves would be preferable, although that must not come at the cost of effectiveness of the tool.\n\n\n\n\nThe CNVs should be generated randomly but still be accessible to me in the form of a list file.\n\n\n\n\nKind regards"},{"context_id":"116098","html":"<p>Someone appears to have made a tool specifically for this: <a href=\"https://github.com/pughlab/bamgineer\" rel=\"nofollow noreferrer\">Bamgineer</a>.</p>\n<p>This does not seem to me to be a good idea (see my comment), but nonetheless the tool does exist.</p>\n<p>There are some papers on this topic, e.g. <a href=\"https://www.sciencedirect.com/science/article/pii/S2949774424009646\" rel=\"nofollow noreferrer\">here</a>. I'd suggest searching PubMed.</p>\n","text":"Someone appears to have made a tool specifically for this: Bamgineer (https://github.com/pughlab/bamgineer).\n\n\n\n\nThis does not seem to me to be a good idea (see my comment), but nonetheless the tool does exist.\n\n\n\n\nThere are some papers on this topic, e.g. here (https://www.sciencedirect.com/science/article/pii/S2949774424009646). I'd suggest searching PubMed."}],"domain":"biology","external_citations":["https://github.com/pughlab/bamgineer","https://www.sciencedirect.com/science/article/pii/S2949774424009646"],"ground_truth_type":"metadata_grounded","group_id":"ea46a4e1b97b107087af210a93ad412b34defde7f942e11c7d6d889ba700d755","hard_case_family":["multiple_sources"],"id":"RHM-44b790c36666bbffeabd0462","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":"Yonatan Wolberg","profile_url":"https://biology.stackexchange.com/users/100747/yonatan-wolberg","user_type":"registered"},"created_at":"2025-02-12T14:07:31+00:00","raw_file":"raw/codex_api_v1/b5cf9e7681589fdd0a03b17b5d31b32f33f38a7cf6e5ac27090a128a163b0540_1790824132485859700_0.json","raw_sha256":"0ba2d7bf8064037255ed7e8ce785d71d15061c9d80c66749fdabc38844ca42a2","revision_guid":"D390822C-D2C5-4C39-A567-7946DDCCC608","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D390822C-D2C5-4C39-A567-7946DDCCC608/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":"116097","source_record_sha256":"554e280094e56d61bdee2b8f354a903303bff9b4af70659fa2566c52b8e27cb8","source_url":"https://biology.stackexchange.com/questions/116097/generating-cnvs-del-dup-for-exome-sequencing-data-bam-and-inserting-them-int","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Generating CNVs (DEL/DUP) for exome sequencing data (BAM) and inserting them into BAM\nI'm looking at a way of simulating CNVs in exome sequencing data. The CNVs should be random, but cover any region in the exome and there can be several of them per individual. The CNVs must be of varying sizes, preferably at least 50 - 100 kb in size. Preferably, I would want to generate both deletions and duplications, of equal proportions and of variable copy number, although the limit is 6.\n\n\n\n\nI'm looking at using one tool to generate the CNVs and another to insert them into the exome sequencing BAM files. I understand that generating duplications and inserting them into the BAM file is tricky, but I would appreciate any advice about what tools to use for generating the CNVs and for inserting them into the BAM files.\n\n\n\n\nI'm not the most experienced with bioinformatics and so tools with a gentler learning curves would be preferable, although that must not come at the cost of effectiveness of the tool.\n\n\n\n\nThe CNVs should be generated randomly but still be accessible to me in the form of a list file.\n\n\n\n\nKind regards","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116098,"score":0}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>These are most likely Carpet beetle larvae exoskeletons. Carpet beetle are from the family <a href=\"https://en.wikipedia.org/wiki/Dermestidae\" rel=\"nofollow noreferrer\">Dermestidae</a> and are found world wide. There are about 1800 species within the family, many of which are pests of both household and industrial facilities, where they scavenge all manner of animal- and plant-derived materials. The most commonly found one in these sorts of situations is the <a href=\"https://en.wikipedia.org/wiki/Varied_carpet_beetle\" rel=\"nofollow noreferrer\">varied carpet beetle</a>, which can eat holes in your woolen and cotton clothes.</p>\n<p>The larvae are quite hairy and sort of striped, as can be seen in your picture, particularly the largest one in the middle. They are typically found in dark spots and will attempt to escape the light. Their movement is hunched, a bit like a caterpillar.</p>\n<p>I think you have several instars here, which means that the adults will have hatched. The adults shaped a bit like a lady-bird/lady-bug, but are typically quite small; a few millimetres at most and are patterned in various shades of brown, buff and black.</p>\n<p>These are very commonly asked about here: so here's some other posts with carpet beetles, which mean that this will likely be closed as a duplicate:</p>\n<p><a href=\"https://biology.stackexchange.com/questions/79183/what-kind-of-insect-can-this-be-this-appears-to-be-just-a-shell-after-and-insec\">What kind of insect can this be? This appears to be just a shell after and insect went through a metamorphosis process</a></p>\n<p><a href=\"https://biology.stackexchange.com/questions/103321/what-is-this-very-tiny-insect-that-was-in-my-bedsheets/103323#103323\">What is this very tiny insect that was in my bedsheets?</a></p>\n","answer_id":116269,"answer_text":"These are most likely Carpet beetle larvae exoskeletons. Carpet beetle are from the family Dermestidae (https://en.wikipedia.org/wiki/Dermestidae) and are found world wide. There are about 1800 species within the family, many of which are pests of both household and industrial facilities, where they scavenge all manner of animal- and plant-derived materials. The most commonly found one in these sorts of situations is the varied carpet beetle (https://en.wikipedia.org/wiki/Varied_carpet_beetle), which can eat holes in your woolen and cotton clothes.\n\n\n\n\nThe larvae are quite hairy and sort of striped, as can be seen in your picture, particularly the largest one in the middle. They are typically found in dark spots and will attempt to escape the light. Their movement is hunched, a bit like a caterpillar.\n\n\n\n\nI think you have several instars here, which means that the adults will have hatched. The adults shaped a bit like a lady-bird/lady-bug, but are typically quite small; a few millimetres at most and are patterned in various shades of brown, buff and black.\n\n\n\n\nThese are very commonly asked about here: so here's some other posts with carpet beetles, which mean that this will likely be closed as a duplicate:\n\n\n\n\nWhat kind of insect can this be? This appears to be just a shell after and insect went through a metamorphosis process (https://biology.stackexchange.com/questions/79183/what-kind-of-insect-can-this-be-this-appears-to-be-just-a-shell-after-and-insec)\n\n\n\n\nWhat is this very tiny insect that was in my bedsheets? (https://biology.stackexchange.com/questions/103321/what-is-this-very-tiny-insect-that-was-in-my-bedsheets/103323#103323)","answer_url":"https://biology.stackexchange.com/a/116269","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2025-03-22T06:57:12+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":116267,"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":"2025-03-22T06:57:12+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"85CE6AE6-4FC1-49EC-9EA6-27B9C20F4D58","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/85CE6AE6-4FC1-49EC-9EA6-27B9C20F4D58/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"user103134","author_url":"https://biology.stackexchange.com/users/103134/user103134","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"user103134","profile_url":"https://biology.stackexchange.com/users/103134/user103134","user_type":"registered"},"created_at":"2025-03-21T19:02:24+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"89A9C380-57CF-4191-A13F-77EE04A075C9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/89A9C380-57CF-4191-A13F-77EE04A075C9/view-source"}],"url":"https://biology.stackexchange.com/questions/116267/can-anyone-id-these-exoskeletons"},{"author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","context_id":"116269","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":"2025-03-22T06:57:12+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"85CE6AE6-4FC1-49EC-9EA6-27B9C20F4D58","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/85CE6AE6-4FC1-49EC-9EA6-27B9C20F4D58/view-source"}],"url":"https://biology.stackexchange.com/a/116269"}],"contexts":[{"context_id":"question","html":"<p>I was cleaning our bed mattress and box springs and found a few exoskeletons that look the same.  Not sure if they are bed bugs?  No other signs of bedbugs - and do not appear to be to me.  Any help is appreciated!</p>\n<p><a href=\"https://i.sstatic.net/oTtT394A.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/oTtT394A.jpg\" alt=\"enter image description here\" /></a></p>\n","text":"I was cleaning our bed mattress and box springs and found a few exoskeletons that look the same.  Not sure if they are bed bugs?  No other signs of bedbugs - and do not appear to be to me.  Any help is appreciated!\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/oTtT394A.jpg] (https://i.sstatic.net/oTtT394A.jpg)"},{"context_id":"116269","html":"<p>These are most likely Carpet beetle larvae exoskeletons. Carpet beetle are from the family <a href=\"https://en.wikipedia.org/wiki/Dermestidae\" rel=\"nofollow noreferrer\">Dermestidae</a> and are found world wide. There are about 1800 species within the family, many of which are pests of both household and industrial facilities, where they scavenge all manner of animal- and plant-derived materials. The most commonly found one in these sorts of situations is the <a href=\"https://en.wikipedia.org/wiki/Varied_carpet_beetle\" rel=\"nofollow noreferrer\">varied carpet beetle</a>, which can eat holes in your woolen and cotton clothes.</p>\n<p>The larvae are quite hairy and sort of striped, as can be seen in your picture, particularly the largest one in the middle. They are typically found in dark spots and will attempt to escape the light. Their movement is hunched, a bit like a caterpillar.</p>\n<p>I think you have several instars here, which means that the adults will have hatched. The adults shaped a bit like a lady-bird/lady-bug, but are typically quite small; a few millimetres at most and are patterned in various shades of brown, buff and black.</p>\n<p>These are very commonly asked about here: so here's some other posts with carpet beetles, which mean that this will likely be closed as a duplicate:</p>\n<p><a href=\"https://biology.stackexchange.com/questions/79183/what-kind-of-insect-can-this-be-this-appears-to-be-just-a-shell-after-and-insec\">What kind of insect can this be? This appears to be just a shell after and insect went through a metamorphosis process</a></p>\n<p><a href=\"https://biology.stackexchange.com/questions/103321/what-is-this-very-tiny-insect-that-was-in-my-bedsheets/103323#103323\">What is this very tiny insect that was in my bedsheets?</a></p>\n","text":"These are most likely Carpet beetle larvae exoskeletons. Carpet beetle are from the family Dermestidae (https://en.wikipedia.org/wiki/Dermestidae) and are found world wide. There are about 1800 species within the family, many of which are pests of both household and industrial facilities, where they scavenge all manner of animal- and plant-derived materials. The most commonly found one in these sorts of situations is the varied carpet beetle (https://en.wikipedia.org/wiki/Varied_carpet_beetle), which can eat holes in your woolen and cotton clothes.\n\n\n\n\nThe larvae are quite hairy and sort of striped, as can be seen in your picture, particularly the largest one in the middle. They are typically found in dark spots and will attempt to escape the light. Their movement is hunched, a bit like a caterpillar.\n\n\n\n\nI think you have several instars here, which means that the adults will have hatched. The adults shaped a bit like a lady-bird/lady-bug, but are typically quite small; a few millimetres at most and are patterned in various shades of brown, buff and black.\n\n\n\n\nThese are very commonly asked about here: so here's some other posts with carpet beetles, which mean that this will likely be closed as a duplicate:\n\n\n\n\nWhat kind of insect can this be? This appears to be just a shell after and insect went through a metamorphosis process (https://biology.stackexchange.com/questions/79183/what-kind-of-insect-can-this-be-this-appears-to-be-just-a-shell-after-and-insec)\n\n\n\n\nWhat is this very tiny insect that was in my bedsheets? (https://biology.stackexchange.com/questions/103321/what-is-this-very-tiny-insect-that-was-in-my-bedsheets/103323#103323)"}],"domain":"biology","external_citations":["https://biology.stackexchange.com/questions/103321/what-is-this-very-tiny-insect-that-was-in-my-bedsheets/103323#103323","https://biology.stackexchange.com/questions/79183/what-kind-of-insect-can-this-be-this-appears-to-be-just-a-shell-after-and-insec","https://en.wikipedia.org/wiki/Dermestidae","https://en.wikipedia.org/wiki/Varied_carpet_beetle","https://i.sstatic.net/oTtT394A.jpg"],"ground_truth_type":"metadata_grounded","group_id":"571288de26711e452c23fe768cc449aded02669c27c9ec61e786cac9c24cde77","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-aae656ce4b937dde609be719","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":"user103134","profile_url":"https://biology.stackexchange.com/users/103134/user103134","user_type":"registered"},"created_at":"2025-03-21T19:02:24+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"89A9C380-57CF-4191-A13F-77EE04A075C9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/89A9C380-57CF-4191-A13F-77EE04A075C9/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":"116267","source_record_sha256":"89d4e42276fd564940ce1dd5ca337a4428f36683748092868c4256f075ccd49f","source_url":"https://biology.stackexchange.com/questions/116267/can-anyone-id-these-exoskeletons","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Can anyone ID these exoskeletons?\nI was cleaning our bed mattress and box springs and found a few exoskeletons that look the same.  Not sure if they are bed bugs?  No other signs of bedbugs - and do not appear to be to me.  Any help is appreciated!\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/oTtT394A.jpg] (https://i.sstatic.net/oTtT394A.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116269,"score":3}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":116275,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Something implied but unstated in your question is that many platyhelminthes have no anus (and thus no true gut).</p>\n<p>However, <a href=\"https://en.wikipedia.org/wiki/Flatworm#cite_note-RuppertBarnes2004Platyhelminthes-13\" rel=\"nofollow noreferrer\">some of them do have a complete gut</a>:</p>\n<blockquote>\n<p>Most platyhelminths have no anus and regurgitate undigested material through the mouth. The genus Paracatenula, whose members include tiny flatworms living in symbiosis with bacteria, is even missing a mouth and a gut.[16] <strong>However, some long species have an anus and some with complex, branched guts have more than one anus,</strong> since excretion only through the mouth would be difficult for them.[13] The gut is lined with a single layer of endodermal cells that absorb and digest food. Some species break up and soften food first by secreting enzymes in the gut or pharynx (throat).[5]</p>\n</blockquote>\n<p>Thus, the feature is variable within this clade. This requires logically that the gut has been lost (and/or gained) within the clade, not in its common ancestor, unless we go on to assert that the clade is polyphyletic.</p>\n","answer_id":116275,"answer_text":"Something implied but unstated in your question is that many platyhelminthes have no anus (and thus no true gut).\n\n\n\n\nHowever, some of them do have a complete gut (https://en.wikipedia.org/wiki/Flatworm#cite_note-RuppertBarnes2004Platyhelminthes-13):\n\n\n\n\n\n\n\nMost platyhelminths have no anus and regurgitate undigested material through the mouth. The genus Paracatenula, whose members include tiny flatworms living in symbiosis with bacteria, is even missing a mouth and a gut.[16] However, some long species have an anus and some with complex, branched guts have more than one anus, since excretion only through the mouth would be difficult for them.[13] The gut is lined with a single layer of endodermal cells that absorb and digest food. Some species break up and soften food first by secreting enzymes in the gut or pharynx (throat).[5]\n\n\n\n\n\n\n\nThus, the feature is variable within this clade. This requires logically that the gut has been lost (and/or gained) within the clade, not in its common ancestor, unless we go on to assert that the clade is polyphyletic.","answer_url":"https://biology.stackexchange.com/a/116275","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2025-03-24T19:42:39+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":116270,"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":"2025-03-24T19:42:39+00:00","raw_file":"raw/codex_api_v1/6a8d1217a71337b035f168c28f3cef00c95606938297595ce7816a6ee2aabc47_1790824139846857200_0.json","raw_sha256":"915362f28bff22e7e44f536acc7b10e33f23a77bbb5e547906a8fdc7cf7e3e89","revision_guid":"81ED3CB3-285D-453C-84F1-57651E1E21DE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/81ED3CB3-285D-453C-84F1-57651E1E21DE/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":"2025-03-24T21:32:53+00:00","raw_file":"raw/codex_api_v1/6a8d1217a71337b035f168c28f3cef00c95606938297595ce7816a6ee2aabc47_1790824139846857200_0.json","raw_sha256":"915362f28bff22e7e44f536acc7b10e33f23a77bbb5e547906a8fdc7cf7e3e89","revision_guid":"429CB024-3177-48EC-82D2-4EE57C892927","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/429CB024-3177-48EC-82D2-4EE57C892927/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":"2025-04-01T19:01:02+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"363A0C1D-7261-4CAD-AC78-206353E08590","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/363A0C1D-7261-4CAD-AC78-206353E08590/view-source"}],"score":3},{"answer_html":"<p>This question was addressed by <a href=\"https://www.sciencedirect.com/science/article/pii/S0012160611000650?via%3Dihub\" rel=\"nofollow noreferrer\">José María Martín-Durán and Rafael Romero (2011)</a></p>\n<p>To quote from their conclusions:</p>\n<blockquote>\n<p>The expression of foxA suggests that the pharynx of triclads could be considered homologous to either the foregut or the anterior midgut of other bilaterians with a through-gut. However, important foregut markers like brachyury or gsx have been lost, and other foregut-related genes including NK2.1 and otx (Garcia-Fernàndez et al., 1993, Umesono et al., 1999) are not expressed in the pharynx (Fig. 8A). The determination of the endoderm through a GATA456-dependent mechanism seems to be conserved in triclads, but not the specification of a main midgut region, since Xlox is not expressed in the digestive system. Finally, other hindgut-associated genes do not show gut-associated expression either, whether due to the physical loss of the gene in the genome (the case of brachyury or caudal) or the absence of the expression domain in the developing embryo (loss of the hindgut domain of foxA or orthopedia) (Umesono et al., 1997). Accordingly, we propose that the antero-posterior gut-regionalization present in those bilaterians with a through-gut is not present in triclads. In our model, the digestive system is only patterned in two main regions, namely, the pharynx and the blind gut.</p>\n</blockquote>\n<p>Note that <a href=\"https://en.wikipedia.org/wiki/Platyhelminthes\" rel=\"nofollow noreferrer\">Platyhelminthes</a> have undergone some redefinition, so I'm going to leave aside the consideration of members outside Spiralia.</p>\n","answer_id":116278,"answer_text":"This question was addressed by José María Martín-Durán and Rafael Romero (2011) (https://www.sciencedirect.com/science/article/pii/S0012160611000650?via%3Dihub)\n\n\n\n\nTo quote from their conclusions:\n\n\n\n\n\n\n\nThe expression of foxA suggests that the pharynx of triclads could be considered homologous to either the foregut or the anterior midgut of other bilaterians with a through-gut. However, important foregut markers like brachyury or gsx have been lost, and other foregut-related genes including NK2.1 and otx (Garcia-Fernàndez et al., 1993, Umesono et al., 1999) are not expressed in the pharynx (Fig. 8A). The determination of the endoderm through a GATA456-dependent mechanism seems to be conserved in triclads, but not the specification of a main midgut region, since Xlox is not expressed in the digestive system. Finally, other hindgut-associated genes do not show gut-associated expression either, whether due to the physical loss of the gene in the genome (the case of brachyury or caudal) or the absence of the expression domain in the developing embryo (loss of the hindgut domain of foxA or orthopedia) (Umesono et al., 1997). Accordingly, we propose that the antero-posterior gut-regionalization present in those bilaterians with a through-gut is not present in triclads. In our model, the digestive system is only patterned in two main regions, namely, the pharynx and the blind gut.\n\n\n\n\n\n\n\nNote that Platyhelminthes (https://en.wikipedia.org/wiki/Platyhelminthes) have undergone some redefinition, so I'm going to leave aside the consideration of members outside Spiralia.","answer_url":"https://biology.stackexchange.com/a/116278","author":"Mike Serfas","author_url":"https://biology.stackexchange.com/users/57271/mike-serfas","content_license":"CC BY-SA 4.0","created_at":"2025-03-25T03:44:27+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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Kostlan","profile_url":"https://biology.stackexchange.com/users/4321/kevin-kostlan","user_type":"registered"},"created_at":"2025-03-23T05:36:34+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"75ACE4CF-3FCD-4CEF-958E-3DA3CF1DFD68","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/75ACE4CF-3FCD-4CEF-958E-3DA3CF1DFD68/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Kevin Kostlan","profile_url":"https://biology.stackexchange.com/users/4321/kevin-kostlan","user_type":"registered"},"created_at":"2025-03-23T05:42:15+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"96C8D56A-4C2F-4B74-B002-0561E51CF6A4","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/96C8D56A-4C2F-4B74-B002-0561E51CF6A4/view-source"}],"url":"https://biology.stackexchange.com/questions/116270/did-flatworms-lose-an-ancestral-one-way-digestive-tract"},{"author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"116275","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":"2025-03-24T19:42:39+00:00","raw_file":"raw/codex_api_v1/6a8d1217a71337b035f168c28f3cef00c95606938297595ce7816a6ee2aabc47_1790824139846857200_0.json","raw_sha256":"915362f28bff22e7e44f536acc7b10e33f23a77bbb5e547906a8fdc7cf7e3e89","revision_guid":"81ED3CB3-285D-453C-84F1-57651E1E21DE","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/81ED3CB3-285D-453C-84F1-57651E1E21DE/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":"2025-03-24T21:32:53+00:00","raw_file":"raw/codex_api_v1/6a8d1217a71337b035f168c28f3cef00c95606938297595ce7816a6ee2aabc47_1790824139846857200_0.json","raw_sha256":"915362f28bff22e7e44f536acc7b10e33f23a77bbb5e547906a8fdc7cf7e3e89","revision_guid":"429CB024-3177-48EC-82D2-4EE57C892927","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/429CB024-3177-48EC-82D2-4EE57C892927/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":"2025-04-01T19:01:02+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"363A0C1D-7261-4CAD-AC78-206353E08590","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/363A0C1D-7261-4CAD-AC78-206353E08590/view-source"}],"url":"https://biology.stackexchange.com/a/116275"},{"author":"Mike Serfas","author_url":"https://biology.stackexchange.com/users/57271/mike-serfas","content_license":"CC BY-SA 4.0","context_id":"116278","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":"2025-03-25T03:44:27+00:00","raw_file":"raw/codex_api_v1/6a8d1217a71337b035f168c28f3cef00c95606938297595ce7816a6ee2aabc47_1790824139846857200_0.json","raw_sha256":"915362f28bff22e7e44f536acc7b10e33f23a77bbb5e547906a8fdc7cf7e3e89","revision_guid":"F92A05C4-71D9-4CA5-A6EE-3F383633A001","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F92A05C4-71D9-4CA5-A6EE-3F383633A001/view-source"}],"url":"https://biology.stackexchange.com/a/116278"}],"contexts":[{"context_id":"question","html":"<p>Planarians are in the <a href=\"https://en.m.wikipedia.org/wiki/Spiralia\" rel=\"nofollow noreferrer\">Spiralia</a> clade, which is more closely related to mollusks than arthropods.</p>\n<p>Both mollusks and arthropods are <em>protostomes</em> with a mouth and anus with a one-way transfer of food through their digestive system. Having a proper &quot;gut&quot; is considered a major evolutionary advantage which contributed to the extreme success of these two phyla.</p>\n<p>Did planarians and other platyhelminthes lose the ancestral protostome gut while mollusks and arthropods kept it? Or did mollusks and arthropods independently evolve one-way digestive tracts?</p>\n","text":"Planarians are in the Spiralia (https://en.m.wikipedia.org/wiki/Spiralia) clade, which is more closely related to mollusks than arthropods.\n\n\n\n\nBoth mollusks and arthropods are protostomes with a mouth and anus with a one-way transfer of food through their digestive system. Having a proper \"gut\" is considered a major evolutionary advantage which contributed to the extreme success of these two phyla.\n\n\n\n\nDid planarians and other platyhelminthes lose the ancestral protostome gut while mollusks and arthropods kept it? Or did mollusks and arthropods independently evolve one-way digestive tracts?"},{"context_id":"116275","html":"<p>Something implied but unstated in your question is that many platyhelminthes have no anus (and thus no true gut).</p>\n<p>However, <a href=\"https://en.wikipedia.org/wiki/Flatworm#cite_note-RuppertBarnes2004Platyhelminthes-13\" rel=\"nofollow noreferrer\">some of them do have a complete gut</a>:</p>\n<blockquote>\n<p>Most platyhelminths have no anus and regurgitate undigested material through the mouth. The genus Paracatenula, whose members include tiny flatworms living in symbiosis with bacteria, is even missing a mouth and a gut.[16] <strong>However, some long species have an anus and some with complex, branched guts have more than one anus,</strong> since excretion only through the mouth would be difficult for them.[13] The gut is lined with a single layer of endodermal cells that absorb and digest food. Some species break up and soften food first by secreting enzymes in the gut or pharynx (throat).[5]</p>\n</blockquote>\n<p>Thus, the feature is variable within this clade. This requires logically that the gut has been lost (and/or gained) within the clade, not in its common ancestor, unless we go on to assert that the clade is polyphyletic.</p>\n","text":"Something implied but unstated in your question is that many platyhelminthes have no anus (and thus no true gut).\n\n\n\n\nHowever, some of them do have a complete gut (https://en.wikipedia.org/wiki/Flatworm#cite_note-RuppertBarnes2004Platyhelminthes-13):\n\n\n\n\n\n\n\nMost platyhelminths have no anus and regurgitate undigested material through the mouth. The genus Paracatenula, whose members include tiny flatworms living in symbiosis with bacteria, is even missing a mouth and a gut.[16] However, some long species have an anus and some with complex, branched guts have more than one anus, since excretion only through the mouth would be difficult for them.[13] The gut is lined with a single layer of endodermal cells that absorb and digest food. Some species break up and soften food first by secreting enzymes in the gut or pharynx (throat).[5]\n\n\n\n\n\n\n\nThus, the feature is variable within this clade. This requires logically that the gut has been lost (and/or gained) within the clade, not in its common ancestor, unless we go on to assert that the clade is polyphyletic."},{"context_id":"116278","html":"<p>This question was addressed by <a href=\"https://www.sciencedirect.com/science/article/pii/S0012160611000650?via%3Dihub\" rel=\"nofollow noreferrer\">José María Martín-Durán and Rafael Romero (2011)</a></p>\n<p>To quote from their conclusions:</p>\n<blockquote>\n<p>The expression of foxA suggests that the pharynx of triclads could be considered homologous to either the foregut or the anterior midgut of other bilaterians with a through-gut. However, important foregut markers like brachyury or gsx have been lost, and other foregut-related genes including NK2.1 and otx (Garcia-Fernàndez et al., 1993, Umesono et al., 1999) are not expressed in the pharynx (Fig. 8A). The determination of the endoderm through a GATA456-dependent mechanism seems to be conserved in triclads, but not the specification of a main midgut region, since Xlox is not expressed in the digestive system. Finally, other hindgut-associated genes do not show gut-associated expression either, whether due to the physical loss of the gene in the genome (the case of brachyury or caudal) or the absence of the expression domain in the developing embryo (loss of the hindgut domain of foxA or orthopedia) (Umesono et al., 1997). Accordingly, we propose that the antero-posterior gut-regionalization present in those bilaterians with a through-gut is not present in triclads. In our model, the digestive system is only patterned in two main regions, namely, the pharynx and the blind gut.</p>\n</blockquote>\n<p>Note that <a href=\"https://en.wikipedia.org/wiki/Platyhelminthes\" rel=\"nofollow noreferrer\">Platyhelminthes</a> have undergone some redefinition, so I'm going to leave aside the consideration of members outside Spiralia.</p>\n","text":"This question was addressed by José María Martín-Durán and Rafael Romero (2011) (https://www.sciencedirect.com/science/article/pii/S0012160611000650?via%3Dihub)\n\n\n\n\nTo quote from their conclusions:\n\n\n\n\n\n\n\nThe expression of foxA suggests that the pharynx of triclads could be considered homologous to either the foregut or the anterior midgut of other bilaterians with a through-gut. However, important foregut markers like brachyury or gsx have been lost, and other foregut-related genes including NK2.1 and otx (Garcia-Fernàndez et al., 1993, Umesono et al., 1999) are not expressed in the pharynx (Fig. 8A). The determination of the endoderm through a GATA456-dependent mechanism seems to be conserved in triclads, but not the specification of a main midgut region, since Xlox is not expressed in the digestive system. Finally, other hindgut-associated genes do not show gut-associated expression either, whether due to the physical loss of the gene in the genome (the case of brachyury or caudal) or the absence of the expression domain in the developing embryo (loss of the hindgut domain of foxA or orthopedia) (Umesono et al., 1997). Accordingly, we propose that the antero-posterior gut-regionalization present in those bilaterians with a through-gut is not present in triclads. In our model, the digestive system is only patterned in two main regions, namely, the pharynx and the blind gut.\n\n\n\n\n\n\n\nNote that Platyhelminthes (https://en.wikipedia.org/wiki/Platyhelminthes) have undergone some redefinition, so I'm going to leave aside the consideration of members outside Spiralia."}],"domain":"biology","external_citations":["https://en.m.wikipedia.org/wiki/Spiralia","https://en.wikipedia.org/wiki/Flatworm#cite_note-RuppertBarnes2004Platyhelminthes-13","https://en.wikipedia.org/wiki/Platyhelminthes","https://www.sciencedirect.com/science/article/pii/S0012160611000650?via%3Dihub"],"ground_truth_type":"metadata_grounded","group_id":"3e051bbc85c50d44544ddcf3acdb30a875dbc3c01b3a6b9ec357f935f330a57e","hard_case_family":["multiple_sources","multiple_answer_candidates"],"id":"RHM-fd93f0783dd84a494f0eca55","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":"Kevin Kostlan","profile_url":"https://biology.stackexchange.com/users/4321/kevin-kostlan","user_type":"registered"},"created_at":"2025-03-23T05:36:34+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"75ACE4CF-3FCD-4CEF-958E-3DA3CF1DFD68","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/75ACE4CF-3FCD-4CEF-958E-3DA3CF1DFD68/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Kevin Kostlan","profile_url":"https://biology.stackexchange.com/users/4321/kevin-kostlan","user_type":"registered"},"created_at":"2025-03-23T05:42:15+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"96C8D56A-4C2F-4B74-B002-0561E51CF6A4","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/96C8D56A-4C2F-4B74-B002-0561E51CF6A4/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":"116270","source_record_sha256":"030513f9a75cffa2138c0ef518dc1f5de70a26383064fc7a7f7279061f8ff52f","source_url":"https://biology.stackexchange.com/questions/116270/did-flatworms-lose-an-ancestral-one-way-digestive-tract","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Did flatworms lose an ancestral one-way digestive tract?\nPlanarians are in the Spiralia (https://en.m.wikipedia.org/wiki/Spiralia) clade, which is more closely related to mollusks than arthropods.\n\n\n\n\nBoth mollusks and arthropods are protostomes with a mouth and anus with a one-way transfer of food through their digestive system. Having a proper \"gut\" is considered a major evolutionary advantage which contributed to the extreme success of these two phyla.\n\n\n\n\nDid planarians and other platyhelminthes lose the ancestral protostome gut while mollusks and arthropods kept it? Or did mollusks and arthropods independently evolve one-way digestive tracts?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116275,"score":3},{"answer_id":116278,"score":2}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":116285,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p><strong>To clarify and close the question:</strong></p>\n<p>Most papers on mathematical compost modeling assume that the compost mass remains constant, which I will refer to as the wet mass. This assumption is generally valid for an in-vessel compost reactor (a closed system), where moisture is assumed to remain contained within the system.</p>\n<p>The confusion may arise because some papers refer to the compost substrate <span class=\"math-container\">$S$</span>, which is not the same as the wet mass. The substrate typically refers to the BVS (Biodegradable Volatile Solids), which decays over time, while the wet mass includes both the BVS and the inert or non-degradable mass, as well as moisture in the compost.</p>\n<p>When deriving the heat balance equation:</p>\n<p><span class=\"math-container\">$$\\frac{d(cmT)}{dt} = \\sum \\dot{Q}$$</span></p>\n<p>It logically follows that any heat generated from the BVS (Biodegradable Volatile Solids)—which represents the energy-producing portion of the compost—will be absorbed by the entire mass, including the wet mass. This accounts for the fact that heat energy is distributed across the total system, not just the decaying BVS fraction.</p>\n","answer_id":116285,"answer_text":"To clarify and close the question:\n\n\n\n\nMost papers on mathematical compost modeling assume that the compost mass remains constant, which I will refer to as the wet mass. This assumption is generally valid for an in-vessel compost reactor (a closed system), where moisture is assumed to remain contained within the system.\n\n\n\n\nThe confusion may arise because some papers refer to the compost substrate $S$, which is not the same as the wet mass. The substrate typically refers to the BVS (Biodegradable Volatile Solids), which decays over time, while the wet mass includes both the BVS and the inert or non-degradable mass, as well as moisture in the compost.\n\n\n\n\nWhen deriving the heat balance equation:\n\n\n\n\n$$\\frac{d(cmT)}{dt} = \\sum \\dot{Q}$$\n\n\n\n\nIt logically follows that any heat generated from the BVS (Biodegradable Volatile Solids)—which represents the energy-producing portion of the compost—will be absorbed by the entire mass, including the wet mass. This accounts for the fact that heat energy is distributed across the total system, not just the decaying BVS fraction.","answer_url":"https://biology.stackexchange.com/a/116285","author":"user51811","author_url":"https://biology.stackexchange.com/users/103271/user51811","content_license":"CC BY-SA 4.0","created_at":"2025-03-26T09:28:53+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 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an engineer by background and have been exploring the mathematical models in compost science. One common equation I’ve come across is the energy balance:<span class=\"math-container\">$$\\frac{d(mcT)}{dt} = G(H_i - H_o) - UA(T-T_a) + Q_{bio}$$</span>\nWhere <span class=\"math-container\">$m$</span> is the mass, <span class=\"math-container\">$c$</span> the specific heat capacity, <span class=\"math-container\">$T$</span> the temperature, <span class=\"math-container\">$G$</span> the airflow, <span class=\"math-container\">$H_i$</span> and <span class=\"math-container\">$H_o$</span> the inlet and outlet enthalpies, <span class=\"math-container\">$U$</span> a general heat transfer coefficient, <span class=\"math-container\">$A$</span> the system area, <span class=\"math-container\">$T_a$</span> the ambient temperature, and <span class=\"math-container\">$Q_{bio}$</span> the biological heat production.</p>\n<p>For the mass, I wonder how this assumption can be made valid. I assume that it's the dry mass, although some papers use wet mass, which wouldn't make a strong assumption in theory, as from start (mesophilic) to end (maturation finalisation) the moisture loss alone can cause a significant mass loss.</p>\n<p>A frequent assumption in many papers is that <span class=\"math-container\">$m$</span> and <span class=\"math-container\">$c$</span> remain constant over time. However, considering that composting involves significant changes—especially moisture loss—it’s unclear how valid this assumption is. Is the idea that the model uses the dry mass rather than the wet mass, or is there another justification? How might this simplification impact the model’s accuracy given the considerable mass loss from moisture evaporation?</p>\n<p>I’ve referenced a few papers discussing this approach:</p>\n<ol>\n<li><a href=\"https://www.sciencedirect.com/science/article/pii/S0956053X20303287\" rel=\"noreferrer\">Source 1</a></li>\n<li><a href=\"https://www.sciencedirect.com/science/article/pii/S0956053X05000668?ref=pdf_download&amp;fr=RR-2&amp;rr=9250491949a594c0\" rel=\"noreferrer\">Source 2</a></li>\n<li><a href=\"https://www.researchgate.net/publication/269609693_Mathematical_Model_of_Compost_Pile_Temperature_Prediction\" rel=\"noreferrer\">Source 3</a></li>\n</ol>\n","text":"I’m an engineer by background and have been exploring the mathematical models in compost science. One common equation I’ve come across is the energy balance:$$\\frac{d(mcT)}{dt} = G(H_i - H_o) - UA(T-T_a) + Q_{bio}$$\nWhere $m$ is the mass, $c$ the specific heat capacity, $T$ the temperature, $G$ the airflow, $H_i$ and $H_o$ the inlet and outlet enthalpies, $U$ a general heat transfer coefficient, $A$ the system area, $T_a$ the ambient temperature, and $Q_{bio}$ the biological heat production.\n\n\n\n\nFor the mass, I wonder how this assumption can be made valid. I assume that it's the dry mass, although some papers use wet mass, which wouldn't make a strong assumption in theory, as from start (mesophilic) to end (maturation finalisation) the moisture loss alone can cause a significant mass loss.\n\n\n\n\nA frequent assumption in many papers is that $m$ and $c$ remain constant over time. However, considering that composting involves significant changes—especially moisture loss—it’s unclear how valid this assumption is. Is the idea that the model uses the dry mass rather than the wet mass, or is there another justification? How might this simplification impact the model’s accuracy given the considerable mass loss from moisture evaporation?\n\n\n\n\nI’ve referenced a few papers discussing this approach:\n\n\n\n\n\nSource 1 (https://www.sciencedirect.com/science/article/pii/S0956053X20303287)\n\n\n\n\nSource 2 (https://www.sciencedirect.com/science/article/pii/S0956053X05000668?ref=pdf_download&fr=RR-2&rr=9250491949a594c0)\n\n\n\n\nSource 3 (https://www.researchgate.net/publication/269609693_Mathematical_Model_of_Compost_Pile_Temperature_Prediction)"},{"context_id":"116285","html":"<p><strong>To clarify and close the question:</strong></p>\n<p>Most papers on mathematical compost modeling assume that the compost mass remains constant, which I will refer to as the wet mass. This assumption is generally valid for an in-vessel compost reactor (a closed system), where moisture is assumed to remain contained within the system.</p>\n<p>The confusion may arise because some papers refer to the compost substrate <span class=\"math-container\">$S$</span>, which is not the same as the wet mass. The substrate typically refers to the BVS (Biodegradable Volatile Solids), which decays over time, while the wet mass includes both the BVS and the inert or non-degradable mass, as well as moisture in the compost.</p>\n<p>When deriving the heat balance equation:</p>\n<p><span class=\"math-container\">$$\\frac{d(cmT)}{dt} = \\sum \\dot{Q}$$</span></p>\n<p>It logically follows that any heat generated from the BVS (Biodegradable Volatile Solids)—which represents the energy-producing portion of the compost—will be absorbed by the entire mass, including the wet mass. This accounts for the fact that heat energy is distributed across the total system, not just the decaying BVS fraction.</p>\n","text":"To clarify and close the question:\n\n\n\n\nMost papers on mathematical compost modeling assume that the compost mass remains constant, which I will refer to as the wet mass. This assumption is generally valid for an in-vessel compost reactor (a closed system), where moisture is assumed to remain contained within the system.\n\n\n\n\nThe confusion may arise because some papers refer to the compost substrate $S$, which is not the same as the wet mass. The substrate typically refers to the BVS (Biodegradable Volatile Solids), which decays over time, while the wet mass includes both the BVS and the inert or non-degradable mass, as well as moisture in the compost.\n\n\n\n\nWhen deriving the heat balance equation:\n\n\n\n\n$$\\frac{d(cmT)}{dt} = \\sum \\dot{Q}$$\n\n\n\n\nIt logically follows that any heat generated from the BVS (Biodegradable Volatile Solids)—which represents the energy-producing portion of the compost—will be absorbed by the entire mass, including the wet mass. This accounts for the fact that heat energy is distributed across the total system, not just the decaying BVS fraction."}],"domain":"biology","external_citations":["https://www.researchgate.net/publication/269609693_Mathematical_Model_of_Compost_Pile_Temperature_Prediction","https://www.sciencedirect.com/science/article/pii/S0956053X05000668?ref=pdf_download&fr=RR-2&rr=9250491949a594c0","https://www.sciencedirect.com/science/article/pii/S0956053X20303287"],"ground_truth_type":"metadata_grounded","group_id":"2eb0959b98d7eef4f5f3a5026777cf0a97f179bcd979362e392380e7807f7416","hard_case_family":["multiple_sources"],"id":"RHM-9a890d2c9357c0b69eef3bf1","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":"user51811","profile_url":"https://biology.stackexchange.com/users/103271/user51811","user_type":"registered"},"created_at":"2025-03-23T19:29:28+00:00","raw_file":"raw/codex_api_v1/d15f4865285273ae6317f3f3c349227e1b259d6015b55aa14ef5accac806b399_1790824130296338000_0.json","raw_sha256":"611d5d0f66539d270d10e88493add03469f6e7c1f54b654a8efbaea5fbbc2960","revision_guid":"DE5C7257-9894-43BA-B311-C6A0107FF967","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DE5C7257-9894-43BA-B311-C6A0107FF967/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":"116271","source_record_sha256":"0b77e25065311a5753f0303d8c1456b3930c3f015ec0bb99354a8ca2ea6a0b39","source_url":"https://biology.stackexchange.com/questions/116271/compost-mathematical-model-mass-assumption","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Compost Mathematical Model - Mass Assumption\nI’m an engineer by background and have been exploring the mathematical models in compost science. One common equation I’ve come across is the energy balance:$$\\frac{d(mcT)}{dt} = G(H_i - H_o) - UA(T-T_a) + Q_{bio}$$\nWhere $m$ is the mass, $c$ the specific heat capacity, $T$ the temperature, $G$ the airflow, $H_i$ and $H_o$ the inlet and outlet enthalpies, $U$ a general heat transfer coefficient, $A$ the system area, $T_a$ the ambient temperature, and $Q_{bio}$ the biological heat production.\n\n\n\n\nFor the mass, I wonder how this assumption can be made valid. I assume that it's the dry mass, although some papers use wet mass, which wouldn't make a strong assumption in theory, as from start (mesophilic) to end (maturation finalisation) the moisture loss alone can cause a significant mass loss.\n\n\n\n\nA frequent assumption in many papers is that $m$ and $c$ remain constant over time. However, considering that composting involves significant changes—especially moisture loss—it’s unclear how valid this assumption is. Is the idea that the model uses the dry mass rather than the wet mass, or is there another justification? How might this simplification impact the model’s accuracy given the considerable mass loss from moisture evaporation?\n\n\n\n\nI’ve referenced a few papers discussing this approach:\n\n\n\n\n\nSource 1 (https://www.sciencedirect.com/science/article/pii/S0956053X20303287)\n\n\n\n\nSource 2 (https://www.sciencedirect.com/science/article/pii/S0956053X05000668?ref=pdf_download&fr=RR-2&rr=9250491949a594c0)\n\n\n\n\nSource 3 (https://www.researchgate.net/publication/269609693_Mathematical_Model_of_Compost_Pile_Temperature_Prediction)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116285,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":116341,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I've not read the press release, but I can tell you unequivocally that these are not dire wolves (<em><a href=\"https://en.wikipedia.org/wiki/Dire_wolf\" rel=\"noreferrer\">Aenocyon dirus</a></em>). These are grey wolves tweaked for some characteristics.</p>\n<p>Simply put, they have taken a grey wolf (<em><a href=\"https://en.wikipedia.org/wiki/Wolf\" rel=\"noreferrer\">Canis lupus lupus</a></em>) and tweaked some genes, I think around 20ish genes from the media stories I have seen. These genes are particularly those that make the head larger and muscles stronger. These alter the external appearance of the wolf to look more like dire wolves.</p>\n<p>Grey wolves and dire wolves, as you can see from the scientific names, are from separate genera within the dog (<a href=\"https://en.wikipedia.org/wiki/Canidae\" rel=\"noreferrer\">Canidae</a>) family. This means that, while they are related, there is a distant genetic relationship. You could think of this as being similar to the relationship between humans (genus <em><a href=\"https://en.wikipedia.org/wiki/Homo\" rel=\"noreferrer\">Homo</a></em>) and chimpanzees (genus <em><a href=\"https://en.wikipedia.org/wiki/Pan_(genus)\" rel=\"noreferrer\">Pan</a></em>).</p>\n<p>The genomes of humans and chimpanzees are very similar, at around 98-99% similarity. However, tweaking a few genes of a human to make them shorter, with longer, coarser hair, longer arms, different pelvis shape and greater strength does not make them a chimpanzee. By the same logic tweaking some genes in a wolf does not make it a dire wolf.</p>\n<p>In addition, while dire wolves and wolves co-existed recently, we really only have sub-fossil remains with ancient DNA in them. This means fragmented DNA which is hard to extract and is very difficult to work with. The technology to work with ancient DNA is amazing and advancing rapidly, but the very nature of it means working with partial samples and a lot of reconstruction bioinformatically.</p>\n<p>Further supporting my point, a 2021 study from Perri <em>et al.</em><sup>1</sup> found that the genomes of dire wolves and grey wolves were highly divergent, and that dire wolves were the last of an ancient divergent lineage of canids, with little genetic relatedness to members of the <em>Canis</em> genus, and that there is no evidence of gene flow between the two genera.</p>\n<p>A third complication is that, while we have the genomes and could potentially tweak genes to suit, a whole lot of what goes into making a species a species is all the bits of the genome that aren't encoded in the genes. Only a few years ago, these bits of the genome were called &quot;junk DNA&quot;, and were thought to not do much, but recent evidence is that they do plenty. There are all sorts of gene regulations that go on in these regions (promoters, epigenetic modifications and many more) and it all alters how genes behave and hence how the animal looks, behaves and many other factors.  Currently, we don't know a huge amount how these regions of the genome work, even for such well studied organisms as mice, but people are working on it. This lack of knowledge means that we can't currently make anything that we can actually call a dire wolf, merely something that looks like one.</p>\n<p>So, to answer your questions in your second to last paragraph - they are the species that was modified - grey wolf, they are not a new species at all. They are very close to grey wolves genetically, with modifications to only a handful of genes, whereas the dire wolf was quite genetically distinct from the grey wolf it would seem. I could see an argument for these being hybrids, but I would say most hybrids have more genetic mixing going on than we see here. Perhaps &quot;variant&quot; might be a better description, but even that might be too strong a word.</p>\n<p>Refs:</p>\n<ol>\n<li>Perri AR, Mitchell KJ, Mouton A, Álvarez-Carretero S, Hulme-Beaman A, Haile J, Jamieson A, Meachen J, Lin AT, Schubert BW, Ameen C, Antipina EE, Bover P, Brace S, Carmagnini A, Carøe C, Samaniego Castruita JA, Chatters JC, Dobney K, Dos Reis M, Evin A, Gaubert P, Gopalakrishnan S, Gower G, Heiniger H, Helgen KM, Kapp J, Kosintsev PA, Linderholm A, Ozga AT, Presslee S, Salis AT, Saremi NF, Shew C, Skerry K, Taranenko DE, Thompson M, Sablin MV, Kuzmin YV, Collins MJ, Sinding MS, Gilbert MTP, Stone AC, Shapiro B, Van Valkenburgh B, Wayne RK, Larson G, Cooper A, Frantz LAF. Dire wolves were the last of an ancient New World canid lineage. Nature. 2021 Mar;591(7848):87-91. doi: 10.1038/s41586-020-03082-x. Epub 2021 Jan 13. <a href=\"https://pubmed.ncbi.nlm.nih.gov/33442059/\" rel=\"noreferrer\">PMID: 33442059</a>.</li>\n</ol>\n","answer_id":116341,"answer_text":"I've not read the press release, but I can tell you unequivocally that these are not dire wolves (Aenocyon dirus (https://en.wikipedia.org/wiki/Dire_wolf)). These are grey wolves tweaked for some characteristics.\n\n\n\n\nSimply put, they have taken a grey wolf (Canis lupus lupus (https://en.wikipedia.org/wiki/Wolf)) and tweaked some genes, I think around 20ish genes from the media stories I have seen. These genes are particularly those that make the head larger and muscles stronger. These alter the external appearance of the wolf to look more like dire wolves.\n\n\n\n\nGrey wolves and dire wolves, as you can see from the scientific names, are from separate genera within the dog (Canidae (https://en.wikipedia.org/wiki/Canidae)) family. This means that, while they are related, there is a distant genetic relationship. You could think of this as being similar to the relationship between humans (genus Homo (https://en.wikipedia.org/wiki/Homo)) and chimpanzees (genus Pan (https://en.wikipedia.org/wiki/Pan_(genus))).\n\n\n\n\nThe genomes of humans and chimpanzees are very similar, at around 98-99% similarity. However, tweaking a few genes of a human to make them shorter, with longer, coarser hair, longer arms, different pelvis shape and greater strength does not make them a chimpanzee. By the same logic tweaking some genes in a wolf does not make it a dire wolf.\n\n\n\n\nIn addition, while dire wolves and wolves co-existed recently, we really only have sub-fossil remains with ancient DNA in them. This means fragmented DNA which is hard to extract and is very difficult to work with. The technology to work with ancient DNA is amazing and advancing rapidly, but the very nature of it means working with partial samples and a lot of reconstruction bioinformatically.\n\n\n\n\nFurther supporting my point, a 2021 study from Perri et al.1 found that the genomes of dire wolves and grey wolves were highly divergent, and that dire wolves were the last of an ancient divergent lineage of canids, with little genetic relatedness to members of the Canis genus, and that there is no evidence of gene flow between the two genera.\n\n\n\n\nA third complication is that, while we have the genomes and could potentially tweak genes to suit, a whole lot of what goes into making a species a species is all the bits of the genome that aren't encoded in the genes. Only a few years ago, these bits of the genome were called \"junk DNA\", and were thought to not do much, but recent evidence is that they do plenty. There are all sorts of gene regulations that go on in these regions (promoters, epigenetic modifications and many more) and it all alters how genes behave and hence how the animal looks, behaves and many other factors.  Currently, we don't know a huge amount how these regions of the genome work, even for such well studied organisms as mice, but people are working on it. This lack of knowledge means that we can't currently make anything that we can actually call a dire wolf, merely something that looks like one.\n\n\n\n\nSo, to answer your questions in your second to last paragraph - they are the species that was modified - grey wolf, they are not a new species at all. They are very close to grey wolves genetically, with modifications to only a handful of genes, whereas the dire wolf was quite genetically distinct from the grey wolf it would seem. I could see an argument for these being hybrids, but I would say most hybrids have more genetic mixing going on than we see here. Perhaps \"variant\" might be a better description, but even that might be too strong a word.\n\n\n\n\nRefs:\n\n\n\n\n\nPerri AR, Mitchell KJ, Mouton A, Álvarez-Carretero S, Hulme-Beaman A, Haile J, Jamieson A, Meachen J, Lin AT, Schubert BW, Ameen C, Antipina EE, Bover P, Brace S, Carmagnini A, Carøe C, Samaniego Castruita JA, Chatters JC, Dobney K, Dos Reis M, Evin A, Gaubert P, Gopalakrishnan S, Gower G, Heiniger H, Helgen KM, Kapp J, Kosintsev PA, Linderholm A, Ozga AT, Presslee S, Salis AT, Saremi NF, Shew C, Skerry K, Taranenko DE, Thompson M, Sablin MV, Kuzmin YV, Collins MJ, Sinding MS, Gilbert MTP, Stone AC, Shapiro B, Van Valkenburgh B, Wayne RK, Larson G, Cooper A, Frantz LAF. Dire wolves were the last of an ancient New World canid lineage. Nature. 2021 Mar;591(7848):87-91. doi: 10.1038/s41586-020-03082-x. Epub 2021 Jan 13. PMID: 33442059 (https://pubmed.ncbi.nlm.nih.gov/33442059/).","answer_url":"https://biology.stackexchange.com/a/116341","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2025-04-09T00:15:36+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":116338,"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":"2025-04-09T00:15:36+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"43B674EA-B94E-4EBE-AE59-38E63EFC14DA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/43B674EA-B94E-4EBE-AE59-38E63EFC14DA/view-source"},{"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":"2025-04-09T02:08:57+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"745EDB77-5ABC-4925-8574-DFC9A72FAB3B","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/745EDB77-5ABC-4925-8574-DFC9A72FAB3B/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":"2025-04-09T02:55:04+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"E7BE8CA8-93BB-47F4-A1A6-7359C481EBC9","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/E7BE8CA8-93BB-47F4-A1A6-7359C481EBC9/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":"2025-04-09T09:10:02+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"0F0D9D83-1B20-43D1-8A64-FB5958B8BBFE","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0F0D9D83-1B20-43D1-8A64-FB5958B8BBFE/view-source"}],"score":34}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"G. 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But since it's currently a highly discussed topic in the media, I’d really like to understand it better — and I imagine others might be wondering about the same thing.</p>\n<p>In recent years, there have been increasing reports of attempts on the &quot;<a href=\"https://en.wikipedia.org/wiki/De-extinction\" rel=\"noreferrer\">de-extinction</a>&quot; of species using techniques from biotechnology. While earlier efforts like the <a href=\"https://en.wikipedia.org/wiki/Pyrenean_ibex#Cloning_project\" rel=\"noreferrer\">cloning of the Pyrenean ibex</a> or the human-assistet germination of the <a href=\"https://en.wikipedia.org/wiki/Judean_date_palm\" rel=\"noreferrer\">Judean palm</a> relied on preserved cells, modern approaches appear to focus more on genome editing, of course, due to the fact that it is quite rare to have preserved cells as in the examples just mentioned.</p>\n<p>Two recent examples from <a href=\"https://colossal.com/\" rel=\"noreferrer\">Colossal Biosciences</a> in particular caused high media attention:</p>\n<ol>\n<li><p>In April 2025 (this week actually), they announced the &quot;de-extinction&quot; of the dire wolf\n(see also <a href=\"https://en.wikipedia.org/wiki/Romulus,_Remus,_and_Khaleesi\" rel=\"noreferrer\">Wikipedia</a>). In their <a href=\"https://colossal.com/direwolf/\" rel=\"noreferrer\">official statement</a>, the\nfollowing is written:</p>\n<blockquote>\n<p>On October 1, 2024, for the first time in human history, Colossal successfully restored a once-eradicated species through the science\nof de-extinction. After a 10,000+ year absence, our team is proud to\nreturn the dire wolf to its rightful place in the ecosystem</p>\n</blockquote>\n<p>However, many scientists have questioned the claim, arguing that the\nresulting animal is more of a genetically modified grey wolf rather\nthan a true dire wolf (see e.g. <a href=\"https://www.bbc.com/news/articles/c4g9ejy3gdvo\" rel=\"noreferrer\">here</a>).</p>\n</li>\n<li><p>In March 2025, they introduced &quot;<a href=\"https://en.wikipedia.org/wiki/Woolly_mouse\" rel=\"noreferrer\">woolly mice</a>&quot; (official <a href=\"https://colossal.com/scientists-have-bred-woolly-mice-on-their-journey-to-bring-back-the-mammoth/\" rel=\"noreferrer\">announcement</a>), namely genetically modified laboratory mice developed as part of efforts toward the eventual de-extinction of the woolly mammoth.</p>\n</li>\n</ol>\n<p>So here is my question: From what I understand, this approach involves analyzing the genome of extinct species, such as the dire wolf or the woolly mammoth, to identify key genes responsible for traits that characterized them, like the woolly coats and other genetic modifications aimed at cold tolerance in the example of the mammoth. Scientists then use genome editing techniques to introduce these traits into closely related living species, resulting in what is being referred to as a &quot;de-extinct&quot; species.</p>\n<blockquote>\n<p><strong>Question:</strong> Genetically speaking, how different are de-extinct animals created through genome editing from the modern living species they are based on? How &quot;close&quot; are genome-edited &quot;de-extinct&quot; animals to their extinct counterparts?</p>\n</blockquote>\n<p>In other words, how far reaching are those modifications performed on the genetic level, for example in the two cases listed above? <strong>Are they still in the same species</strong> (e.g. according to the biological species concept; does it even make sense to talk about the biological species concept in this context?), or are they genetically speaking close to their extinct counterpart. Or can they even be considered hybrids? Or even a new species?</p>\n<p>Of course, I know that the concept of a species is a bit subtle, but I would like to get a better feeling of what de-extinction in this sense really means on the academic side.</p>\n","text":"I'm not a biologist, so I apologize if this question is a bit vague. But since it's currently a highly discussed topic in the media, I’d really like to understand it better — and I imagine others might be wondering about the same thing.\n\n\n\n\nIn recent years, there have been increasing reports of attempts on the \"de-extinction (https://en.wikipedia.org/wiki/De-extinction)\" of species using techniques from biotechnology. While earlier efforts like the cloning of the Pyrenean ibex (https://en.wikipedia.org/wiki/Pyrenean_ibex#Cloning_project) or the human-assistet germination of the Judean palm (https://en.wikipedia.org/wiki/Judean_date_palm) relied on preserved cells, modern approaches appear to focus more on genome editing, of course, due to the fact that it is quite rare to have preserved cells as in the examples just mentioned.\n\n\n\n\nTwo recent examples from Colossal Biosciences (https://colossal.com/) in particular caused high media attention:\n\n\n\n\n\n\n\nIn April 2025 (this week actually), they announced the \"de-extinction\" of the dire wolf\n(see also Wikipedia (https://en.wikipedia.org/wiki/Romulus,_Remus,_and_Khaleesi)). In their official statement (https://colossal.com/direwolf/), the\nfollowing is written:\n\n\n\n\n\n\n\nOn October 1, 2024, for the first time in human history, Colossal successfully restored a once-eradicated species through the science\nof de-extinction. After a 10,000+ year absence, our team is proud to\nreturn the dire wolf to its rightful place in the ecosystem\n\n\n\n\n\n\n\nHowever, many scientists have questioned the claim, arguing that the\nresulting animal is more of a genetically modified grey wolf rather\nthan a true dire wolf (see e.g. here (https://www.bbc.com/news/articles/c4g9ejy3gdvo)).\n\n\n\n\n\n\n\n\n\nIn March 2025, they introduced \"woolly mice (https://en.wikipedia.org/wiki/Woolly_mouse)\" (official announcement (https://colossal.com/scientists-have-bred-woolly-mice-on-their-journey-to-bring-back-the-mammoth/)), namely genetically modified laboratory mice developed as part of efforts toward the eventual de-extinction of the woolly mammoth.\n\n\n\n\n\n\n\n\nSo here is my question: From what I understand, this approach involves analyzing the genome of extinct species, such as the dire wolf or the woolly mammoth, to identify key genes responsible for traits that characterized them, like the woolly coats and other genetic modifications aimed at cold tolerance in the example of the mammoth. Scientists then use genome editing techniques to introduce these traits into closely related living species, resulting in what is being referred to as a \"de-extinct\" species.\n\n\n\n\n\n\n\nQuestion: Genetically speaking, how different are de-extinct animals created through genome editing from the modern living species they are based on? How \"close\" are genome-edited \"de-extinct\" animals to their extinct counterparts?\n\n\n\n\n\n\n\nIn other words, how far reaching are those modifications performed on the genetic level, for example in the two cases listed above? Are they still in the same species (e.g. according to the biological species concept; does it even make sense to talk about the biological species concept in this context?), or are they genetically speaking close to their extinct counterpart. Or can they even be considered hybrids? Or even a new species?\n\n\n\n\nOf course, I know that the concept of a species is a bit subtle, but I would like to get a better feeling of what de-extinction in this sense really means on the academic side."},{"context_id":"116341","html":"<p>I've not read the press release, but I can tell you unequivocally that these are not dire wolves (<em><a href=\"https://en.wikipedia.org/wiki/Dire_wolf\" rel=\"noreferrer\">Aenocyon dirus</a></em>). These are grey wolves tweaked for some characteristics.</p>\n<p>Simply put, they have taken a grey wolf (<em><a href=\"https://en.wikipedia.org/wiki/Wolf\" rel=\"noreferrer\">Canis lupus lupus</a></em>) and tweaked some genes, I think around 20ish genes from the media stories I have seen. These genes are particularly those that make the head larger and muscles stronger. These alter the external appearance of the wolf to look more like dire wolves.</p>\n<p>Grey wolves and dire wolves, as you can see from the scientific names, are from separate genera within the dog (<a href=\"https://en.wikipedia.org/wiki/Canidae\" rel=\"noreferrer\">Canidae</a>) family. This means that, while they are related, there is a distant genetic relationship. You could think of this as being similar to the relationship between humans (genus <em><a href=\"https://en.wikipedia.org/wiki/Homo\" rel=\"noreferrer\">Homo</a></em>) and chimpanzees (genus <em><a href=\"https://en.wikipedia.org/wiki/Pan_(genus)\" rel=\"noreferrer\">Pan</a></em>).</p>\n<p>The genomes of humans and chimpanzees are very similar, at around 98-99% similarity. However, tweaking a few genes of a human to make them shorter, with longer, coarser hair, longer arms, different pelvis shape and greater strength does not make them a chimpanzee. By the same logic tweaking some genes in a wolf does not make it a dire wolf.</p>\n<p>In addition, while dire wolves and wolves co-existed recently, we really only have sub-fossil remains with ancient DNA in them. This means fragmented DNA which is hard to extract and is very difficult to work with. The technology to work with ancient DNA is amazing and advancing rapidly, but the very nature of it means working with partial samples and a lot of reconstruction bioinformatically.</p>\n<p>Further supporting my point, a 2021 study from Perri <em>et al.</em><sup>1</sup> found that the genomes of dire wolves and grey wolves were highly divergent, and that dire wolves were the last of an ancient divergent lineage of canids, with little genetic relatedness to members of the <em>Canis</em> genus, and that there is no evidence of gene flow between the two genera.</p>\n<p>A third complication is that, while we have the genomes and could potentially tweak genes to suit, a whole lot of what goes into making a species a species is all the bits of the genome that aren't encoded in the genes. Only a few years ago, these bits of the genome were called &quot;junk DNA&quot;, and were thought to not do much, but recent evidence is that they do plenty. There are all sorts of gene regulations that go on in these regions (promoters, epigenetic modifications and many more) and it all alters how genes behave and hence how the animal looks, behaves and many other factors.  Currently, we don't know a huge amount how these regions of the genome work, even for such well studied organisms as mice, but people are working on it. This lack of knowledge means that we can't currently make anything that we can actually call a dire wolf, merely something that looks like one.</p>\n<p>So, to answer your questions in your second to last paragraph - they are the species that was modified - grey wolf, they are not a new species at all. They are very close to grey wolves genetically, with modifications to only a handful of genes, whereas the dire wolf was quite genetically distinct from the grey wolf it would seem. I could see an argument for these being hybrids, but I would say most hybrids have more genetic mixing going on than we see here. Perhaps &quot;variant&quot; might be a better description, but even that might be too strong a word.</p>\n<p>Refs:</p>\n<ol>\n<li>Perri AR, Mitchell KJ, Mouton A, Álvarez-Carretero S, Hulme-Beaman A, Haile J, Jamieson A, Meachen J, Lin AT, Schubert BW, Ameen C, Antipina EE, Bover P, Brace S, Carmagnini A, Carøe C, Samaniego Castruita JA, Chatters JC, Dobney K, Dos Reis M, Evin A, Gaubert P, Gopalakrishnan S, Gower G, Heiniger H, Helgen KM, Kapp J, Kosintsev PA, Linderholm A, Ozga AT, Presslee S, Salis AT, Saremi NF, Shew C, Skerry K, Taranenko DE, Thompson M, Sablin MV, Kuzmin YV, Collins MJ, Sinding MS, Gilbert MTP, Stone AC, Shapiro B, Van Valkenburgh B, Wayne RK, Larson G, Cooper A, Frantz LAF. Dire wolves were the last of an ancient New World canid lineage. Nature. 2021 Mar;591(7848):87-91. doi: 10.1038/s41586-020-03082-x. Epub 2021 Jan 13. <a href=\"https://pubmed.ncbi.nlm.nih.gov/33442059/\" rel=\"noreferrer\">PMID: 33442059</a>.</li>\n</ol>\n","text":"I've not read the press release, but I can tell you unequivocally that these are not dire wolves (Aenocyon dirus (https://en.wikipedia.org/wiki/Dire_wolf)). These are grey wolves tweaked for some characteristics.\n\n\n\n\nSimply put, they have taken a grey wolf (Canis lupus lupus (https://en.wikipedia.org/wiki/Wolf)) and tweaked some genes, I think around 20ish genes from the media stories I have seen. These genes are particularly those that make the head larger and muscles stronger. These alter the external appearance of the wolf to look more like dire wolves.\n\n\n\n\nGrey wolves and dire wolves, as you can see from the scientific names, are from separate genera within the dog (Canidae (https://en.wikipedia.org/wiki/Canidae)) family. This means that, while they are related, there is a distant genetic relationship. You could think of this as being similar to the relationship between humans (genus Homo (https://en.wikipedia.org/wiki/Homo)) and chimpanzees (genus Pan (https://en.wikipedia.org/wiki/Pan_(genus))).\n\n\n\n\nThe genomes of humans and chimpanzees are very similar, at around 98-99% similarity. However, tweaking a few genes of a human to make them shorter, with longer, coarser hair, longer arms, different pelvis shape and greater strength does not make them a chimpanzee. By the same logic tweaking some genes in a wolf does not make it a dire wolf.\n\n\n\n\nIn addition, while dire wolves and wolves co-existed recently, we really only have sub-fossil remains with ancient DNA in them. This means fragmented DNA which is hard to extract and is very difficult to work with. The technology to work with ancient DNA is amazing and advancing rapidly, but the very nature of it means working with partial samples and a lot of reconstruction bioinformatically.\n\n\n\n\nFurther supporting my point, a 2021 study from Perri et al.1 found that the genomes of dire wolves and grey wolves were highly divergent, and that dire wolves were the last of an ancient divergent lineage of canids, with little genetic relatedness to members of the Canis genus, and that there is no evidence of gene flow between the two genera.\n\n\n\n\nA third complication is that, while we have the genomes and could potentially tweak genes to suit, a whole lot of what goes into making a species a species is all the bits of the genome that aren't encoded in the genes. Only a few years ago, these bits of the genome were called \"junk DNA\", and were thought to not do much, but recent evidence is that they do plenty. There are all sorts of gene regulations that go on in these regions (promoters, epigenetic modifications and many more) and it all alters how genes behave and hence how the animal looks, behaves and many other factors.  Currently, we don't know a huge amount how these regions of the genome work, even for such well studied organisms as mice, but people are working on it. This lack of knowledge means that we can't currently make anything that we can actually call a dire wolf, merely something that looks like one.\n\n\n\n\nSo, to answer your questions in your second to last paragraph - they are the species that was modified - grey wolf, they are not a new species at all. They are very close to grey wolves genetically, with modifications to only a handful of genes, whereas the dire wolf was quite genetically distinct from the grey wolf it would seem. I could see an argument for these being hybrids, but I would say most hybrids have more genetic mixing going on than we see here. Perhaps \"variant\" might be a better description, but even that might be too strong a word.\n\n\n\n\nRefs:\n\n\n\n\n\nPerri AR, Mitchell KJ, Mouton A, Álvarez-Carretero S, Hulme-Beaman A, Haile J, Jamieson A, Meachen J, Lin AT, Schubert BW, Ameen C, Antipina EE, Bover P, Brace S, Carmagnini A, Carøe C, Samaniego Castruita JA, Chatters JC, Dobney K, Dos Reis M, Evin A, Gaubert P, Gopalakrishnan S, Gower G, Heiniger H, Helgen KM, Kapp J, Kosintsev PA, Linderholm A, Ozga AT, Presslee S, Salis AT, Saremi NF, Shew C, Skerry K, Taranenko DE, Thompson M, Sablin MV, Kuzmin YV, Collins MJ, Sinding MS, Gilbert MTP, Stone AC, Shapiro B, Van Valkenburgh B, Wayne RK, Larson G, Cooper A, Frantz LAF. Dire wolves were the last of an ancient New World canid lineage. Nature. 2021 Mar;591(7848):87-91. doi: 10.1038/s41586-020-03082-x. Epub 2021 Jan 13. PMID: 33442059 (https://pubmed.ncbi.nlm.nih.gov/33442059/)."}],"domain":"biology","external_citations":["https://colossal.com/","https://colossal.com/direwolf/","https://colossal.com/scientists-have-bred-woolly-mice-on-their-journey-to-bring-back-the-mammoth/","https://en.wikipedia.org/wiki/Canidae","https://en.wikipedia.org/wiki/De-extinction","https://en.wikipedia.org/wiki/Dire_wolf","https://en.wikipedia.org/wiki/Homo","https://en.wikipedia.org/wiki/Judean_date_palm","https://en.wikipedia.org/wiki/Pan_(genus)","https://en.wikipedia.org/wiki/Pyrenean_ibex#Cloning_project","https://en.wikipedia.org/wiki/Romulus,_Remus,_and_Khaleesi","https://en.wikipedia.org/wiki/Wolf","https://en.wikipedia.org/wiki/Woolly_mouse","https://pubmed.ncbi.nlm.nih.gov/33442059/","https://www.bbc.com/news/articles/c4g9ejy3gdvo"],"ground_truth_type":"metadata_grounded","group_id":"b5de0a18fa7af1ad6243e98852bab3629c80b161942677ff5d9c17c892b2afee","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-de3eadeb36a570e5bc4d6fd7","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":"G. Blaickner","profile_url":"https://biology.stackexchange.com/users/76678/g-blaickner","user_type":"registered"},"created_at":"2025-04-08T16:27:37+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"8B334220-1244-4A6B-B023-5933EA484BE3","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8B334220-1244-4A6B-B023-5933EA484BE3/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":"2025-04-08T17:04:24+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"275BA413-4719-4BD6-8C2C-C2EEAA152654","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/275BA413-4719-4BD6-8C2C-C2EEAA152654/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-04-09T02:23:39+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"93B9F52F-EF8A-4792-ACCC-5F354D420907","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/93B9F52F-EF8A-4792-ACCC-5F354D420907/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":"116338","source_record_sha256":"8d6d4b9009e25e3b059932d9bf0f7f55acc975e2b04af61fa84a206a12f7a992","source_url":"https://biology.stackexchange.com/questions/116338/how-close-are-genome-edited-de-extinct-animals-to-their-extinct-counterparts","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How \"close\" are genome-edited \"de-extinct\" animals to their extinct counterparts?\nI'm not a biologist, so I apologize if this question is a bit vague. But since it's currently a highly discussed topic in the media, I’d really like to understand it better — and I imagine others might be wondering about the same thing.\n\n\n\n\nIn recent years, there have been increasing reports of attempts on the \"de-extinction (https://en.wikipedia.org/wiki/De-extinction)\" of species using techniques from biotechnology. While earlier efforts like the cloning of the Pyrenean ibex (https://en.wikipedia.org/wiki/Pyrenean_ibex#Cloning_project) or the human-assistet germination of the Judean palm (https://en.wikipedia.org/wiki/Judean_date_palm) relied on preserved cells, modern approaches appear to focus more on genome editing, of course, due to the fact that it is quite rare to have preserved cells as in the examples just mentioned.\n\n\n\n\nTwo recent examples from Colossal Biosciences (https://colossal.com/) in particular caused high media attention:\n\n\n\n\n\n\n\nIn April 2025 (this week actually), they announced the \"de-extinction\" of the dire wolf\n(see also Wikipedia (https://en.wikipedia.org/wiki/Romulus,_Remus,_and_Khaleesi)). In their official statement (https://colossal.com/direwolf/), the\nfollowing is written:\n\n\n\n\n\n\n\nOn October 1, 2024, for the first time in human history, Colossal successfully restored a once-eradicated species through the science\nof de-extinction. After a 10,000+ year absence, our team is proud to\nreturn the dire wolf to its rightful place in the ecosystem\n\n\n\n\n\n\n\nHowever, many scientists have questioned the claim, arguing that the\nresulting animal is more of a genetically modified grey wolf rather\nthan a true dire wolf (see e.g. here (https://www.bbc.com/news/articles/c4g9ejy3gdvo)).\n\n\n\n\n\n\n\n\n\nIn March 2025, they introduced \"woolly mice (https://en.wikipedia.org/wiki/Woolly_mouse)\" (official announcement (https://colossal.com/scientists-have-bred-woolly-mice-on-their-journey-to-bring-back-the-mammoth/)), namely genetically modified laboratory mice developed as part of efforts toward the eventual de-extinction of the woolly mammoth.\n\n\n\n\n\n\n\n\nSo here is my question: From what I understand, this approach involves analyzing the genome of extinct species, such as the dire wolf or the woolly mammoth, to identify key genes responsible for traits that characterized them, like the woolly coats and other genetic modifications aimed at cold tolerance in the example of the mammoth. Scientists then use genome editing techniques to introduce these traits into closely related living species, resulting in what is being referred to as a \"de-extinct\" species.\n\n\n\n\n\n\n\nQuestion: Genetically speaking, how different are de-extinct animals created through genome editing from the modern living species they are based on? How \"close\" are genome-edited \"de-extinct\" animals to their extinct counterparts?\n\n\n\n\n\n\n\nIn other words, how far reaching are those modifications performed on the genetic level, for example in the two cases listed above? Are they still in the same species (e.g. according to the biological species concept; does it even make sense to talk about the biological species concept in this context?), or are they genetically speaking close to their extinct counterpart. Or can they even be considered hybrids? Or even a new species?\n\n\n\n\nOf course, I know that the concept of a species is a bit subtle, but I would like to get a better feeling of what de-extinction in this sense really means on the academic side.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116341,"score":34}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The descending limb section of the loop of Henle enables passage of water but blocks the movement of solutes during the process of filtrate-ECF equilibration. The filtrate descends through the loop while water leaves the permeable structure to enter the hyperosmotic medullary interstitium which results in filtrate equilibration with the extracellular fluid. The osmolarity grows stronger because of the descending filtration direction. The glomerulus sends a 300 mOsm/L filtrate which immediately adjusts its composition through medullary interstitial osmotic pressure while also ascending in osmolarity.</p>\n<p>Your doubt about the circled 300 mOsm/L value is valid and you are correct to do so. The osmotic pressure at the beginning of the descending limb should be 400 mOsm/L instead of 300 mOsm/L according to the diagram provided by Guyton and Hall because of the equilibration mechanism. The shown value of 300 mOsm/L at this point should be considered an oversight or a simplification by the diagram authors.\nThe ascending limb acts to remove ions during Step 3 at the same time it prevents the movement of water when its osmolarity remains steady. The removal of solutes in the process lowers osmotic pressure but the filtrate solution gradually grows less concentrated not more concentrated. The steady osmolarity condition in the ascending limb exists because medullary interstitium ion transport preserves the osmotic gradient instead of changing filtrate osmolarity inside the limb.</p>\n","answer_id":116374,"answer_text":"The descending limb section of the loop of Henle enables passage of water but blocks the movement of solutes during the process of filtrate-ECF equilibration. The filtrate descends through the loop while water leaves the permeable structure to enter the hyperosmotic medullary interstitium which results in filtrate equilibration with the extracellular fluid. The osmolarity grows stronger because of the descending filtration direction. The glomerulus sends a 300 mOsm/L filtrate which immediately adjusts its composition through medullary interstitial osmotic pressure while also ascending in osmolarity.\n\n\n\n\nYour doubt about the circled 300 mOsm/L value is valid and you are correct to do so. The osmotic pressure at the beginning of the descending limb should be 400 mOsm/L instead of 300 mOsm/L according to the diagram provided by Guyton and Hall because of the equilibration mechanism. The shown value of 300 mOsm/L at this point should be considered an oversight or a simplification by the diagram authors.\nThe ascending limb acts to remove ions during Step 3 at the same time it prevents the movement of water when its osmolarity remains steady. The removal of solutes in the process lowers osmotic pressure but the filtrate solution gradually grows less concentrated not more concentrated. The steady osmolarity condition in the ascending limb exists because medullary interstitium ion transport preserves the osmotic gradient instead of changing filtrate osmolarity inside the limb.","answer_url":"https://biology.stackexchange.com/a/116374","author":"Nithya Gopakumar","author_url":"https://biology.stackexchange.com/users/104994/nithya-gopakumar","content_license":"CC BY-SA 4.0","created_at":"2025-04-17T09:14:42+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":116370,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Nithya Gopakumar","profile_url":"https://biology.stackexchange.com/users/104994/nithya-gopakumar","user_type":"registered"},"created_at":"2025-04-17T09:14:42+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"7C1713DC-6FC4-4782-8BB4-306FDA605FC7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7C1713DC-6FC4-4782-8BB4-306FDA605FC7/view-source"}],"score":2},{"answer_html":"<p>The ascending limb of the loop of Henle is responsible for actively transporting ions (like sodium, potassium, and chloride) out of the filtrate into the surrounding medullary interstitium (the tissue surrounding the loop). Unlike the descending limb, the ascending limb is impermeable to water, meaning water cannot follow the ions that are being moved.</p>\n<p>Why does osmolarity stay steady in the ascending limb?\nThe medullary interstitium has a high osmolarity due to the continuous transport of ions from the ascending limb.</p>\n<p>Even though solutes (ions) are leaving the filtrate, water cannot follow, which prevents further dilution or concentration of the filtrate in the ascending limb.</p>\n<p>Instead of dramatically changing the filtrate’s osmolarity inside the ascending limb, the transported ions maintain the osmotic gradient in the surrounding medullary interstitium.</p>\n<p>This osmotic gradient is critical because it allows the kidney to efficiently concentrate urine when needed.</p>\n<p>What would happen if this mechanism didn't work?\nIf the ascending limb didn’t transport ions out effectively, the medullary interstitium would lose its osmotic gradient, meaning the kidney wouldn't be able to concentrate urine properly, leading to excessive water loss and inefficient filtration.</p>\n<p>Summary:\nThe steady osmolarity condition in the ascending limb exists because instead of directly altering the filtrate’s osmolarity inside the limb, the movement of ions out into the medullary interstitium maintains the osmotic gradient needed for water reabsorption in other kidney regions.</p>\n","answer_id":116379,"answer_text":"The ascending limb of the loop of Henle is responsible for actively transporting ions (like sodium, potassium, and chloride) out of the filtrate into the surrounding medullary interstitium (the tissue surrounding the loop). Unlike the descending limb, the ascending limb is impermeable to water, meaning water cannot follow the ions that are being moved.\n\n\n\n\nWhy does osmolarity stay steady in the ascending limb?\nThe medullary interstitium has a high osmolarity due to the continuous transport of ions from the ascending limb.\n\n\n\n\nEven though solutes (ions) are leaving the filtrate, water cannot follow, which prevents further dilution or concentration of the filtrate in the ascending limb.\n\n\n\n\nInstead of dramatically changing the filtrate’s osmolarity inside the ascending limb, the transported ions maintain the osmotic gradient in the surrounding medullary interstitium.\n\n\n\n\nThis osmotic gradient is critical because it allows the kidney to efficiently concentrate urine when needed.\n\n\n\n\nWhat would happen if this mechanism didn't work?\nIf the ascending limb didn’t transport ions out effectively, the medullary interstitium would lose its osmotic gradient, meaning the kidney wouldn't be able to concentrate urine properly, leading to excessive water loss and inefficient filtration.\n\n\n\n\nSummary:\nThe steady osmolarity condition in the ascending limb exists because instead of directly altering the filtrate’s osmolarity inside the limb, the movement of ions out into the medullary interstitium maintains the osmotic gradient needed for water reabsorption in other kidney regions.","answer_url":"https://biology.stackexchange.com/a/116379","author":"Nithya Gopakumar","author_url":"https://biology.stackexchange.com/users/104994/nithya-gopakumar","content_license":"CC BY-SA 4.0","created_at":"2025-04-18T16:50:24+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":116370,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Nithya Gopakumar","profile_url":"https://biology.stackexchange.com/users/104994/nithya-gopakumar","user_type":"registered"},"created_at":"2025-04-18T16:50:24+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"257ECA55-A9E4-44B5-9A25-BB5E3A8F7160","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/257ECA55-A9E4-44B5-9A25-BB5E3A8F7160/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Kutuka K","author_url":"https://biology.stackexchange.com/users/104939/kutuka-k","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Kutuka K","profile_url":"https://biology.stackexchange.com/users/104939/kutuka-k","user_type":"registered"},"created_at":"2025-04-16T16:50:34+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"B154B6D6-3102-4827-AC63-1A4A03449E0E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B154B6D6-3102-4827-AC63-1A4A03449E0E/view-source"}],"url":"https://biology.stackexchange.com/questions/116370/during-countercurrent-multiplication-how-does-filtrate-arriving-from-the-proxim"},{"author":"Nithya Gopakumar","author_url":"https://biology.stackexchange.com/users/104994/nithya-gopakumar","content_license":"CC BY-SA 4.0","context_id":"116374","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Nithya Gopakumar","profile_url":"https://biology.stackexchange.com/users/104994/nithya-gopakumar","user_type":"registered"},"created_at":"2025-04-17T09:14:42+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"7C1713DC-6FC4-4782-8BB4-306FDA605FC7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7C1713DC-6FC4-4782-8BB4-306FDA605FC7/view-source"}],"url":"https://biology.stackexchange.com/a/116374"},{"author":"Nithya Gopakumar","author_url":"https://biology.stackexchange.com/users/104994/nithya-gopakumar","content_license":"CC BY-SA 4.0","context_id":"116379","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Nithya Gopakumar","profile_url":"https://biology.stackexchange.com/users/104994/nithya-gopakumar","user_type":"registered"},"created_at":"2025-04-18T16:50:24+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"257ECA55-A9E4-44B5-9A25-BB5E3A8F7160","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/257ECA55-A9E4-44B5-9A25-BB5E3A8F7160/view-source"}],"url":"https://biology.stackexchange.com/a/116379"}],"contexts":[{"context_id":"question","html":"<p>Undergrad student here. Kind of confused about this. User de Novo wrote in <a href=\"https://biology.stackexchange.com/a/76217/104939\">an answer</a> of theirs that ”when fluid moves, 300 mOsm filtrate flows in from the glomerulus, replacing the 400 mOsm filtrate at the beginning of the descending limb (which equilibrates with the ECF)”, but I didn’t exactly understand how the equilibration occurs.\nI’ve attached some images from Guyton and Hall to clarify my question. Isn’t that circled 300 supposed to be 400 mOsm/L?</p>\n<p>I might as well also mention here that Guyton states that the interstitial medullary osmolarity during Step 3 because ions are continously actively transported out of the ascending limb. But why don’t we see a corresponding change in the osmolarities of the ascending limb in the diagram? Any input from you all on this end would be greatly appreciated. Thank you all in advance.</p>\n<p>[<img src=\"https://i.sstatic.net/LhVxroTd.jpg\" alt=\"Snippet from Guyton and Hall, 14th edition, page 369\" />]</p>\n","text":"Undergrad student here. Kind of confused about this. User de Novo wrote in an answer (https://biology.stackexchange.com/a/76217/104939) of theirs that ”when fluid moves, 300 mOsm filtrate flows in from the glomerulus, replacing the 400 mOsm filtrate at the beginning of the descending limb (which equilibrates with the ECF)”, but I didn’t exactly understand how the equilibration occurs.\nI’ve attached some images from Guyton and Hall to clarify my question. Isn’t that circled 300 supposed to be 400 mOsm/L?\n\n\n\n\nI might as well also mention here that Guyton states that the interstitial medullary osmolarity during Step 3 because ions are continously actively transported out of the ascending limb. But why don’t we see a corresponding change in the osmolarities of the ascending limb in the diagram? Any input from you all on this end would be greatly appreciated. Thank you all in advance.\n\n\n\n\n[[image: Snippet from Guyton and Hall, 14th edition, page 369; source: https://i.sstatic.net/LhVxroTd.jpg]]"},{"context_id":"116374","html":"<p>The descending limb section of the loop of Henle enables passage of water but blocks the movement of solutes during the process of filtrate-ECF equilibration. The filtrate descends through the loop while water leaves the permeable structure to enter the hyperosmotic medullary interstitium which results in filtrate equilibration with the extracellular fluid. The osmolarity grows stronger because of the descending filtration direction. The glomerulus sends a 300 mOsm/L filtrate which immediately adjusts its composition through medullary interstitial osmotic pressure while also ascending in osmolarity.</p>\n<p>Your doubt about the circled 300 mOsm/L value is valid and you are correct to do so. The osmotic pressure at the beginning of the descending limb should be 400 mOsm/L instead of 300 mOsm/L according to the diagram provided by Guyton and Hall because of the equilibration mechanism. The shown value of 300 mOsm/L at this point should be considered an oversight or a simplification by the diagram authors.\nThe ascending limb acts to remove ions during Step 3 at the same time it prevents the movement of water when its osmolarity remains steady. The removal of solutes in the process lowers osmotic pressure but the filtrate solution gradually grows less concentrated not more concentrated. The steady osmolarity condition in the ascending limb exists because medullary interstitium ion transport preserves the osmotic gradient instead of changing filtrate osmolarity inside the limb.</p>\n","text":"The descending limb section of the loop of Henle enables passage of water but blocks the movement of solutes during the process of filtrate-ECF equilibration. The filtrate descends through the loop while water leaves the permeable structure to enter the hyperosmotic medullary interstitium which results in filtrate equilibration with the extracellular fluid. The osmolarity grows stronger because of the descending filtration direction. The glomerulus sends a 300 mOsm/L filtrate which immediately adjusts its composition through medullary interstitial osmotic pressure while also ascending in osmolarity.\n\n\n\n\nYour doubt about the circled 300 mOsm/L value is valid and you are correct to do so. The osmotic pressure at the beginning of the descending limb should be 400 mOsm/L instead of 300 mOsm/L according to the diagram provided by Guyton and Hall because of the equilibration mechanism. The shown value of 300 mOsm/L at this point should be considered an oversight or a simplification by the diagram authors.\nThe ascending limb acts to remove ions during Step 3 at the same time it prevents the movement of water when its osmolarity remains steady. The removal of solutes in the process lowers osmotic pressure but the filtrate solution gradually grows less concentrated not more concentrated. The steady osmolarity condition in the ascending limb exists because medullary interstitium ion transport preserves the osmotic gradient instead of changing filtrate osmolarity inside the limb."},{"context_id":"116379","html":"<p>The ascending limb of the loop of Henle is responsible for actively transporting ions (like sodium, potassium, and chloride) out of the filtrate into the surrounding medullary interstitium (the tissue surrounding the loop). Unlike the descending limb, the ascending limb is impermeable to water, meaning water cannot follow the ions that are being moved.</p>\n<p>Why does osmolarity stay steady in the ascending limb?\nThe medullary interstitium has a high osmolarity due to the continuous transport of ions from the ascending limb.</p>\n<p>Even though solutes (ions) are leaving the filtrate, water cannot follow, which prevents further dilution or concentration of the filtrate in the ascending limb.</p>\n<p>Instead of dramatically changing the filtrate’s osmolarity inside the ascending limb, the transported ions maintain the osmotic gradient in the surrounding medullary interstitium.</p>\n<p>This osmotic gradient is critical because it allows the kidney to efficiently concentrate urine when needed.</p>\n<p>What would happen if this mechanism didn't work?\nIf the ascending limb didn’t transport ions out effectively, the medullary interstitium would lose its osmotic gradient, meaning the kidney wouldn't be able to concentrate urine properly, leading to excessive water loss and inefficient filtration.</p>\n<p>Summary:\nThe steady osmolarity condition in the ascending limb exists because instead of directly altering the filtrate’s osmolarity inside the limb, the movement of ions out into the medullary interstitium maintains the osmotic gradient needed for water reabsorption in other kidney regions.</p>\n","text":"The ascending limb of the loop of Henle is responsible for actively transporting ions (like sodium, potassium, and chloride) out of the filtrate into the surrounding medullary interstitium (the tissue surrounding the loop). Unlike the descending limb, the ascending limb is impermeable to water, meaning water cannot follow the ions that are being moved.\n\n\n\n\nWhy does osmolarity stay steady in the ascending limb?\nThe medullary interstitium has a high osmolarity due to the continuous transport of ions from the ascending limb.\n\n\n\n\nEven though solutes (ions) are leaving the filtrate, water cannot follow, which prevents further dilution or concentration of the filtrate in the ascending limb.\n\n\n\n\nInstead of dramatically changing the filtrate’s osmolarity inside the ascending limb, the transported ions maintain the osmotic gradient in the surrounding medullary interstitium.\n\n\n\n\nThis osmotic gradient is critical because it allows the kidney to efficiently concentrate urine when needed.\n\n\n\n\nWhat would happen if this mechanism didn't work?\nIf the ascending limb didn’t transport ions out effectively, the medullary interstitium would lose its osmotic gradient, meaning the kidney wouldn't be able to concentrate urine properly, leading to excessive water loss and inefficient filtration.\n\n\n\n\nSummary:\nThe steady osmolarity condition in the ascending limb exists because instead of directly altering the filtrate’s osmolarity inside the limb, the movement of ions out into the medullary interstitium maintains the osmotic gradient needed for water reabsorption in other kidney regions."}],"domain":"biology","external_citations":["https://biology.stackexchange.com/a/76217/104939"],"ground_truth_type":"metadata_grounded","group_id":"dbf331b1d52342c0fa16d081ea2d066979c2a210e1dc95c04960942820ff0463","hard_case_family":["no_accepted_answer","multiple_answer_candidates"],"id":"RHM-5754717855a0250b95fc9fd0","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":"Kutuka K","profile_url":"https://biology.stackexchange.com/users/104939/kutuka-k","user_type":"registered"},"created_at":"2025-04-16T16:50:34+00:00","raw_file":"raw/codex_api_v1/2e46271dd42cc68e540cd93745d874445294455a8c8fc89effd7f36ed497eee4_1790824137680573300_0.json","raw_sha256":"21274b3e65918ff952c3e3901f10b15b146be4d989ae74907eaed06f2a54ef5e","revision_guid":"B154B6D6-3102-4827-AC63-1A4A03449E0E","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B154B6D6-3102-4827-AC63-1A4A03449E0E/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":"116370","source_record_sha256":"3a2a6605bd73a1a65647bf73ea7bf9c2e1e079cc7f44afb2164e8d7eedb0969d","source_url":"https://biology.stackexchange.com/questions/116370/during-countercurrent-multiplication-how-does-filtrate-arriving-from-the-proxim","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"During countercurrent multiplication, how does filtrate arriving from the proximal tubule equilibrate with the ECF?\nUndergrad student here. Kind of confused about this. User de Novo wrote in an answer (https://biology.stackexchange.com/a/76217/104939) of theirs that ”when fluid moves, 300 mOsm filtrate flows in from the glomerulus, replacing the 400 mOsm filtrate at the beginning of the descending limb (which equilibrates with the ECF)”, but I didn’t exactly understand how the equilibration occurs.\nI’ve attached some images from Guyton and Hall to clarify my question. Isn’t that circled 300 supposed to be 400 mOsm/L?\n\n\n\n\nI might as well also mention here that Guyton states that the interstitial medullary osmolarity during Step 3 because ions are continously actively transported out of the ascending limb. But why don’t we see a corresponding change in the osmolarities of the ascending limb in the diagram? Any input from you all on this end would be greatly appreciated. Thank you all in advance.\n\n\n\n\n[[image: Snippet from Guyton and Hall, 14th edition, page 369; source: https://i.sstatic.net/LhVxroTd.jpg]]","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116374,"score":2},{"answer_id":116379,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>IMO this is a very good question.</p>\n<p>The paper <a href=\"https://www.nature.com/articles/191810a0\" rel=\"nofollow noreferrer\">Relative Sweetness of α and β-Forms of Selected Sugars</a> by Rose Marie Pangborn &amp; Sandra C. Gee, published in <em>Nature</em> in 1961    states, <strong>and provides very strong evidence</strong>,  that a freshly dissolved solution of β-D-glucose becomes sweeter after mutarotation.</p>\n<p>But what of the paper <a href=\"https://pubs.acs.org/doi/10.1021/ba-1971-0117.ch015#:%7E:text=The%20saporous%20unit%20for%20sweet,and%20an%20intramolecular%20hydrogen%20bond\" rel=\"nofollow noreferrer\">Sugar Structure and Taste</a> by R. S. Shallenberger which apparently states the   opposite?</p>\n<p>I'll give the full quote, as it may be important:</p>\n<blockquote>\n<p>α-D-Glucopyranose is about\ntwo-thirds as sweet as sucrose, but the mutarotated solution is even less sweet</p>\n</blockquote>\n<blockquote>\n<p>Yet crystalline β-D-glucopyranose is sweeter than the α-anomer,\nand the mutarotated solution is again less sweet.</p>\n</blockquote>\n<blockquote>\n<p>In the first one would\nconclude that the α-anomer is sweeter than the β-anomer, but in the\nsecond the reverse conclusion could be reached.</p>\n</blockquote>\n<p>To be pedantic (and charitable), the second sentence of this quote refers to the crystalline forms, <em>not</em> the forms in solution, and Shallenberger does not actually state that a freshly prepared solution of β-D-glucopyranose becomes less sweet upon mutarotation.</p>\n<p>But if this interpretation is correct, the third sentence of the above quote is surely at least very misleading?</p>\n<p>The situation is clarified in a paper <a href=\"https://doi.org/10.1111/j.1365-2621.1965.tb01802.x\" rel=\"nofollow noreferrer\">Configuration, Conformation, and Sweetness of Hexose Anomers</a> by Shallenberger, Acree and Guild where the authors acknowledge that Pangborn and Gee are correct on this point.</p>\n<p>The relevant quote is as follows:</p>\n<blockquote>\n<p>Studies of sugars in solution (Pangborn and Gee, 1961; Schutz and Pilgrim, 1957; Cameron, 1947) show that freshly prepared of α-D-glucose are sweeter than mutarotated solutions</p>\n</blockquote>\n<blockquote>\n<p>Moreover, mutarotated glucose solutions are sweeter than freshly prepared\nβ-D-glucose (Pangborn and Gee, 1961).</p>\n</blockquote>\n<blockquote>\n<p>However, Shallenberer (1963) reported that crystalline β-D-glucose appears to taste sweeter than crystalline α-D-glucose</p>\n</blockquote>\n<p>Thus, to clarify: a freshly prepared solution of α-D-glucose becomes less sweet upon mutarotation, and a freshly prepared solutions of β-D-glucose becomes <strong>more sweet</strong> upon mutarotation, as correctly stated by Pangborn and Gee in their 1961 paper</p>\n","answer_id":116409,"answer_text":"IMO this is a very good question.\n\n\n\n\nThe paper Relative Sweetness of α and β-Forms of Selected Sugars (https://www.nature.com/articles/191810a0) by Rose Marie Pangborn & Sandra C. Gee, published in Nature in 1961    states, and provides very strong evidence,  that a freshly dissolved solution of β-D-glucose becomes sweeter after mutarotation.\n\n\n\n\nBut what of the paper Sugar Structure and Taste (https://pubs.acs.org/doi/10.1021/ba-1971-0117.ch015#:%7E:text=The%20saporous%20unit%20for%20sweet,and%20an%20intramolecular%20hydrogen%20bond) by R. S. Shallenberger which apparently states the   opposite?\n\n\n\n\nI'll give the full quote, as it may be important:\n\n\n\n\n\n\n\nα-D-Glucopyranose is about\ntwo-thirds as sweet as sucrose, but the mutarotated solution is even less sweet\n\n\n\n\n\n\n\n\n\n\nYet crystalline β-D-glucopyranose is sweeter than the α-anomer,\nand the mutarotated solution is again less sweet.\n\n\n\n\n\n\n\n\n\n\nIn the first one would\nconclude that the α-anomer is sweeter than the β-anomer, but in the\nsecond the reverse conclusion could be reached.\n\n\n\n\n\n\n\nTo be pedantic (and charitable), the second sentence of this quote refers to the crystalline forms, not the forms in solution, and Shallenberger does not actually state that a freshly prepared solution of β-D-glucopyranose becomes less sweet upon mutarotation.\n\n\n\n\nBut if this interpretation is correct, the third sentence of the above quote is surely at least very misleading?\n\n\n\n\nThe situation is clarified in a paper Configuration, Conformation, and Sweetness of Hexose Anomers (https://doi.org/10.1111/j.1365-2621.1965.tb01802.x) by Shallenberger, Acree and Guild where the authors acknowledge that Pangborn and Gee are correct on this point.\n\n\n\n\nThe relevant quote is as follows:\n\n\n\n\n\n\n\nStudies of sugars in solution (Pangborn and Gee, 1961; Schutz and Pilgrim, 1957; Cameron, 1947) show that freshly prepared of α-D-glucose are sweeter than mutarotated solutions\n\n\n\n\n\n\n\n\n\n\nMoreover, mutarotated glucose solutions are sweeter than freshly prepared\nβ-D-glucose (Pangborn and Gee, 1961).\n\n\n\n\n\n\n\n\n\n\nHowever, Shallenberer (1963) reported that crystalline β-D-glucose appears to taste sweeter than crystalline α-D-glucose\n\n\n\n\n\n\n\nThus, to clarify: a freshly prepared solution of α-D-glucose becomes less sweet upon mutarotation, and a freshly prepared solutions of β-D-glucose becomes more sweet upon mutarotation, as correctly stated by Pangborn and Gee in their 1961 paper","answer_url":"https://biology.stackexchange.com/a/116409","author":"tersorium","author_url":"https://biology.stackexchange.com/users/1136/tersorium","content_license":"CC BY-SA 4.0","created_at":"2025-04-26T07:51:06+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":"116409","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"tersorium","profile_url":"https://biology.stackexchange.com/users/1136/tersorium","user_type":"registered"},"created_at":"2025-04-26T07:51:06+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"807D42D6-933A-42CE-8585-D7B5EC415422","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/807D42D6-933A-42CE-8585-D7B5EC415422/view-source"}],"url":"https://biology.stackexchange.com/a/116409"}],"contexts":[{"context_id":"question","html":"<p>The article <a href=\"https://www.nature.com/articles/191810a0\" rel=\"nofollow noreferrer\">Relative Sweetness of α and β-Forms of Selected Sugars</a>, published in <em>Nature</em> (a leading scientific journal) in 1961 states that a freshly dissolved solution of β-D-glucose becomes sweeter after mutarotation whereas the article <a href=\"https://pubs.acs.org/doi/10.1021/ba-1971-0117.ch015#:%7E:text=The%20saporous%20unit%20for%20sweet,and%20an%20intramolecular%20hydrogen%20bond\" rel=\"nofollow noreferrer\">Sugar Structure and Taste</a> by R. S. Shallenberger ( a <a href=\"https://link.springer.com/book/10.1007/978-1-4615-2666-7\" rel=\"nofollow noreferrer\">leading researcher in the field of taste chemistry</a>) states the exact opposite is true.</p>\n<p>Which article is correct, please provide evidence?</p>\n<p>Edit: here is the exact quote from <code>Sugar Structure and Taste</code> paper:</p>\n<blockquote>\n<p>crystalline β-ᴅ-glucopyranose is sweeter than the α-anomer, yet the mutarotated solution is again less sweet</p>\n</blockquote>\n","text":"The article Relative Sweetness of α and β-Forms of Selected Sugars (https://www.nature.com/articles/191810a0), published in Nature (a leading scientific journal) in 1961 states that a freshly dissolved solution of β-D-glucose becomes sweeter after mutarotation whereas the article Sugar Structure and Taste (https://pubs.acs.org/doi/10.1021/ba-1971-0117.ch015#:%7E:text=The%20saporous%20unit%20for%20sweet,and%20an%20intramolecular%20hydrogen%20bond) by R. S. Shallenberger ( a leading researcher in the field of taste chemistry (https://link.springer.com/book/10.1007/978-1-4615-2666-7)) states the exact opposite is true.\n\n\n\n\nWhich article is correct, please provide evidence?\n\n\n\n\nEdit: here is the exact quote from Sugar Structure and Taste paper:\n\n\n\n\n\n\n\ncrystalline β-ᴅ-glucopyranose is sweeter than the α-anomer, yet the mutarotated solution is again less sweet"},{"context_id":"116409","html":"<p>IMO this is a very good question.</p>\n<p>The paper <a href=\"https://www.nature.com/articles/191810a0\" rel=\"nofollow noreferrer\">Relative Sweetness of α and β-Forms of Selected Sugars</a> by Rose Marie Pangborn &amp; Sandra C. Gee, published in <em>Nature</em> in 1961    states, <strong>and provides very strong evidence</strong>,  that a freshly dissolved solution of β-D-glucose becomes sweeter after mutarotation.</p>\n<p>But what of the paper <a href=\"https://pubs.acs.org/doi/10.1021/ba-1971-0117.ch015#:%7E:text=The%20saporous%20unit%20for%20sweet,and%20an%20intramolecular%20hydrogen%20bond\" rel=\"nofollow noreferrer\">Sugar Structure and Taste</a> by R. S. Shallenberger which apparently states the   opposite?</p>\n<p>I'll give the full quote, as it may be important:</p>\n<blockquote>\n<p>α-D-Glucopyranose is about\ntwo-thirds as sweet as sucrose, but the mutarotated solution is even less sweet</p>\n</blockquote>\n<blockquote>\n<p>Yet crystalline β-D-glucopyranose is sweeter than the α-anomer,\nand the mutarotated solution is again less sweet.</p>\n</blockquote>\n<blockquote>\n<p>In the first one would\nconclude that the α-anomer is sweeter than the β-anomer, but in the\nsecond the reverse conclusion could be reached.</p>\n</blockquote>\n<p>To be pedantic (and charitable), the second sentence of this quote refers to the crystalline forms, <em>not</em> the forms in solution, and Shallenberger does not actually state that a freshly prepared solution of β-D-glucopyranose becomes less sweet upon mutarotation.</p>\n<p>But if this interpretation is correct, the third sentence of the above quote is surely at least very misleading?</p>\n<p>The situation is clarified in a paper <a href=\"https://doi.org/10.1111/j.1365-2621.1965.tb01802.x\" rel=\"nofollow noreferrer\">Configuration, Conformation, and Sweetness of Hexose Anomers</a> by Shallenberger, Acree and Guild where the authors acknowledge that Pangborn and Gee are correct on this point.</p>\n<p>The relevant quote is as follows:</p>\n<blockquote>\n<p>Studies of sugars in solution (Pangborn and Gee, 1961; Schutz and Pilgrim, 1957; Cameron, 1947) show that freshly prepared of α-D-glucose are sweeter than mutarotated solutions</p>\n</blockquote>\n<blockquote>\n<p>Moreover, mutarotated glucose solutions are sweeter than freshly prepared\nβ-D-glucose (Pangborn and Gee, 1961).</p>\n</blockquote>\n<blockquote>\n<p>However, Shallenberer (1963) reported that crystalline β-D-glucose appears to taste sweeter than crystalline α-D-glucose</p>\n</blockquote>\n<p>Thus, to clarify: a freshly prepared solution of α-D-glucose becomes less sweet upon mutarotation, and a freshly prepared solutions of β-D-glucose becomes <strong>more sweet</strong> upon mutarotation, as correctly stated by Pangborn and Gee in their 1961 paper</p>\n","text":"IMO this is a very good question.\n\n\n\n\nThe paper Relative Sweetness of α and β-Forms of Selected Sugars (https://www.nature.com/articles/191810a0) by Rose Marie Pangborn & Sandra C. Gee, published in Nature in 1961    states, and provides very strong evidence,  that a freshly dissolved solution of β-D-glucose becomes sweeter after mutarotation.\n\n\n\n\nBut what of the paper Sugar Structure and Taste (https://pubs.acs.org/doi/10.1021/ba-1971-0117.ch015#:%7E:text=The%20saporous%20unit%20for%20sweet,and%20an%20intramolecular%20hydrogen%20bond) by R. S. Shallenberger which apparently states the   opposite?\n\n\n\n\nI'll give the full quote, as it may be important:\n\n\n\n\n\n\n\nα-D-Glucopyranose is about\ntwo-thirds as sweet as sucrose, but the mutarotated solution is even less sweet\n\n\n\n\n\n\n\n\n\n\nYet crystalline β-D-glucopyranose is sweeter than the α-anomer,\nand the mutarotated solution is again less sweet.\n\n\n\n\n\n\n\n\n\n\nIn the first one would\nconclude that the α-anomer is sweeter than the β-anomer, but in the\nsecond the reverse conclusion could be reached.\n\n\n\n\n\n\n\nTo be pedantic (and charitable), the second sentence of this quote refers to the crystalline forms, not the forms in solution, and Shallenberger does not actually state that a freshly prepared solution of β-D-glucopyranose becomes less sweet upon mutarotation.\n\n\n\n\nBut if this interpretation is correct, the third sentence of the above quote is surely at least very misleading?\n\n\n\n\nThe situation is clarified in a paper Configuration, Conformation, and Sweetness of Hexose Anomers (https://doi.org/10.1111/j.1365-2621.1965.tb01802.x) by Shallenberger, Acree and Guild where the authors acknowledge that Pangborn and Gee are correct on this point.\n\n\n\n\nThe relevant quote is as follows:\n\n\n\n\n\n\n\nStudies of sugars in solution (Pangborn and Gee, 1961; Schutz and Pilgrim, 1957; Cameron, 1947) show that freshly prepared of α-D-glucose are sweeter than mutarotated solutions\n\n\n\n\n\n\n\n\n\n\nMoreover, mutarotated glucose solutions are sweeter than freshly prepared\nβ-D-glucose (Pangborn and Gee, 1961).\n\n\n\n\n\n\n\n\n\n\nHowever, Shallenberer (1963) reported that crystalline β-D-glucose appears to taste sweeter than crystalline α-D-glucose\n\n\n\n\n\n\n\nThus, to clarify: a freshly prepared solution of α-D-glucose becomes less sweet upon mutarotation, and a freshly prepared solutions of β-D-glucose becomes more sweet upon mutarotation, as correctly stated by Pangborn and Gee in their 1961 paper"}],"domain":"biology","external_citations":["https://doi.org/10.1111/j.1365-2621.1965.tb01802.x","https://link.springer.com/book/10.1007/978-1-4615-2666-7","https://pubs.acs.org/doi/10.1021/ba-1971-0117.ch015#:%7E:text=The%20saporous%20unit%20for%20sweet,and%20an%20intramolecular%20hydrogen%20bond","https://www.nature.com/articles/191810a0"],"ground_truth_type":"metadata_grounded","group_id":"c75d2483a38cba61d3cf7cefd6a6a00202e4e2264058d222822e230dd0c53d4e","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-2d54378a6534a06481d9264a","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":"user394522","profile_url":"https://biology.stackexchange.com/users/78594/user394522","user_type":"registered"},"created_at":"2025-04-25T06:43:29+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"C0C3E95C-C79B-4032-866B-AD1F24131E39","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/C0C3E95C-C79B-4032-866B-AD1F24131E39/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":"2025-04-25T22:33:52+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"8E24EB6A-A04D-4E4E-A59D-6C4B6E00ECDD","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8E24EB6A-A04D-4E4E-A59D-6C4B6E00ECDD/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"tersorium","profile_url":"https://biology.stackexchange.com/users/1136/tersorium","user_type":"registered"},"created_at":"2025-04-26T07:52:55+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"483A0BAC-082E-4406-8526-06DE79A3A14C","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/483A0BAC-082E-4406-8526-06DE79A3A14C/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2025-05-26T08:06:15+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"7A07BAEE-0885-4B89-BCF3-E6D4AA92AD33","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/7A07BAEE-0885-4B89-BCF3-E6D4AA92AD33/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2025-09-23T09:05:55+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"00218711-C917-4A20-A97C-E8D65E348903","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/00218711-C917-4A20-A97C-E8D65E348903/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2026-01-21T09:06:05+00:00","raw_file":"raw/codex_api_v1/00f792a35cd1fe53cc744b44d1c7f5a2081648f5d4403a4e8f1d570c00e5dc95_1790824135500262400_0.json","raw_sha256":"0face46f22b53414ff8968bb035acf71d0f5c1f84da8d6f0813602f842802d98","revision_guid":"A83A6FD5-6380-4946-9327-ED03AF0210E8","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/A83A6FD5-6380-4946-9327-ED03AF0210E8/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":"116406","source_record_sha256":"3f0b8234de3fc4bc0770701acef23e2bc8a48f528abba207305afae069e1d0d5","source_url":"https://biology.stackexchange.com/questions/116406/does-%ce%b2-d-glucose-become-more-or-less-sweet-after-mutarotation","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Does β-D-glucose become more or less sweet after mutarotation\nThe article Relative Sweetness of α and β-Forms of Selected Sugars (https://www.nature.com/articles/191810a0), published in Nature (a leading scientific journal) in 1961 states that a freshly dissolved solution of β-D-glucose becomes sweeter after mutarotation whereas the article Sugar Structure and Taste (https://pubs.acs.org/doi/10.1021/ba-1971-0117.ch015#:%7E:text=The%20saporous%20unit%20for%20sweet,and%20an%20intramolecular%20hydrogen%20bond) by R. S. Shallenberger ( a leading researcher in the field of taste chemistry (https://link.springer.com/book/10.1007/978-1-4615-2666-7)) states the exact opposite is true.\n\n\n\n\nWhich article is correct, please provide evidence?\n\n\n\n\nEdit: here is the exact quote from Sugar Structure and Taste paper:\n\n\n\n\n\n\n\ncrystalline β-ᴅ-glucopyranose is sweeter than the α-anomer, yet the mutarotated solution is again less sweet","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":116409,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Cherries are drupes, which apparently mean that by definition the pit is formed from the superior ovary, i.e. the central bit of the flower:</p>\n<p><a href=\"https://courses.botany.wisc.edu/botany_400/Lab/LabWK03Fruitkey.html\" rel=\"noreferrer\">https://courses.botany.wisc.edu/botany_400/Lab/LabWK03Fruitkey.html</a></p>\n<p><a href=\"https://en.wikipedia.org/wiki/Ovary_(botany)#Superior_ovary\" rel=\"noreferrer\">https://en.wikipedia.org/wiki/Ovary_(botany)#Superior_ovary</a></p>\n<p>Diagram of the ovary's relationship to the flower:\n<a href=\"https://i.sstatic.net/Lhn3Ezfd.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/Lhn3Ezfd.png\" alt=\"Diagram of different ovary positions in a flower\" /></a></p>\n<p><a href=\"https://en.wikipedia.org/wiki/Drupe\" rel=\"noreferrer\">https://en.wikipedia.org/wiki/Drupe</a></p>\n<p>From the last Wikipedia link:</p>\n<blockquote>\n<p>The definitive characteristic of a drupe is that the hard, woody (lignified) stone is derived from the ovary wall of the flower.</p>\n</blockquote>\n<p>From your photo it seems clear that those cherries have two separate pits which would have formed from two separate ovaries, so even if those ovaries happened to have identical DNA (which could be, I haven't looked into how the ovaries form to see why they'd be conjoined like this) they'd have been fertilized independently with different pollen, meaning the seeds will have different genetics.</p>\n","answer_id":117713,"answer_text":"Cherries are drupes, which apparently mean that by definition the pit is formed from the superior ovary, i.e. the central bit of the flower:\n\n\n\n\nhttps://courses.botany.wisc.edu/botany_400/Lab/LabWK03Fruitkey.html (https://courses.botany.wisc.edu/botany_400/Lab/LabWK03Fruitkey.html)\n\n\n\n\nhttps://en.wikipedia.org/wiki/Ovary_(botany)#Superior_ovary (https://en.wikipedia.org/wiki/Ovary_(botany)#Superior_ovary)\n\n\n\n\nDiagram of the ovary's relationship to the flower:\n[image: Diagram of different ovary positions in a flower; source: https://i.sstatic.net/Lhn3Ezfd.png] (https://i.sstatic.net/Lhn3Ezfd.png)\n\n\n\n\nhttps://en.wikipedia.org/wiki/Drupe (https://en.wikipedia.org/wiki/Drupe)\n\n\n\n\nFrom the last Wikipedia link:\n\n\n\n\n\n\n\nThe definitive characteristic of a drupe is that the hard, woody (lignified) stone is derived from the ovary wall of the flower.\n\n\n\n\n\n\n\nFrom your photo it seems clear that those cherries have two separate pits which would have formed from two separate ovaries, so even if those ovaries happened to have identical DNA (which could be, I haven't looked into how the ovaries form to see why they'd be conjoined like this) they'd have been fertilized independently with different pollen, meaning the seeds will have different genetics.","answer_url":"https://biology.stackexchange.com/a/117713","author":"Oosaka","author_url":"https://biology.stackexchange.com/users/30356/oosaka","content_license":"CC BY-SA 4.0","created_at":"2025-07-22T10:38:47+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":117677,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Oosaka","profile_url":"https://biology.stackexchange.com/users/30356/oosaka","user_type":"registered"},"created_at":"2025-07-22T10:38:47+00:00","raw_file":"raw/codex_api_v1/01815689c0e6362f8bdf7b8393d418437539b76345e52b5c663d1613602784aa_1790824154537857800_0.json","raw_sha256":"b2f446369df60a45c452a5be0d5e0c462ff7455589d79062d4d1f36a4c5e5880","revision_guid":"EC47AAF8-2AFB-4BB9-8A8B-219820BE3167","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/EC47AAF8-2AFB-4BB9-8A8B-219820BE3167/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Oosaka","profile_url":"https://biology.stackexchange.com/users/30356/oosaka","user_type":"registered"},"created_at":"2025-07-22T10:43:48+00:00","raw_file":"raw/codex_api_v1/01815689c0e6362f8bdf7b8393d418437539b76345e52b5c663d1613602784aa_1790824154537857800_0.json","raw_sha256":"b2f446369df60a45c452a5be0d5e0c462ff7455589d79062d4d1f36a4c5e5880","revision_guid":"A87412F5-4570-49FE-8005-6C928195FC61","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A87412F5-4570-49FE-8005-6C928195FC61/view-source"}],"score":6}],"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":"2025-07-10T19:45:02+00:00","raw_file":"raw/codex_api_v1/80ec0626e4dca1e373c0bba13c4761d1214a376d40d05a99b2449abc3be980f1_1790824142842265700_0.json","raw_sha256":"33eeba97fc2f78c2f9362274c5b7e2be011563807fed5b756d22d51f059bffce","revision_guid":"4DDAA8C4-A33F-4781-9BB3-B17331941F7C","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4DDAA8C4-A33F-4781-9BB3-B17331941F7C/view-source"}],"url":"https://biology.stackexchange.com/questions/117677/conjoined-yellow-cherries-do-the-pits-have-identical-dna"},{"author":"Oosaka","author_url":"https://biology.stackexchange.com/users/30356/oosaka","content_license":"CC BY-SA 4.0","context_id":"117713","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Oosaka","profile_url":"https://biology.stackexchange.com/users/30356/oosaka","user_type":"registered"},"created_at":"2025-07-22T10:38:47+00:00","raw_file":"raw/codex_api_v1/01815689c0e6362f8bdf7b8393d418437539b76345e52b5c663d1613602784aa_1790824154537857800_0.json","raw_sha256":"b2f446369df60a45c452a5be0d5e0c462ff7455589d79062d4d1f36a4c5e5880","revision_guid":"EC47AAF8-2AFB-4BB9-8A8B-219820BE3167","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/EC47AAF8-2AFB-4BB9-8A8B-219820BE3167/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Oosaka","profile_url":"https://biology.stackexchange.com/users/30356/oosaka","user_type":"registered"},"created_at":"2025-07-22T10:43:48+00:00","raw_file":"raw/codex_api_v1/01815689c0e6362f8bdf7b8393d418437539b76345e52b5c663d1613602784aa_1790824154537857800_0.json","raw_sha256":"b2f446369df60a45c452a5be0d5e0c462ff7455589d79062d4d1f36a4c5e5880","revision_guid":"A87412F5-4570-49FE-8005-6C928195FC61","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/A87412F5-4570-49FE-8005-6C928195FC61/view-source"}],"url":"https://biology.stackexchange.com/a/117713"}],"contexts":[{"context_id":"question","html":"<p>I bought some yellow sweet cherries from a grocery store in Ontario, Canada. One of the cherries was actually two cherries combined with a single stem. (Size: 1.5 inches wide total; product of USA.)</p>\n<p><a href=\"https://i.sstatic.net/AJDZo7d8.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/AJDZo7d8.png\" alt=\"enter image description here\" /></a></p>\n<p>Do the seeds have identical genetics? Or different genetics?</p>\n<p>Related: <a href=\"https://biology.stackexchange.com/questions/70233/peach-pits-with-two-seeds-are-the-seeds-identical-twins\">Peach pits with two seeds: Are the seeds identical twins?</a></p>\n","text":"I bought some yellow sweet cherries from a grocery store in Ontario, Canada. One of the cherries was actually two cherries combined with a single stem. (Size: 1.5 inches wide total; product of USA.)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/AJDZo7d8.png] (https://i.sstatic.net/AJDZo7d8.png)\n\n\n\n\nDo the seeds have identical genetics? Or different genetics?\n\n\n\n\nRelated: Peach pits with two seeds: Are the seeds identical twins? (https://biology.stackexchange.com/questions/70233/peach-pits-with-two-seeds-are-the-seeds-identical-twins)"},{"context_id":"117713","html":"<p>Cherries are drupes, which apparently mean that by definition the pit is formed from the superior ovary, i.e. the central bit of the flower:</p>\n<p><a href=\"https://courses.botany.wisc.edu/botany_400/Lab/LabWK03Fruitkey.html\" rel=\"noreferrer\">https://courses.botany.wisc.edu/botany_400/Lab/LabWK03Fruitkey.html</a></p>\n<p><a href=\"https://en.wikipedia.org/wiki/Ovary_(botany)#Superior_ovary\" rel=\"noreferrer\">https://en.wikipedia.org/wiki/Ovary_(botany)#Superior_ovary</a></p>\n<p>Diagram of the ovary's relationship to the flower:\n<a href=\"https://i.sstatic.net/Lhn3Ezfd.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/Lhn3Ezfd.png\" alt=\"Diagram of different ovary positions in a flower\" /></a></p>\n<p><a href=\"https://en.wikipedia.org/wiki/Drupe\" rel=\"noreferrer\">https://en.wikipedia.org/wiki/Drupe</a></p>\n<p>From the last Wikipedia link:</p>\n<blockquote>\n<p>The definitive characteristic of a drupe is that the hard, woody (lignified) stone is derived from the ovary wall of the flower.</p>\n</blockquote>\n<p>From your photo it seems clear that those cherries have two separate pits which would have formed from two separate ovaries, so even if those ovaries happened to have identical DNA (which could be, I haven't looked into how the ovaries form to see why they'd be conjoined like this) they'd have been fertilized independently with different pollen, meaning the seeds will have different genetics.</p>\n","text":"Cherries are drupes, which apparently mean that by definition the pit is formed from the superior ovary, i.e. the central bit of the flower:\n\n\n\n\nhttps://courses.botany.wisc.edu/botany_400/Lab/LabWK03Fruitkey.html (https://courses.botany.wisc.edu/botany_400/Lab/LabWK03Fruitkey.html)\n\n\n\n\nhttps://en.wikipedia.org/wiki/Ovary_(botany)#Superior_ovary (https://en.wikipedia.org/wiki/Ovary_(botany)#Superior_ovary)\n\n\n\n\nDiagram of the ovary's relationship to the flower:\n[image: Diagram of different ovary positions in a flower; source: https://i.sstatic.net/Lhn3Ezfd.png] (https://i.sstatic.net/Lhn3Ezfd.png)\n\n\n\n\nhttps://en.wikipedia.org/wiki/Drupe (https://en.wikipedia.org/wiki/Drupe)\n\n\n\n\nFrom the last Wikipedia link:\n\n\n\n\n\n\n\nThe definitive characteristic of a drupe is that the hard, woody (lignified) stone is derived from the ovary wall of the flower.\n\n\n\n\n\n\n\nFrom your photo it seems clear that those cherries have two separate pits which would have formed from two separate ovaries, so even if those ovaries happened to have identical DNA (which could be, I haven't looked into how the ovaries form to see why they'd be conjoined like this) they'd have been fertilized independently with different pollen, meaning the seeds will have different genetics."}],"domain":"biology","external_citations":["https://biology.stackexchange.com/questions/70233/peach-pits-with-two-seeds-are-the-seeds-identical-twins","https://courses.botany.wisc.edu/botany_400/Lab/LabWK03Fruitkey.html","https://en.wikipedia.org/wiki/Drupe","https://en.wikipedia.org/wiki/Ovary_(botany)#Superior_ovary","https://i.sstatic.net/AJDZo7d8.png","https://i.sstatic.net/Lhn3Ezfd.png"],"ground_truth_type":"metadata_grounded","group_id":"4fcad0bc7bc97d41d6d39accca0f89e6f5fe6545b4d98a26b04b4733cd2b3428","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-b52ccf2be568248ac99b959c","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":"User1974","profile_url":"https://biology.stackexchange.com/users/31741/user1974","user_type":"registered"},"created_at":"2025-07-10T19:45:02+00:00","raw_file":"raw/codex_api_v1/80ec0626e4dca1e373c0bba13c4761d1214a376d40d05a99b2449abc3be980f1_1790824142842265700_0.json","raw_sha256":"33eeba97fc2f78c2f9362274c5b7e2be011563807fed5b756d22d51f059bffce","revision_guid":"4DDAA8C4-A33F-4781-9BB3-B17331941F7C","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/4DDAA8C4-A33F-4781-9BB3-B17331941F7C/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":"117677","source_record_sha256":"56863734e017adc237a83cda27790b735bdbec3172a901a6dc5b72d6d0a94870","source_url":"https://biology.stackexchange.com/questions/117677/conjoined-yellow-cherries-do-the-pits-have-identical-dna","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Conjoined yellow cherries — Do the pits have identical DNA?\nI bought some yellow sweet cherries from a grocery store in Ontario, Canada. One of the cherries was actually two cherries combined with a single stem. (Size: 1.5 inches wide total; product of USA.)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/AJDZo7d8.png] (https://i.sstatic.net/AJDZo7d8.png)\n\n\n\n\nDo the seeds have identical genetics? Or different genetics?\n\n\n\n\nRelated: Peach pits with two seeds: Are the seeds identical twins? (https://biology.stackexchange.com/questions/70233/peach-pits-with-two-seeds-are-the-seeds-identical-twins)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":117713,"score":6}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I recommend <a href=\"https://www.nature.com/articles/s41586-024-08450-5\" rel=\"nofollow noreferrer\">this recent publication</a> (Palsson et al. 2025 Nature). THe method is of supposedly much higher accuracy due to the presence of the more numerous non-crossover recombination events.</p>\n<p>They have deposited maps on <a href=\"https://zenodo.org/records/14025565\" rel=\"nofollow noreferrer\">zenodo</a>.</p>\n<p>Looking at the maps they are not at the resolution that you want, but you should be able to interpolate map distances from the provided information if you really need to.</p>\n<p>I am guessing that they don't get that fine due to the sparsity of the crossover data. For a derivation of the limits of resolution to maps, I suggest this <a href=\"https://pubmed.ncbi.nlm.nih.gov/8037215/\" rel=\"nofollow noreferrer\">paper</a>. They refer to their maps as &quot;high-resolution&quot;.</p>\n<p>I suggest also references therein.</p>\n","answer_id":117696,"answer_text":"I recommend this recent publication (https://www.nature.com/articles/s41586-024-08450-5) (Palsson et al. 2025 Nature). THe method is of supposedly much higher accuracy due to the presence of the more numerous non-crossover recombination events.\n\n\n\n\nThey have deposited maps on zenodo (https://zenodo.org/records/14025565).\n\n\n\n\nLooking at the maps they are not at the resolution that you want, but you should be able to interpolate map distances from the provided information if you really need to.\n\n\n\n\nI am guessing that they don't get that fine due to the sparsity of the crossover data. For a derivation of the limits of resolution to maps, I suggest this paper (https://pubmed.ncbi.nlm.nih.gov/8037215/). They refer to their maps as \"high-resolution\".\n\n\n\n\nI suggest also references therein.","answer_url":"https://biology.stackexchange.com/a/117696","author":"Maximilian Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","created_at":"2025-07-16T20:05:35+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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Press","author_url":"https://biology.stackexchange.com/users/22392/maximilian-press","content_license":"CC BY-SA 4.0","context_id":"117696","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":"2025-07-16T20:05:35+00:00","raw_file":"raw/codex_api_v1/80ec0626e4dca1e373c0bba13c4761d1214a376d40d05a99b2449abc3be980f1_1790824142842265700_0.json","raw_sha256":"33eeba97fc2f78c2f9362274c5b7e2be011563807fed5b756d22d51f059bffce","revision_guid":"749E9F49-0B97-4F20-815E-727E357316D7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/749E9F49-0B97-4F20-815E-727E357316D7/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":"2025-07-16T20:12:43+00:00","raw_file":"raw/codex_api_v1/80ec0626e4dca1e373c0bba13c4761d1214a376d40d05a99b2449abc3be980f1_1790824142842265700_0.json","raw_sha256":"33eeba97fc2f78c2f9362274c5b7e2be011563807fed5b756d22d51f059bffce","revision_guid":"F00C4C12-71C5-43D4-A8B1-984173FD9E74","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F00C4C12-71C5-43D4-A8B1-984173FD9E74/view-source"}],"url":"https://biology.stackexchange.com/a/117696"}],"contexts":[{"context_id":"question","html":"<p>For some work I've been doing, I've been spending a lot of time looking for linkage and/or recombination maps that meet these criteria:</p>\n<ol>\n<li>Very fine-scale, to the point that the typical resolution or inter-SNP distance is around 1 kb or below</li>\n<li>The genetic/recombination map has actually been released by the authors, in a supplementary file, or a database, or something like that.</li>\n<li>If possible, though not necessary, I'd like this to be a genetic or recombination map for a non-PRDM9 organism.</li>\n</ol>\n<p>After lots of searching, I've still only found one paper which meets these criteria: &quot;Stable recombination hotspots in birds&quot; in Science (2015). Whatever additional papers there are that have this data available for download and use, I would appreciate it if they could be shared.</p>\n","text":"For some work I've been doing, I've been spending a lot of time looking for linkage and/or recombination maps that meet these criteria:\n\n\n\n\n\nVery fine-scale, to the point that the typical resolution or inter-SNP distance is around 1 kb or below\n\n\n\n\nThe genetic/recombination map has actually been released by the authors, in a supplementary file, or a database, or something like that.\n\n\n\n\nIf possible, though not necessary, I'd like this to be a genetic or recombination map for a non-PRDM9 organism.\n\n\n\n\n\nAfter lots of searching, I've still only found one paper which meets these criteria: \"Stable recombination hotspots in birds\" in Science (2015). Whatever additional papers there are that have this data available for download and use, I would appreciate it if they could be shared."},{"context_id":"117696","html":"<p>I recommend <a href=\"https://www.nature.com/articles/s41586-024-08450-5\" rel=\"nofollow noreferrer\">this recent publication</a> (Palsson et al. 2025 Nature). THe method is of supposedly much higher accuracy due to the presence of the more numerous non-crossover recombination events.</p>\n<p>They have deposited maps on <a href=\"https://zenodo.org/records/14025565\" rel=\"nofollow noreferrer\">zenodo</a>.</p>\n<p>Looking at the maps they are not at the resolution that you want, but you should be able to interpolate map distances from the provided information if you really need to.</p>\n<p>I am guessing that they don't get that fine due to the sparsity of the crossover data. For a derivation of the limits of resolution to maps, I suggest this <a href=\"https://pubmed.ncbi.nlm.nih.gov/8037215/\" rel=\"nofollow noreferrer\">paper</a>. They refer to their maps as &quot;high-resolution&quot;.</p>\n<p>I suggest also references therein.</p>\n","text":"I recommend this recent publication (https://www.nature.com/articles/s41586-024-08450-5) (Palsson et al. 2025 Nature). THe method is of supposedly much higher accuracy due to the presence of the more numerous non-crossover recombination events.\n\n\n\n\nThey have deposited maps on zenodo (https://zenodo.org/records/14025565).\n\n\n\n\nLooking at the maps they are not at the resolution that you want, but you should be able to interpolate map distances from the provided information if you really need to.\n\n\n\n\nI am guessing that they don't get that fine due to the sparsity of the crossover data. For a derivation of the limits of resolution to maps, I suggest this paper (https://pubmed.ncbi.nlm.nih.gov/8037215/). They refer to their maps as \"high-resolution\".\n\n\n\n\nI suggest also references therein."}],"domain":"biology","external_citations":["https://pubmed.ncbi.nlm.nih.gov/8037215/","https://www.nature.com/articles/s41586-024-08450-5","https://zenodo.org/records/14025565"],"ground_truth_type":"metadata_grounded","group_id":"1db04d9f3bda4c4dc9904fd16cf4bc10d1cfc7184e71d421ff3096f1ff2f183e","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-190e08b63e5942b66b022c47","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":"Rick Schwartz","profile_url":"https://biology.stackexchange.com/users/112622/rick-schwartz","user_type":"registered"},"created_at":"2025-07-16T16:22:47+00:00","raw_file":"raw/codex_api_v1/80ec0626e4dca1e373c0bba13c4761d1214a376d40d05a99b2449abc3be980f1_1790824142842265700_0.json","raw_sha256":"33eeba97fc2f78c2f9362274c5b7e2be011563807fed5b756d22d51f059bffce","revision_guid":"99697870-5196-45C1-8F42-FA8DAAA71A47","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/99697870-5196-45C1-8F42-FA8DAAA71A47/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2025-08-15T21:01:30+00:00","raw_file":"raw/codex_api_v1/80ec0626e4dca1e373c0bba13c4761d1214a376d40d05a99b2449abc3be980f1_1790824142842265700_0.json","raw_sha256":"33eeba97fc2f78c2f9362274c5b7e2be011563807fed5b756d22d51f059bffce","revision_guid":"7DFE2914-A9E6-4775-AE88-A6934721738A","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/7DFE2914-A9E6-4775-AE88-A6934721738A/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2025-12-13T21:07:45+00:00","raw_file":"raw/codex_api_v1/80ec0626e4dca1e373c0bba13c4761d1214a376d40d05a99b2449abc3be980f1_1790824142842265700_0.json","raw_sha256":"33eeba97fc2f78c2f9362274c5b7e2be011563807fed5b756d22d51f059bffce","revision_guid":"D1E2E1FA-788A-4A43-9762-3377D385DEA8","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/D1E2E1FA-788A-4A43-9762-3377D385DEA8/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2026-04-12T22:01:30+00:00","raw_file":"raw/codex_api_v1/80ec0626e4dca1e373c0bba13c4761d1214a376d40d05a99b2449abc3be980f1_1790824142842265700_0.json","raw_sha256":"33eeba97fc2f78c2f9362274c5b7e2be011563807fed5b756d22d51f059bffce","revision_guid":"64D24B07-5FD5-4FA0-A4C8-4264147896E8","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/64D24B07-5FD5-4FA0-A4C8-4264147896E8/view-source"},{"content_license":null,"contributor":{"display_name":"Community","profile_url":"https://biology.stackexchange.com/users/-1/community","user_type":"moderator"},"created_at":"2026-08-10T22:06:10+00:00","raw_file":"raw/codex_api_v1/80ec0626e4dca1e373c0bba13c4761d1214a376d40d05a99b2449abc3be980f1_1790824142842265700_0.json","raw_sha256":"33eeba97fc2f78c2f9362274c5b7e2be011563807fed5b756d22d51f059bffce","revision_guid":"019377E9-CE0F-491D-B037-8D27922EEE71","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/019377E9-CE0F-491D-B037-8D27922EEE71/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":"117694","source_record_sha256":"eab9ad10940c16df70d28b1a56f170e4af5ea35c3e13c29f523324e9af8c4dc9","source_url":"https://biology.stackexchange.com/questions/117694/are-there-any-fine-scale-1-kb-resolution-genetic-or-recombination-maps-with","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Are there any fine-scale (< 1 kb resolution) genetic or recombination maps with data released?\nFor some work I've been doing, I've been spending a lot of time looking for linkage and/or recombination maps that meet these criteria:\n\n\n\n\n\nVery fine-scale, to the point that the typical resolution or inter-SNP distance is around 1 kb or below\n\n\n\n\nThe genetic/recombination map has actually been released by the authors, in a supplementary file, or a database, or something like that.\n\n\n\n\nIf possible, though not necessary, I'd like this to be a genetic or recombination map for a non-PRDM9 organism.\n\n\n\n\n\nAfter lots of searching, I've still only found one paper which meets these criteria: \"Stable recombination hotspots in birds\" in Science (2015). Whatever additional papers there are that have this data available for download and use, I would appreciate it if they could be shared.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":117696,"score":0}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Short oligos are extremely cheap from commercial vendors like IDT. You could probably get both strands of that sequence synthesized for around $10 and anneal them yourself. You can also order them already annealed for an additional cost.</p>\n<p>You might also consider having it fluorescently labelled. This would add cost but could aid in detection in EMSA or allow for techniques like fluorescence polarization.</p>\n","answer_id":117758,"answer_text":"Short oligos are extremely cheap from commercial vendors like IDT. You could probably get both strands of that sequence synthesized for around $10 and anneal them yourself. You can also order them already annealed for an additional cost.\n\n\n\n\nYou might also consider having it fluorescently labelled. This would add cost but could aid in detection in EMSA or allow for techniques like fluorescence polarization.","answer_url":"https://biology.stackexchange.com/a/117758","author":"canadianer","author_url":"https://biology.stackexchange.com/users/6307/canadianer","content_license":"CC BY-SA 4.0","created_at":"2025-07-31T23:18:20+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 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":117756,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"canadianer","profile_url":"https://biology.stackexchange.com/users/6307/canadianer","user_type":"registered"},"created_at":"2025-07-31T23:18:20+00:00","raw_file":"raw/codex_api_v1/01815689c0e6362f8bdf7b8393d418437539b76345e52b5c663d1613602784aa_1790824154537857800_0.json","raw_sha256":"b2f446369df60a45c452a5be0d5e0c462ff7455589d79062d4d1f36a4c5e5880","revision_guid":"932F00E7-89D4-4092-B6C5-77D76525AF14","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/932F00E7-89D4-4092-B6C5-77D76525AF14/view-source"}],"score":1}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Dmitry","author_url":"https://biology.stackexchange.com/users/113531/dmitry","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Dmitry","profile_url":"https://biology.stackexchange.com/users/113531/dmitry","user_type":"registered"},"created_at":"2025-07-31T16:44:38+00:00","raw_file":"raw/codex_api_v1/01815689c0e6362f8bdf7b8393d418437539b76345e52b5c663d1613602784aa_1790824154537857800_0.json","raw_sha256":"b2f446369df60a45c452a5be0d5e0c462ff7455589d79062d4d1f36a4c5e5880","revision_guid":"B5A0B3E5-1950-497A-A44C-C58D8E0B2ACA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B5A0B3E5-1950-497A-A44C-C58D8E0B2ACA/view-source"}],"url":"https://biology.stackexchange.com/questions/117756/detecting-if-a-specific-dna-region-has-high-affinity-with-a-specific-transcripti"},{"author":"canadianer","author_url":"https://biology.stackexchange.com/users/6307/canadianer","content_license":"CC BY-SA 4.0","context_id":"117758","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"canadianer","profile_url":"https://biology.stackexchange.com/users/6307/canadianer","user_type":"registered"},"created_at":"2025-07-31T23:18:20+00:00","raw_file":"raw/codex_api_v1/01815689c0e6362f8bdf7b8393d418437539b76345e52b5c663d1613602784aa_1790824154537857800_0.json","raw_sha256":"b2f446369df60a45c452a5be0d5e0c462ff7455589d79062d4d1f36a4c5e5880","revision_guid":"932F00E7-89D4-4092-B6C5-77D76525AF14","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/932F00E7-89D4-4092-B6C5-77D76525AF14/view-source"}],"url":"https://biology.stackexchange.com/a/117758"}],"contexts":[{"context_id":"question","html":"<p>I know a sequence of presumable GC-rich binding site of some specific transcription factor (e.g. GCGGGCGG). I know it's between -300 and -100 from the start codone of the given gene. How can I confirm that the TF has affinity with GCGGGCGG ? Of course EMSA is good for detecting affinity but how do I get the given oligonucleotide to do EMSA? Is it cheaper to synthesise the sequence using any technique or cut it out by some pre-calculated set of restriction enzymes</p>\n","text":"I know a sequence of presumable GC-rich binding site of some specific transcription factor (e.g. GCGGGCGG). I know it's between -300 and -100 from the start codone of the given gene. How can I confirm that the TF has affinity with GCGGGCGG ? Of course EMSA is good for detecting affinity but how do I get the given oligonucleotide to do EMSA? Is it cheaper to synthesise the sequence using any technique or cut it out by some pre-calculated set of restriction enzymes"},{"context_id":"117758","html":"<p>Short oligos are extremely cheap from commercial vendors like IDT. You could probably get both strands of that sequence synthesized for around $10 and anneal them yourself. You can also order them already annealed for an additional cost.</p>\n<p>You might also consider having it fluorescently labelled. This would add cost but could aid in detection in EMSA or allow for techniques like fluorescence polarization.</p>\n","text":"Short oligos are extremely cheap from commercial vendors like IDT. You could probably get both strands of that sequence synthesized for around $10 and anneal them yourself. You can also order them already annealed for an additional cost.\n\n\n\n\nYou might also consider having it fluorescently labelled. This would add cost but could aid in detection in EMSA or allow for techniques like fluorescence polarization."}],"domain":"biology","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"e41a19596814aea5a8a0a55f6caf05195a482ba9366879b46507f9a967c6cfa7","hard_case_family":["no_accepted_answer"],"id":"RHM-f6b5036f03153c957af9b255","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":"Dmitry","profile_url":"https://biology.stackexchange.com/users/113531/dmitry","user_type":"registered"},"created_at":"2025-07-31T16:44:38+00:00","raw_file":"raw/codex_api_v1/01815689c0e6362f8bdf7b8393d418437539b76345e52b5c663d1613602784aa_1790824154537857800_0.json","raw_sha256":"b2f446369df60a45c452a5be0d5e0c462ff7455589d79062d4d1f36a4c5e5880","revision_guid":"B5A0B3E5-1950-497A-A44C-C58D8E0B2ACA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B5A0B3E5-1950-497A-A44C-C58D8E0B2ACA/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":"117756","source_record_sha256":"e0638cc8975850fc6ddeb7abf792b008fde9a97877ba51749bc8038c1ff53b22","source_url":"https://biology.stackexchange.com/questions/117756/detecting-if-a-specific-dna-region-has-high-affinity-with-a-specific-transcripti","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Detecting if a specific DNA region has high affinity with a specific transcription factor\nI know a sequence of presumable GC-rich binding site of some specific transcription factor (e.g. GCGGGCGG). I know it's between -300 and -100 from the start codone of the given gene. How can I confirm that the TF has affinity with GCGGGCGG ? Of course EMSA is good for detecting affinity but how do I get the given oligonucleotide to do EMSA? Is it cheaper to synthesise the sequence using any technique or cut it out by some pre-calculated set of restriction enzymes","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":117758,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":117921,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<blockquote>\n<p>Often in popular explanations, we hear that organisms evolved these features &quot;because they needed them&quot; for survival.</p>\n</blockquote>\n<p>Ya, that's <em>very, very</em> wrong. Evolution is a <strong>stochastic or chance</strong> process. According to <a href=\"https://www.google.com/url?sa=t&amp;source=web&amp;rct=j&amp;opi=89978449&amp;url=https://anthroholic.com/theory-of-mutation-in-evolution%3Fsrsltid%3DAfmBOorNk1lQV8zP_J6MCIGBc96DzWXOj_n4GFKVyNSCogwEA3O04HhJ&amp;ved=2ahUKEwjCg8KXtdiPAxU3lK8BHdHNIX8QFnoECGEQAQ&amp;usg=AOvVaw1dI_5lDaduAfSxGhCZrnoy\" rel=\"nofollow noreferrer\">Hugo de Vries theory of evolution</a>, evolution occurs due to <strong>random</strong> sudden huge mutations <strong>that occur in any random direction.</strong> So evolution is not at all a directed process.</p>\n<p>When these variations occur, they could either benefit the organism or harm it. In case of useful variations, the organisms have a benefit over other organisms of its type. For example, if there are a group of herbivores without eyes, and one of them suddenly develops eyes, it would surely have a benefit because it can see where vegetation is to feed upon. (Point to note here is that this is just an example, and evolution of the eye has been described below) This in Darwin's terms, is often known as <em>&quot;Survival of the fittest&quot;.</em></p>\n<p>So, &quot;need&quot; has no role in this process. &quot;Environmental pressure&quot; does have a role in this, especially for selecting the better traits. For example, in <a href=\"https://www.google.com/url?sa=t&amp;source=web&amp;rct=j&amp;opi=89978449&amp;url=https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/replica-plating&amp;ved=2ahUKEwid0ZCVuNiPAxX8hagCHc4QI0cQFnoFCIMBEAE&amp;usg=AOvVaw3oVRlGq19bdf8TgBFgQHhc\" rel=\"nofollow noreferrer\">Lederberg's replica plating experiment</a>, bacteria which had pre-evolved antibiotic resistance survived due to the selection pressure of the antibiotic environment.</p>\n<p><strong>Darwin's theory and Neo Darwinism</strong></p>\n<p>Neo-Darwinism is the most recent theory of evolution. Let us discuss Darwin's theory first:</p>\n<ol>\n<li>Important role of reproduction: Organisms reproducing at a very high rate make more of themselves, and out compete others.</li>\n<li>Struggle for existence: This high rate of reproduction leads to competition for food, land, etc.</li>\n<li>Variation and their Inheritance: Organism have inbuilt variation for providing benefits to the organism.</li>\n<li>Survival of the fittest and natural selection: Organisms with the best of these characteristics succeed in this competition and produce more organisms with its beneficial characteristics.</li>\n</ol>\n<p>In this case, variations originate randomly. The organism with better characteristics has a reproductive advantage, therefore increasing the number of individuals having that characteristic in the population. Better characteristics get selected and genetically passed on. When the Mendelian genetics are added on this theory, it is known as Neo-Darwinism. In this theory as well, new genes are produced through random mutations. <em>Slow variations over time accumulate to give new characters like eyes.</em> This theory differs from the de Vries theory, as it says that slow variations keep on accumulating rather than a single large variation. This theory is more applicable to your example of the eye, as it evolved slowly from &quot;photospots&quot; to more complex forms like ommatidia and the eyes in case of vertebrates, instead of a sudden huge mutation. This has been described below.</p>\n<hr />\n<p><em><strong>An insight into the evolution of the eye</strong></em></p>\n<p><strong>Short look into the rapid evolution of the eye:</strong> The eye began not as a tool for “seeing” but as a simple light detector, first appearing as photospots or ocelli in euglenoids to gauge light for photosynthesis. Primitive light-sensing structures, such as pigment spot ocelli found in jellyfish, flatworms, and even alongside compound eyes in insects, represent early stages in this journey. In vertebrates, fossil evidence indicates eyes emerged with the first fish during the Cambrian period, with their structure remaining largely unchanged for over 400 million years, as seen in modern lampreys. Nilsson and Pelger’s 1994 modeling suggested that a complex fish-type eye could evolve surprisingly quickly—within half a million years—from a light-sensitive patch of skin. Evolution has repeatedly produced eyes through convergence, leading to striking similarities like those between fish and cephalopods. Biochemically, this innovation rested on opsin proteins, derived from ancestral GPCRs, which bound retinal to enable light sensitivity. While alternative light-absorbing molecules existed, rhodopsins and cryptochromes outcompeted them, forming the foundation for animal vision.</p>\n<p><a href=\"https://i.sstatic.net/Fy1reinV.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/Fy1reinV.jpg\" alt=\"Mollusc evolution\" /></a></p>\n<p>Image of evolution of the eye in Mollusca</p>\n<p><a href=\"https://i.sstatic.net/6vX0WkBM.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/6vX0WkBM.jpg\" alt=\"King sandworm\" /></a></p>\n<p><em>Nereis virens</em>—King sandworm: note the eyecup but no lens. This provides some spatial information for the animal although its vision is poor. Nevertheless, it is a predator. Histologic section by Richard Dubielzig DVM.</p>\n<p><a href=\"https://i.sstatic.net/26PuFi1M.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/26PuFi1M.jpg\" alt=\"Nautilus\" /></a></p>\n<p>Nautilus: note the nautilus eye with a pinhole but no cornea. The eye is embedded with the body with the histology seen in.</p>\n<p><strong>A <em>much, much</em> more detailed one</strong>:</p>\n<p>The eye originally evolved as something we don't think of it as &quot;eyes&quot; today. It evolved the sensation of light (the ability to detect light) in its surrounding rather than &quot;looking at and scanning&quot; it's surroundings. &quot;Photospot&quot; or &quot;stigma&quot; originally evolved in the euglenoids for helping in detection of light intensity for photosynthesis. It contains the chemical astaxanthin. The halophiles (primitive archaea) develop a pigmented membrane composed of a pigment called bacterio-rhodopsin (related to the one found in our own eyes) to harness the sun's energy. The light energy is utilised to carry on ATP production but they cannot use this ATP in food synthesis. Hence, they are heterotrophs. Bacteriorhodopsin is defined as a light-driven ion pump found in the purple membrane of <em>Halobacterium salinarum</em>, consisting of trimers of monomers that contain seven transmembrane <span class=\"math-container\">$\\alpha$</span>-helices and a retinal molecule, facilitating proton pumping through a photochemical cycle linked to retinal photoisomerization and protein conformational changes.</p>\n<p><a href=\"https://en.m.wikipedia.org/wiki/Simple_eye_in_invertebrates\" rel=\"nofollow noreferrer\">Ocellus (&quot;simple eye or photospot&quot;)</a> is a quite primitive form of the eye, although it might not be as simple as the name suggests. Some organisms like some jellyfish, sea stars, flatworms, and ribbonworms may have primitive light sensors as the only means of &quot;seeing&quot;. These light sensing cells are called <em>pigment spot ocelli</em>, which have randomly distributed pigment, and have no other higher structures such as a cornea or lens). In arthropods like cockroaches and wasps, these might be present addition to the complex eye.</p>\n<p><a href=\"https://i.sstatic.net/YMCreQx7.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/YMCreQx7.jpg\" alt=\"Wasp head\" /></a></p>\n<p>Head of Polistes with two compound eyes and three ocelli (circled)</p>\n<p>In the animal kingdom, it evolved in a similar manner (see pictures above for details).</p>\n<blockquote>\n<p>Fish fossils from these periods have eye sockets, indicating that these fish must have had eyes. The lampreys, present-day relatives of these early fish, have eyes that are very similar to those of other fish, leading to the conclusion that very little has happened to the aquatic form of the vertebrate eye for about 400 million years.</p>\n<p>The lower chordates, from which the vertebrates arose, have either simple eyespots or no eyes at all; therefore, presumably the vertebrate eye originated with the first fish and not before.</p>\n</blockquote>\n<p>Discussing about the time required for this evolutionary success I found out this 1994 experiment,</p>\n<blockquote>\n<p>In 1994 Swedish zoologists Dan-Eric Nilsson and Susanne Pelger took up the challenge of “evolving” an eye of the fish type from a patch of photosensitive skin. Using pessimistic estimates of variation, heritability, and selection intensity, Nilsson and Pelger came to the conclusion that it would take 364,000 generations for a fish eye to evolve. Given a generation time of a year, which is typical for moderate-sized animals, a respectable eye could evolve in less than half a million years. Of course, other physiological elements (e.g., competent brains) have to evolve in parallel with eyes. However, at least as far as the eye itself is concerned, very little time is actually required for its evolution.</p>\n</blockquote>\n<p>This evolution mostly occurred in the Cambrian period, with small changes occurring outside of it.</p>\n<p><strong>Evolution of the eye has occurred several times.</strong></p>\n<blockquote>\n<p>Because there are only a limited number of ways that images can be produced, it is not surprising that some of them have been “discovered” more than once. This has led to numerous examples of convergence in the evolutionary history of eyes. The similarity in optical design of the eyes of fish and cephalopod molluscs, such as octopuses and squid, is perhaps the most well-known example.</p>\n</blockquote>\n<p><strong>Biochemical aspect:</strong> (from <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC5811732/\" rel=\"nofollow noreferrer\">The evolution of eyes: major steps. The Keeler lecture 2017</a>)</p>\n<blockquote>\n<p>The opsin in rhodopsin probably evolved from a G-protein coupled receptor (GPCR) protein although this origin is murky. G proteins are rather common and rather easily produced, but the first ‘opsins’ were not true GPCR. Rather these early opsin-like compounds combined with retinal that functioned as a proton pump for energy production for certain Archaea. The passage of such molecules from microbial opsins to metazoan opsins probably came from a common ancestor as these are related, albeit distantly.</p>\n<p>Retinal and its eventual congeners and an opsin served as the basis for the principal family of metazoan photoreceptive compounds—the ciliary opsins, rhabdomeric opsins, and the photoisomerases. These were not the only photoreceptive compounds available to first life as other compounds such as the flavins, porphyrins, biliproteins, and chlorophyll among others could have been sufficient for the transduction of light to the energy to power a biochemical signal. However, under certain circumstances these compounds could be toxic or photosensitizing to cells. These other compounds were not able to compete as successfully with rhodopsin for the principal photoreceptive one although the flavins are retained in many Metazoa as light-sensing molecules in the form of cryptochromes. This biochemistry was crucial to our use of rhodopsin and cryptochromes.</p>\n</blockquote>\n<p>Two other questions that are good to read in the context of the evolution of the eye:</p>\n<ol>\n<li><a href=\"https://biology.stackexchange.com/questions/30214/what-is-the-minimum-eye\">What is the minimum eye?</a></li>\n<li><a href=\"https://biology.stackexchange.com/questions/782/when-did-vision-evolve-for-the-first-time/818#818\">When did vision evolve for the first time?</a></li>\n</ol>\n<p>A para in the 2nd post</p>\n<blockquote>\n<p>One candidate for the &quot;earliest eye&quot; might be urbilatarians - the hypothesized last common ancestor of the clade bilatarians - which probably evolved at the end of the Ediacaran period (~555 Myr). An example would be Kimberella (described here) which might or might not have been a mollusc and might or might not have had photoreceptors!</p>\n</blockquote>\n<p>So, this is the first time it evolved in Animalia.</p>\n<hr />\n<p>Sources and further reads:<br></p>\n<ol>\n<li><a href=\"https://www.britannica.com/science/photoreception/Evolution-of-eyes\" rel=\"nofollow noreferrer\">Britannica</a></li>\n<li><a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC5811732/\" rel=\"nofollow noreferrer\">NCBI</a></li>\n<li><a href=\"https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/bacteriorhodopsin#:%7E:text=Bacteriorhodopsin%20is%20defined%20as%20a,photoisomerization%20and%20protein%20conformational%20changes.&amp;text=How%20useful%20is%20this%20definition?\" rel=\"nofollow noreferrer\">ScienceDirect</a></li>\n</ol>\n","answer_id":117921,"answer_text":"Often in popular explanations, we hear that organisms evolved these features \"because they needed them\" for survival.\n\n\n\n\n\n\n\nYa, that's very, very wrong. Evolution is a stochastic or chance process. According to Hugo de Vries theory of evolution (https://www.google.com/url?sa=t&source=web&rct=j&opi=89978449&url=https://anthroholic.com/theory-of-mutation-in-evolution%3Fsrsltid%3DAfmBOorNk1lQV8zP_J6MCIGBc96DzWXOj_n4GFKVyNSCogwEA3O04HhJ&ved=2ahUKEwjCg8KXtdiPAxU3lK8BHdHNIX8QFnoECGEQAQ&usg=AOvVaw1dI_5lDaduAfSxGhCZrnoy), evolution occurs due to random sudden huge mutations that occur in any random direction. So evolution is not at all a directed process.\n\n\n\n\nWhen these variations occur, they could either benefit the organism or harm it. In case of useful variations, the organisms have a benefit over other organisms of its type. For example, if there are a group of herbivores without eyes, and one of them suddenly develops eyes, it would surely have a benefit because it can see where vegetation is to feed upon. (Point to note here is that this is just an example, and evolution of the eye has been described below) This in Darwin's terms, is often known as \"Survival of the fittest\".\n\n\n\n\nSo, \"need\" has no role in this process. \"Environmental pressure\" does have a role in this, especially for selecting the better traits. For example, in Lederberg's replica plating experiment (https://www.google.com/url?sa=t&source=web&rct=j&opi=89978449&url=https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/replica-plating&ved=2ahUKEwid0ZCVuNiPAxX8hagCHc4QI0cQFnoFCIMBEAE&usg=AOvVaw3oVRlGq19bdf8TgBFgQHhc), bacteria which had pre-evolved antibiotic resistance survived due to the selection pressure of the antibiotic environment.\n\n\n\n\nDarwin's theory and Neo Darwinism\n\n\n\n\nNeo-Darwinism is the most recent theory of evolution. Let us discuss Darwin's theory first:\n\n\n\n\n\nImportant role of reproduction: Organisms reproducing at a very high rate make more of themselves, and out compete others.\n\n\n\n\nStruggle for existence: This high rate of reproduction leads to competition for food, land, etc.\n\n\n\n\nVariation and their Inheritance: Organism have inbuilt variation for providing benefits to the organism.\n\n\n\n\nSurvival of the fittest and natural selection: Organisms with the best of these characteristics succeed in this competition and produce more organisms with its beneficial characteristics.\n\n\n\n\n\nIn this case, variations originate randomly. The organism with better characteristics has a reproductive advantage, therefore increasing the number of individuals having that characteristic in the population. Better characteristics get selected and genetically passed on. When the Mendelian genetics are added on this theory, it is known as Neo-Darwinism. In this theory as well, new genes are produced through random mutations. Slow variations over time accumulate to give new characters like eyes. This theory differs from the de Vries theory, as it says that slow variations keep on accumulating rather than a single large variation. This theory is more applicable to your example of the eye, as it evolved slowly from \"photospots\" to more complex forms like ommatidia and the eyes in case of vertebrates, instead of a sudden huge mutation. This has been described below.\n\n\n\n\n\n\n\nAn insight into the evolution of the eye\n\n\n\n\nShort look into the rapid evolution of the eye: The eye began not as a tool for “seeing” but as a simple light detector, first appearing as photospots or ocelli in euglenoids to gauge light for photosynthesis. Primitive light-sensing structures, such as pigment spot ocelli found in jellyfish, flatworms, and even alongside compound eyes in insects, represent early stages in this journey. In vertebrates, fossil evidence indicates eyes emerged with the first fish during the Cambrian period, with their structure remaining largely unchanged for over 400 million years, as seen in modern lampreys. Nilsson and Pelger’s 1994 modeling suggested that a complex fish-type eye could evolve surprisingly quickly—within half a million years—from a light-sensitive patch of skin. Evolution has repeatedly produced eyes through convergence, leading to striking similarities like those between fish and cephalopods. Biochemically, this innovation rested on opsin proteins, derived from ancestral GPCRs, which bound retinal to enable light sensitivity. While alternative light-absorbing molecules existed, rhodopsins and cryptochromes outcompeted them, forming the foundation for animal vision.\n\n\n\n\n[image: Mollusc evolution; source: https://i.sstatic.net/Fy1reinV.jpg] (https://i.sstatic.net/Fy1reinV.jpg)\n\n\n\n\nImage of evolution of the eye in Mollusca\n\n\n\n\n[image: King sandworm; source: https://i.sstatic.net/6vX0WkBM.jpg] (https://i.sstatic.net/6vX0WkBM.jpg)\n\n\n\n\nNereis virens—King sandworm: note the eyecup but no lens. This provides some spatial information for the animal although its vision is poor. Nevertheless, it is a predator. Histologic section by Richard Dubielzig DVM.\n\n\n\n\n[image: Nautilus; source: https://i.sstatic.net/26PuFi1M.jpg] (https://i.sstatic.net/26PuFi1M.jpg)\n\n\n\n\nNautilus: note the nautilus eye with a pinhole but no cornea. The eye is embedded with the body with the histology seen in.\n\n\n\n\nA much, much more detailed one:\n\n\n\n\nThe eye originally evolved as something we don't think of it as \"eyes\" today. It evolved the sensation of light (the ability to detect light) in its surrounding rather than \"looking at and scanning\" it's surroundings. \"Photospot\" or \"stigma\" originally evolved in the euglenoids for helping in detection of light intensity for photosynthesis. It contains the chemical astaxanthin. The halophiles (primitive archaea) develop a pigmented membrane composed of a pigment called bacterio-rhodopsin (related to the one found in our own eyes) to harness the sun's energy. The light energy is utilised to carry on ATP production but they cannot use this ATP in food synthesis. Hence, they are heterotrophs. Bacteriorhodopsin is defined as a light-driven ion pump found in the purple membrane of Halobacterium salinarum, consisting of trimers of monomers that contain seven transmembrane $\\alpha$-helices and a retinal molecule, facilitating proton pumping through a photochemical cycle linked to retinal photoisomerization and protein conformational changes.\n\n\n\n\nOcellus (\"simple eye or photospot\") (https://en.m.wikipedia.org/wiki/Simple_eye_in_invertebrates) is a quite primitive form of the eye, although it might not be as simple as the name suggests. Some organisms like some jellyfish, sea stars, flatworms, and ribbonworms may have primitive light sensors as the only means of \"seeing\". These light sensing cells are called pigment spot ocelli, which have randomly distributed pigment, and have no other higher structures such as a cornea or lens). In arthropods like cockroaches and wasps, these might be present addition to the complex eye.\n\n\n\n\n[image: Wasp head; source: https://i.sstatic.net/YMCreQx7.jpg] (https://i.sstatic.net/YMCreQx7.jpg)\n\n\n\n\nHead of Polistes with two compound eyes and three ocelli (circled)\n\n\n\n\nIn the animal kingdom, it evolved in a similar manner (see pictures above for details).\n\n\n\n\n\n\n\nFish fossils from these periods have eye sockets, indicating that these fish must have had eyes. The lampreys, present-day relatives of these early fish, have eyes that are very similar to those of other fish, leading to the conclusion that very little has happened to the aquatic form of the vertebrate eye for about 400 million years.\n\n\n\n\nThe lower chordates, from which the vertebrates arose, have either simple eyespots or no eyes at all; therefore, presumably the vertebrate eye originated with the first fish and not before.\n\n\n\n\n\n\n\nDiscussing about the time required for this evolutionary success I found out this 1994 experiment,\n\n\n\n\n\n\n\nIn 1994 Swedish zoologists Dan-Eric Nilsson and Susanne Pelger took up the challenge of “evolving” an eye of the fish type from a patch of photosensitive skin. Using pessimistic estimates of variation, heritability, and selection intensity, Nilsson and Pelger came to the conclusion that it would take 364,000 generations for a fish eye to evolve. Given a generation time of a year, which is typical for moderate-sized animals, a respectable eye could evolve in less than half a million years. Of course, other physiological elements (e.g., competent brains) have to evolve in parallel with eyes. However, at least as far as the eye itself is concerned, very little time is actually required for its evolution.\n\n\n\n\n\n\n\nThis evolution mostly occurred in the Cambrian period, with small changes occurring outside of it.\n\n\n\n\nEvolution of the eye has occurred several times.\n\n\n\n\n\n\n\nBecause there are only a limited number of ways that images can be produced, it is not surprising that some of them have been “discovered” more than once. This has led to numerous examples of convergence in the evolutionary history of eyes. The similarity in optical design of the eyes of fish and cephalopod molluscs, such as octopuses and squid, is perhaps the most well-known example.\n\n\n\n\n\n\n\nBiochemical aspect: (from The evolution of eyes: major steps. The Keeler lecture 2017 (https://pmc.ncbi.nlm.nih.gov/articles/PMC5811732/))\n\n\n\n\n\n\n\nThe opsin in rhodopsin probably evolved from a G-protein coupled receptor (GPCR) protein although this origin is murky. G proteins are rather common and rather easily produced, but the first ‘opsins’ were not true GPCR. Rather these early opsin-like compounds combined with retinal that functioned as a proton pump for energy production for certain Archaea. The passage of such molecules from microbial opsins to metazoan opsins probably came from a common ancestor as these are related, albeit distantly.\n\n\n\n\nRetinal and its eventual congeners and an opsin served as the basis for the principal family of metazoan photoreceptive compounds—the ciliary opsins, rhabdomeric opsins, and the photoisomerases. These were not the only photoreceptive compounds available to first life as other compounds such as the flavins, porphyrins, biliproteins, and chlorophyll among others could have been sufficient for the transduction of light to the energy to power a biochemical signal. However, under certain circumstances these compounds could be toxic or photosensitizing to cells. These other compounds were not able to compete as successfully with rhodopsin for the principal photoreceptive one although the flavins are retained in many Metazoa as light-sensing molecules in the form of cryptochromes. This biochemistry was crucial to our use of rhodopsin and cryptochromes.\n\n\n\n\n\n\n\nTwo other questions that are good to read in the context of the evolution of the eye:\n\n\n\n\n\nWhat is the minimum eye? (https://biology.stackexchange.com/questions/30214/what-is-the-minimum-eye)\n\n\n\n\nWhen did vision evolve for the first time? (https://biology.stackexchange.com/questions/782/when-did-vision-evolve-for-the-first-time/818#818)\n\n\n\n\n\nA para in the 2nd post\n\n\n\n\n\n\n\nOne candidate for the \"earliest eye\" might be urbilatarians - the hypothesized last common ancestor of the clade bilatarians - which probably evolved at the end of the Ediacaran period (~555 Myr). An example would be Kimberella (described here) which might or might not have been a mollusc and might or might not have had photoreceptors!\n\n\n\n\n\n\n\nSo, this is the first time it evolved in Animalia.\n\n\n\n\n\n\n\nSources and further reads:\n\n\n\n\n\n\nBritannica (https://www.britannica.com/science/photoreception/Evolution-of-eyes)\n\n\n\n\nNCBI (https://pmc.ncbi.nlm.nih.gov/articles/PMC5811732/)\n\n\n\n\nScienceDirect (https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/bacteriorhodopsin#:%7E:text=Bacteriorhodopsin%20is%20defined%20as%20a,photoisomerization%20and%20protein%20conformational%20changes.&text=How%20useful%20is%20this%20definition?)","answer_url":"https://biology.stackexchange.com/a/117921","author":"Shayan","author_url":"https://biology.stackexchange.com/users/114723/shayan","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":"2025-10-07T16:56:15+00:00","raw_file":"raw/codex_api_v1/a76d8ab07f874a10eafefc315936b171795ddfe3f4ac47f247a19154460d4acc_1790824150220029700_0.json","raw_sha256":"d1e485076b0bfa0aed0ebdace356f1cab7a9d04a86bc0f38c43c8a253e51cebd","revision_guid":"18BD733F-CDBC-46AC-80F3-ACA944FCB941","revision_number":11,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/18BD733F-CDBC-46AC-80F3-ACA944FCB941/view-source"}],"url":"https://biology.stackexchange.com/a/117921"}],"contexts":[{"context_id":"question","html":"<p>It is widely known that evolution produces complex and highly useful traits, like eyes, ears, or wings, without any kind of foresight or goal.</p>\n<p>Often in popular explanations, we hear that organisms evolved these features &quot;because they needed them&quot; for survival. But this idea seems confusing to me. If an organism has no concept of light or vision, how could it &quot;know&quot; it needs an eye? It reminds me of asking how a person who's never heard of the sky would ever think to grow wings and fly.</p>\n<p>I understand that evolution is not a conscious or goal-directed process. But then how do traits that are so well-suited to the environment appear at all, if there's no &quot;aim&quot; behind their development? It seems like an apparent contradiction between the randomness of mutation and the usefulness (and complexity) of the resulting traits.</p>\n<p>Is there a better way to think about the role of &quot;need&quot; or &quot;environmental pressure&quot; in driving evolution? How do useful traits arise without an organism directing or anticipating them?</p>\n<p>I've read some basic material on natural selection and adaptation (e.g. Wikipedia), but I'm still unclear on how new and complex traits can appear &quot;out of nowhere&quot; without intent.</p>\n","text":"It is widely known that evolution produces complex and highly useful traits, like eyes, ears, or wings, without any kind of foresight or goal.\n\n\n\n\nOften in popular explanations, we hear that organisms evolved these features \"because they needed them\" for survival. But this idea seems confusing to me. If an organism has no concept of light or vision, how could it \"know\" it needs an eye? It reminds me of asking how a person who's never heard of the sky would ever think to grow wings and fly.\n\n\n\n\nI understand that evolution is not a conscious or goal-directed process. But then how do traits that are so well-suited to the environment appear at all, if there's no \"aim\" behind their development? It seems like an apparent contradiction between the randomness of mutation and the usefulness (and complexity) of the resulting traits.\n\n\n\n\nIs there a better way to think about the role of \"need\" or \"environmental pressure\" in driving evolution? How do useful traits arise without an organism directing or anticipating them?\n\n\n\n\nI've read some basic material on natural selection and adaptation (e.g. Wikipedia), but I'm still unclear on how new and complex traits can appear \"out of nowhere\" without intent."},{"context_id":"117921","html":"<blockquote>\n<p>Often in popular explanations, we hear that organisms evolved these features &quot;because they needed them&quot; for survival.</p>\n</blockquote>\n<p>Ya, that's <em>very, very</em> wrong. Evolution is a <strong>stochastic or chance</strong> process. According to <a href=\"https://www.google.com/url?sa=t&amp;source=web&amp;rct=j&amp;opi=89978449&amp;url=https://anthroholic.com/theory-of-mutation-in-evolution%3Fsrsltid%3DAfmBOorNk1lQV8zP_J6MCIGBc96DzWXOj_n4GFKVyNSCogwEA3O04HhJ&amp;ved=2ahUKEwjCg8KXtdiPAxU3lK8BHdHNIX8QFnoECGEQAQ&amp;usg=AOvVaw1dI_5lDaduAfSxGhCZrnoy\" rel=\"nofollow noreferrer\">Hugo de Vries theory of evolution</a>, evolution occurs due to <strong>random</strong> sudden huge mutations <strong>that occur in any random direction.</strong> So evolution is not at all a directed process.</p>\n<p>When these variations occur, they could either benefit the organism or harm it. In case of useful variations, the organisms have a benefit over other organisms of its type. For example, if there are a group of herbivores without eyes, and one of them suddenly develops eyes, it would surely have a benefit because it can see where vegetation is to feed upon. (Point to note here is that this is just an example, and evolution of the eye has been described below) This in Darwin's terms, is often known as <em>&quot;Survival of the fittest&quot;.</em></p>\n<p>So, &quot;need&quot; has no role in this process. &quot;Environmental pressure&quot; does have a role in this, especially for selecting the better traits. For example, in <a href=\"https://www.google.com/url?sa=t&amp;source=web&amp;rct=j&amp;opi=89978449&amp;url=https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/replica-plating&amp;ved=2ahUKEwid0ZCVuNiPAxX8hagCHc4QI0cQFnoFCIMBEAE&amp;usg=AOvVaw3oVRlGq19bdf8TgBFgQHhc\" rel=\"nofollow noreferrer\">Lederberg's replica plating experiment</a>, bacteria which had pre-evolved antibiotic resistance survived due to the selection pressure of the antibiotic environment.</p>\n<p><strong>Darwin's theory and Neo Darwinism</strong></p>\n<p>Neo-Darwinism is the most recent theory of evolution. Let us discuss Darwin's theory first:</p>\n<ol>\n<li>Important role of reproduction: Organisms reproducing at a very high rate make more of themselves, and out compete others.</li>\n<li>Struggle for existence: This high rate of reproduction leads to competition for food, land, etc.</li>\n<li>Variation and their Inheritance: Organism have inbuilt variation for providing benefits to the organism.</li>\n<li>Survival of the fittest and natural selection: Organisms with the best of these characteristics succeed in this competition and produce more organisms with its beneficial characteristics.</li>\n</ol>\n<p>In this case, variations originate randomly. The organism with better characteristics has a reproductive advantage, therefore increasing the number of individuals having that characteristic in the population. Better characteristics get selected and genetically passed on. When the Mendelian genetics are added on this theory, it is known as Neo-Darwinism. In this theory as well, new genes are produced through random mutations. <em>Slow variations over time accumulate to give new characters like eyes.</em> This theory differs from the de Vries theory, as it says that slow variations keep on accumulating rather than a single large variation. This theory is more applicable to your example of the eye, as it evolved slowly from &quot;photospots&quot; to more complex forms like ommatidia and the eyes in case of vertebrates, instead of a sudden huge mutation. This has been described below.</p>\n<hr />\n<p><em><strong>An insight into the evolution of the eye</strong></em></p>\n<p><strong>Short look into the rapid evolution of the eye:</strong> The eye began not as a tool for “seeing” but as a simple light detector, first appearing as photospots or ocelli in euglenoids to gauge light for photosynthesis. Primitive light-sensing structures, such as pigment spot ocelli found in jellyfish, flatworms, and even alongside compound eyes in insects, represent early stages in this journey. In vertebrates, fossil evidence indicates eyes emerged with the first fish during the Cambrian period, with their structure remaining largely unchanged for over 400 million years, as seen in modern lampreys. Nilsson and Pelger’s 1994 modeling suggested that a complex fish-type eye could evolve surprisingly quickly—within half a million years—from a light-sensitive patch of skin. Evolution has repeatedly produced eyes through convergence, leading to striking similarities like those between fish and cephalopods. Biochemically, this innovation rested on opsin proteins, derived from ancestral GPCRs, which bound retinal to enable light sensitivity. While alternative light-absorbing molecules existed, rhodopsins and cryptochromes outcompeted them, forming the foundation for animal vision.</p>\n<p><a href=\"https://i.sstatic.net/Fy1reinV.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/Fy1reinV.jpg\" alt=\"Mollusc evolution\" /></a></p>\n<p>Image of evolution of the eye in Mollusca</p>\n<p><a href=\"https://i.sstatic.net/6vX0WkBM.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/6vX0WkBM.jpg\" alt=\"King sandworm\" /></a></p>\n<p><em>Nereis virens</em>—King sandworm: note the eyecup but no lens. This provides some spatial information for the animal although its vision is poor. Nevertheless, it is a predator. Histologic section by Richard Dubielzig DVM.</p>\n<p><a href=\"https://i.sstatic.net/26PuFi1M.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/26PuFi1M.jpg\" alt=\"Nautilus\" /></a></p>\n<p>Nautilus: note the nautilus eye with a pinhole but no cornea. The eye is embedded with the body with the histology seen in.</p>\n<p><strong>A <em>much, much</em> more detailed one</strong>:</p>\n<p>The eye originally evolved as something we don't think of it as &quot;eyes&quot; today. It evolved the sensation of light (the ability to detect light) in its surrounding rather than &quot;looking at and scanning&quot; it's surroundings. &quot;Photospot&quot; or &quot;stigma&quot; originally evolved in the euglenoids for helping in detection of light intensity for photosynthesis. It contains the chemical astaxanthin. The halophiles (primitive archaea) develop a pigmented membrane composed of a pigment called bacterio-rhodopsin (related to the one found in our own eyes) to harness the sun's energy. The light energy is utilised to carry on ATP production but they cannot use this ATP in food synthesis. Hence, they are heterotrophs. Bacteriorhodopsin is defined as a light-driven ion pump found in the purple membrane of <em>Halobacterium salinarum</em>, consisting of trimers of monomers that contain seven transmembrane <span class=\"math-container\">$\\alpha$</span>-helices and a retinal molecule, facilitating proton pumping through a photochemical cycle linked to retinal photoisomerization and protein conformational changes.</p>\n<p><a href=\"https://en.m.wikipedia.org/wiki/Simple_eye_in_invertebrates\" rel=\"nofollow noreferrer\">Ocellus (&quot;simple eye or photospot&quot;)</a> is a quite primitive form of the eye, although it might not be as simple as the name suggests. Some organisms like some jellyfish, sea stars, flatworms, and ribbonworms may have primitive light sensors as the only means of &quot;seeing&quot;. These light sensing cells are called <em>pigment spot ocelli</em>, which have randomly distributed pigment, and have no other higher structures such as a cornea or lens). In arthropods like cockroaches and wasps, these might be present addition to the complex eye.</p>\n<p><a href=\"https://i.sstatic.net/YMCreQx7.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/YMCreQx7.jpg\" alt=\"Wasp head\" /></a></p>\n<p>Head of Polistes with two compound eyes and three ocelli (circled)</p>\n<p>In the animal kingdom, it evolved in a similar manner (see pictures above for details).</p>\n<blockquote>\n<p>Fish fossils from these periods have eye sockets, indicating that these fish must have had eyes. The lampreys, present-day relatives of these early fish, have eyes that are very similar to those of other fish, leading to the conclusion that very little has happened to the aquatic form of the vertebrate eye for about 400 million years.</p>\n<p>The lower chordates, from which the vertebrates arose, have either simple eyespots or no eyes at all; therefore, presumably the vertebrate eye originated with the first fish and not before.</p>\n</blockquote>\n<p>Discussing about the time required for this evolutionary success I found out this 1994 experiment,</p>\n<blockquote>\n<p>In 1994 Swedish zoologists Dan-Eric Nilsson and Susanne Pelger took up the challenge of “evolving” an eye of the fish type from a patch of photosensitive skin. Using pessimistic estimates of variation, heritability, and selection intensity, Nilsson and Pelger came to the conclusion that it would take 364,000 generations for a fish eye to evolve. Given a generation time of a year, which is typical for moderate-sized animals, a respectable eye could evolve in less than half a million years. Of course, other physiological elements (e.g., competent brains) have to evolve in parallel with eyes. However, at least as far as the eye itself is concerned, very little time is actually required for its evolution.</p>\n</blockquote>\n<p>This evolution mostly occurred in the Cambrian period, with small changes occurring outside of it.</p>\n<p><strong>Evolution of the eye has occurred several times.</strong></p>\n<blockquote>\n<p>Because there are only a limited number of ways that images can be produced, it is not surprising that some of them have been “discovered” more than once. This has led to numerous examples of convergence in the evolutionary history of eyes. The similarity in optical design of the eyes of fish and cephalopod molluscs, such as octopuses and squid, is perhaps the most well-known example.</p>\n</blockquote>\n<p><strong>Biochemical aspect:</strong> (from <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC5811732/\" rel=\"nofollow noreferrer\">The evolution of eyes: major steps. The Keeler lecture 2017</a>)</p>\n<blockquote>\n<p>The opsin in rhodopsin probably evolved from a G-protein coupled receptor (GPCR) protein although this origin is murky. G proteins are rather common and rather easily produced, but the first ‘opsins’ were not true GPCR. Rather these early opsin-like compounds combined with retinal that functioned as a proton pump for energy production for certain Archaea. The passage of such molecules from microbial opsins to metazoan opsins probably came from a common ancestor as these are related, albeit distantly.</p>\n<p>Retinal and its eventual congeners and an opsin served as the basis for the principal family of metazoan photoreceptive compounds—the ciliary opsins, rhabdomeric opsins, and the photoisomerases. These were not the only photoreceptive compounds available to first life as other compounds such as the flavins, porphyrins, biliproteins, and chlorophyll among others could have been sufficient for the transduction of light to the energy to power a biochemical signal. However, under certain circumstances these compounds could be toxic or photosensitizing to cells. These other compounds were not able to compete as successfully with rhodopsin for the principal photoreceptive one although the flavins are retained in many Metazoa as light-sensing molecules in the form of cryptochromes. This biochemistry was crucial to our use of rhodopsin and cryptochromes.</p>\n</blockquote>\n<p>Two other questions that are good to read in the context of the evolution of the eye:</p>\n<ol>\n<li><a href=\"https://biology.stackexchange.com/questions/30214/what-is-the-minimum-eye\">What is the minimum eye?</a></li>\n<li><a href=\"https://biology.stackexchange.com/questions/782/when-did-vision-evolve-for-the-first-time/818#818\">When did vision evolve for the first time?</a></li>\n</ol>\n<p>A para in the 2nd post</p>\n<blockquote>\n<p>One candidate for the &quot;earliest eye&quot; might be urbilatarians - the hypothesized last common ancestor of the clade bilatarians - which probably evolved at the end of the Ediacaran period (~555 Myr). An example would be Kimberella (described here) which might or might not have been a mollusc and might or might not have had photoreceptors!</p>\n</blockquote>\n<p>So, this is the first time it evolved in Animalia.</p>\n<hr />\n<p>Sources and further reads:<br></p>\n<ol>\n<li><a href=\"https://www.britannica.com/science/photoreception/Evolution-of-eyes\" rel=\"nofollow noreferrer\">Britannica</a></li>\n<li><a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC5811732/\" rel=\"nofollow noreferrer\">NCBI</a></li>\n<li><a href=\"https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/bacteriorhodopsin#:%7E:text=Bacteriorhodopsin%20is%20defined%20as%20a,photoisomerization%20and%20protein%20conformational%20changes.&amp;text=How%20useful%20is%20this%20definition?\" rel=\"nofollow noreferrer\">ScienceDirect</a></li>\n</ol>\n","text":"Often in popular explanations, we hear that organisms evolved these features \"because they needed them\" for survival.\n\n\n\n\n\n\n\nYa, that's very, very wrong. Evolution is a stochastic or chance process. According to Hugo de Vries theory of evolution (https://www.google.com/url?sa=t&source=web&rct=j&opi=89978449&url=https://anthroholic.com/theory-of-mutation-in-evolution%3Fsrsltid%3DAfmBOorNk1lQV8zP_J6MCIGBc96DzWXOj_n4GFKVyNSCogwEA3O04HhJ&ved=2ahUKEwjCg8KXtdiPAxU3lK8BHdHNIX8QFnoECGEQAQ&usg=AOvVaw1dI_5lDaduAfSxGhCZrnoy), evolution occurs due to random sudden huge mutations that occur in any random direction. So evolution is not at all a directed process.\n\n\n\n\nWhen these variations occur, they could either benefit the organism or harm it. In case of useful variations, the organisms have a benefit over other organisms of its type. For example, if there are a group of herbivores without eyes, and one of them suddenly develops eyes, it would surely have a benefit because it can see where vegetation is to feed upon. (Point to note here is that this is just an example, and evolution of the eye has been described below) This in Darwin's terms, is often known as \"Survival of the fittest\".\n\n\n\n\nSo, \"need\" has no role in this process. \"Environmental pressure\" does have a role in this, especially for selecting the better traits. For example, in Lederberg's replica plating experiment (https://www.google.com/url?sa=t&source=web&rct=j&opi=89978449&url=https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/replica-plating&ved=2ahUKEwid0ZCVuNiPAxX8hagCHc4QI0cQFnoFCIMBEAE&usg=AOvVaw3oVRlGq19bdf8TgBFgQHhc), bacteria which had pre-evolved antibiotic resistance survived due to the selection pressure of the antibiotic environment.\n\n\n\n\nDarwin's theory and Neo Darwinism\n\n\n\n\nNeo-Darwinism is the most recent theory of evolution. Let us discuss Darwin's theory first:\n\n\n\n\n\nImportant role of reproduction: Organisms reproducing at a very high rate make more of themselves, and out compete others.\n\n\n\n\nStruggle for existence: This high rate of reproduction leads to competition for food, land, etc.\n\n\n\n\nVariation and their Inheritance: Organism have inbuilt variation for providing benefits to the organism.\n\n\n\n\nSurvival of the fittest and natural selection: Organisms with the best of these characteristics succeed in this competition and produce more organisms with its beneficial characteristics.\n\n\n\n\n\nIn this case, variations originate randomly. The organism with better characteristics has a reproductive advantage, therefore increasing the number of individuals having that characteristic in the population. Better characteristics get selected and genetically passed on. When the Mendelian genetics are added on this theory, it is known as Neo-Darwinism. In this theory as well, new genes are produced through random mutations. Slow variations over time accumulate to give new characters like eyes. This theory differs from the de Vries theory, as it says that slow variations keep on accumulating rather than a single large variation. This theory is more applicable to your example of the eye, as it evolved slowly from \"photospots\" to more complex forms like ommatidia and the eyes in case of vertebrates, instead of a sudden huge mutation. This has been described below.\n\n\n\n\n\n\n\nAn insight into the evolution of the eye\n\n\n\n\nShort look into the rapid evolution of the eye: The eye began not as a tool for “seeing” but as a simple light detector, first appearing as photospots or ocelli in euglenoids to gauge light for photosynthesis. Primitive light-sensing structures, such as pigment spot ocelli found in jellyfish, flatworms, and even alongside compound eyes in insects, represent early stages in this journey. In vertebrates, fossil evidence indicates eyes emerged with the first fish during the Cambrian period, with their structure remaining largely unchanged for over 400 million years, as seen in modern lampreys. Nilsson and Pelger’s 1994 modeling suggested that a complex fish-type eye could evolve surprisingly quickly—within half a million years—from a light-sensitive patch of skin. Evolution has repeatedly produced eyes through convergence, leading to striking similarities like those between fish and cephalopods. Biochemically, this innovation rested on opsin proteins, derived from ancestral GPCRs, which bound retinal to enable light sensitivity. While alternative light-absorbing molecules existed, rhodopsins and cryptochromes outcompeted them, forming the foundation for animal vision.\n\n\n\n\n[image: Mollusc evolution; source: https://i.sstatic.net/Fy1reinV.jpg] (https://i.sstatic.net/Fy1reinV.jpg)\n\n\n\n\nImage of evolution of the eye in Mollusca\n\n\n\n\n[image: King sandworm; source: https://i.sstatic.net/6vX0WkBM.jpg] (https://i.sstatic.net/6vX0WkBM.jpg)\n\n\n\n\nNereis virens—King sandworm: note the eyecup but no lens. This provides some spatial information for the animal although its vision is poor. Nevertheless, it is a predator. Histologic section by Richard Dubielzig DVM.\n\n\n\n\n[image: Nautilus; source: https://i.sstatic.net/26PuFi1M.jpg] (https://i.sstatic.net/26PuFi1M.jpg)\n\n\n\n\nNautilus: note the nautilus eye with a pinhole but no cornea. The eye is embedded with the body with the histology seen in.\n\n\n\n\nA much, much more detailed one:\n\n\n\n\nThe eye originally evolved as something we don't think of it as \"eyes\" today. It evolved the sensation of light (the ability to detect light) in its surrounding rather than \"looking at and scanning\" it's surroundings. \"Photospot\" or \"stigma\" originally evolved in the euglenoids for helping in detection of light intensity for photosynthesis. It contains the chemical astaxanthin. The halophiles (primitive archaea) develop a pigmented membrane composed of a pigment called bacterio-rhodopsin (related to the one found in our own eyes) to harness the sun's energy. The light energy is utilised to carry on ATP production but they cannot use this ATP in food synthesis. Hence, they are heterotrophs. Bacteriorhodopsin is defined as a light-driven ion pump found in the purple membrane of Halobacterium salinarum, consisting of trimers of monomers that contain seven transmembrane $\\alpha$-helices and a retinal molecule, facilitating proton pumping through a photochemical cycle linked to retinal photoisomerization and protein conformational changes.\n\n\n\n\nOcellus (\"simple eye or photospot\") (https://en.m.wikipedia.org/wiki/Simple_eye_in_invertebrates) is a quite primitive form of the eye, although it might not be as simple as the name suggests. Some organisms like some jellyfish, sea stars, flatworms, and ribbonworms may have primitive light sensors as the only means of \"seeing\". These light sensing cells are called pigment spot ocelli, which have randomly distributed pigment, and have no other higher structures such as a cornea or lens). In arthropods like cockroaches and wasps, these might be present addition to the complex eye.\n\n\n\n\n[image: Wasp head; source: https://i.sstatic.net/YMCreQx7.jpg] (https://i.sstatic.net/YMCreQx7.jpg)\n\n\n\n\nHead of Polistes with two compound eyes and three ocelli (circled)\n\n\n\n\nIn the animal kingdom, it evolved in a similar manner (see pictures above for details).\n\n\n\n\n\n\n\nFish fossils from these periods have eye sockets, indicating that these fish must have had eyes. The lampreys, present-day relatives of these early fish, have eyes that are very similar to those of other fish, leading to the conclusion that very little has happened to the aquatic form of the vertebrate eye for about 400 million years.\n\n\n\n\nThe lower chordates, from which the vertebrates arose, have either simple eyespots or no eyes at all; therefore, presumably the vertebrate eye originated with the first fish and not before.\n\n\n\n\n\n\n\nDiscussing about the time required for this evolutionary success I found out this 1994 experiment,\n\n\n\n\n\n\n\nIn 1994 Swedish zoologists Dan-Eric Nilsson and Susanne Pelger took up the challenge of “evolving” an eye of the fish type from a patch of photosensitive skin. Using pessimistic estimates of variation, heritability, and selection intensity, Nilsson and Pelger came to the conclusion that it would take 364,000 generations for a fish eye to evolve. Given a generation time of a year, which is typical for moderate-sized animals, a respectable eye could evolve in less than half a million years. Of course, other physiological elements (e.g., competent brains) have to evolve in parallel with eyes. However, at least as far as the eye itself is concerned, very little time is actually required for its evolution.\n\n\n\n\n\n\n\nThis evolution mostly occurred in the Cambrian period, with small changes occurring outside of it.\n\n\n\n\nEvolution of the eye has occurred several times.\n\n\n\n\n\n\n\nBecause there are only a limited number of ways that images can be produced, it is not surprising that some of them have been “discovered” more than once. This has led to numerous examples of convergence in the evolutionary history of eyes. The similarity in optical design of the eyes of fish and cephalopod molluscs, such as octopuses and squid, is perhaps the most well-known example.\n\n\n\n\n\n\n\nBiochemical aspect: (from The evolution of eyes: major steps. The Keeler lecture 2017 (https://pmc.ncbi.nlm.nih.gov/articles/PMC5811732/))\n\n\n\n\n\n\n\nThe opsin in rhodopsin probably evolved from a G-protein coupled receptor (GPCR) protein although this origin is murky. G proteins are rather common and rather easily produced, but the first ‘opsins’ were not true GPCR. Rather these early opsin-like compounds combined with retinal that functioned as a proton pump for energy production for certain Archaea. The passage of such molecules from microbial opsins to metazoan opsins probably came from a common ancestor as these are related, albeit distantly.\n\n\n\n\nRetinal and its eventual congeners and an opsin served as the basis for the principal family of metazoan photoreceptive compounds—the ciliary opsins, rhabdomeric opsins, and the photoisomerases. These were not the only photoreceptive compounds available to first life as other compounds such as the flavins, porphyrins, biliproteins, and chlorophyll among others could have been sufficient for the transduction of light to the energy to power a biochemical signal. However, under certain circumstances these compounds could be toxic or photosensitizing to cells. These other compounds were not able to compete as successfully with rhodopsin for the principal photoreceptive one although the flavins are retained in many Metazoa as light-sensing molecules in the form of cryptochromes. This biochemistry was crucial to our use of rhodopsin and cryptochromes.\n\n\n\n\n\n\n\nTwo other questions that are good to read in the context of the evolution of the eye:\n\n\n\n\n\nWhat is the minimum eye? (https://biology.stackexchange.com/questions/30214/what-is-the-minimum-eye)\n\n\n\n\nWhen did vision evolve for the first time? (https://biology.stackexchange.com/questions/782/when-did-vision-evolve-for-the-first-time/818#818)\n\n\n\n\n\nA para in the 2nd post\n\n\n\n\n\n\n\nOne candidate for the \"earliest eye\" might be urbilatarians - the hypothesized last common ancestor of the clade bilatarians - which probably evolved at the end of the Ediacaran period (~555 Myr). An example would be Kimberella (described here) which might or might not have been a mollusc and might or might not have had photoreceptors!\n\n\n\n\n\n\n\nSo, this is the first time it evolved in Animalia.\n\n\n\n\n\n\n\nSources and further reads:\n\n\n\n\n\n\nBritannica (https://www.britannica.com/science/photoreception/Evolution-of-eyes)\n\n\n\n\nNCBI (https://pmc.ncbi.nlm.nih.gov/articles/PMC5811732/)\n\n\n\n\nScienceDirect 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But this idea seems confusing to me. If an organism has no concept of light or vision, how could it \"know\" it needs an eye? It reminds me of asking how a person who's never heard of the sky would ever think to grow wings and fly.\n\n\n\n\nI understand that evolution is not a conscious or goal-directed process. But then how do traits that are so well-suited to the environment appear at all, if there's no \"aim\" behind their development? It seems like an apparent contradiction between the randomness of mutation and the usefulness (and complexity) of the resulting traits.\n\n\n\n\nIs there a better way to think about the role of \"need\" or \"environmental pressure\" in driving evolution? How do useful traits arise without an organism directing or anticipating them?\n\n\n\n\nI've read some basic material on natural selection and adaptation (e.g. Wikipedia), but I'm still unclear on how new and complex traits can appear \"out of nowhere\" without intent.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":117921,"score":14}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":117993,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I would recommend to be careful about binary thinking. We humans seem naturally drawn to binary, but it's just not often a good description of the real world. I might tweak Wikipedia's definition a bit, something like:</p>\n<blockquote>\n<p>&quot;somatic mosaicism&quot; describes genotypic differences in somatic cells of the body.</p>\n</blockquote>\n<p>That is, to emphasize thinking about this as giving a name to observed differences, rather than being a binary condition that is present or not present.</p>\n<p>So yes, genetic differences between somatic cells are common (and certainly not only in the brain), though also many of these differences are inconsequential, see also: <a href=\"https://biology.stackexchange.com/a/117988/27148\">https://biology.stackexchange.com/a/117988/27148</a></p>\n<blockquote>\n<p>how can we understand what &quot;very different&quot; means in practice?</p>\n</blockquote>\n<p>I would expect biologists to use different meanings of &quot;somatic mosaicism&quot; in different contexts. Usually, biologists are going to be studying some phenomenon or mechanism, and since those are almost certainly going to involve some sort of phenotype then that will be the focus.</p>\n<p>I would also argue that mosaicism is as much about what is <em>shared</em> as it is about what is different. It's not just that a mosaic includes cells with different genotypes, but that because these differences are inherited through cell division, you're talking about populations of cells that are more similar to themselves than to another population.</p>\n","answer_id":117993,"answer_text":"I would recommend to be careful about binary thinking. We humans seem naturally drawn to binary, but it's just not often a good description of the real world. I might tweak Wikipedia's definition a bit, something like:\n\n\n\n\n\n\n\n\"somatic mosaicism\" describes genotypic differences in somatic cells of the body.\n\n\n\n\n\n\n\nThat is, to emphasize thinking about this as giving a name to observed differences, rather than being a binary condition that is present or not present.\n\n\n\n\nSo yes, genetic differences between somatic cells are common (and certainly not only in the brain), though also many of these differences are inconsequential, see also: https://biology.stackexchange.com/a/117988/27148 (https://biology.stackexchange.com/a/117988/27148)\n\n\n\n\n\n\n\nhow can we understand what \"very different\" means in practice?\n\n\n\n\n\n\n\nI would expect biologists to use different meanings of \"somatic mosaicism\" in different contexts. Usually, biologists are going to be studying some phenomenon or mechanism, and since those are almost certainly going to involve some sort of phenotype then that will be the focus.\n\n\n\n\nI would also argue that mosaicism is as much about what is shared as it is about what is different. It's not just that a mosaic includes cells with different genotypes, but that because these differences are inherited through cell division, you're talking about populations of cells that are more similar to themselves than to another population.","answer_url":"https://biology.stackexchange.com/a/117993","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2025-09-30T19:54:58+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 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user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-10-01T14:01:39+00:00","raw_file":"raw/codex_api_v1/e6c4101e2e357aa8c5379bd547ec537e2ae9d3a66d32b72c727e9d2ad82690d6_1790824162028580600_0.json","raw_sha256":"cba09186cd183cf1116bbe2f874d16b08a8bc537baa01c33e34f5c3821229cc5","revision_guid":"5D55E511-64FC-4287-973E-0C379419E0CA","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/5D55E511-64FC-4287-973E-0C379419E0CA/view-source"}],"url":"https://biology.stackexchange.com/questions/117992/is-somatic-mosaicism-ubiquitious-or-is-it-defined-in-practice-in-a-way-that-mak"},{"author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","context_id":"117993","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":"2025-09-30T19:54:58+00:00","raw_file":"raw/codex_api_v1/e6c4101e2e357aa8c5379bd547ec537e2ae9d3a66d32b72c727e9d2ad82690d6_1790824162028580600_0.json","raw_sha256":"cba09186cd183cf1116bbe2f874d16b08a8bc537baa01c33e34f5c3821229cc5","revision_guid":"FE63319A-A0B6-4379-BA97-03E5D02DF149","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/FE63319A-A0B6-4379-BA97-03E5D02DF149/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":"2025-09-30T20:04:56+00:00","raw_file":"raw/codex_api_v1/e6c4101e2e357aa8c5379bd547ec537e2ae9d3a66d32b72c727e9d2ad82690d6_1790824162028580600_0.json","raw_sha256":"cba09186cd183cf1116bbe2f874d16b08a8bc537baa01c33e34f5c3821229cc5","revision_guid":"131752D0-D4A8-4B27-9AFB-44A4F05A21E4","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/131752D0-D4A8-4B27-9AFB-44A4F05A21E4/view-source"}],"url":"https://biology.stackexchange.com/a/117993"}],"contexts":[{"context_id":"question","html":"<p>Wikipedia defines <a href=\"https://en.wikipedia.org/wiki/Mosaic_(genetics)#Somatic_mosaicism\" rel=\"nofollow noreferrer\">&quot;somatic mosaicism&quot;</a> to</p>\n<blockquote>\n<p>occur when the somatic cells of the body are of more than one genotype. In the more common mosaics, different genotypes arise from a single fertilized egg cell, due to mitotic errors at first or later cleavages.</p>\n</blockquote>\n<p>We now know that, at least in the human brain, mitotic mutations are very common, and <a href=\"https://www.scientificamerican.com/article/scientists-surprised-to-find-no-two-neurons-are-genetically-alike/\" rel=\"nofollow noreferrer\">every neuron in the brain probably has a (slightly) distinct DNA sequence</a>. This would superficially seem to indicate that the phenomenon of somatic mosaicism (as defined literally) is completely ubiquitous and occurs in all mice and humans. But other questions on this site indicate that the concept of a &quot;genotype&quot; is more flexible than requiring a literal exact match of DNA sequences. So I want to clarify how the term is used in practice.</p>\n<p>Which of these claims most accurately reflects how the term is used in practice?</p>\n<ol>\n<li>&quot;Mosaicism&quot; refers to any mutation at all, and it's completely ubiquitous in the human (and mouse) brain. It may be &quot;interesting&quot; from a phenotypic perspective, or it may not be.</li>\n</ol>\n<p>1(a). It's also ubiquitous everywhere else in the body.</p>\n<p>1(b). Unlike the brain, other organs' cells' mitotic divisions have replication accuracy that is many, many times higher than neurons', so mosaicism remains rare in other organs even under this strict definition. (Also, non-mitotic mutations would have to be very rare. I don't think this subcase holds.)</p>\n<ol start=\"2\">\n<li>&quot;Mosaicism&quot; uses a looser definition of &quot;more than one genotype&quot;, to mean that different cells' genotypes are &quot;very&quot; different.</li>\n</ol>\n<p>2(a). Mosaicism is much rarer under this more restrictive definition.</p>\n<p>2(b). Mosaicism is still ubiquitous in humans, even under this more restrictive definition.</p>\n<p>If case #2 holds, then how can we understand what &quot;very different&quot; means in practice? (I know, I know, biologists don't do rigorous definitions. I'm not looking for a rigorous definition; I'm looking for some rough intuition.) Does it maybe mean something like &quot;a non-synonymous mutation in a gene that codes for a protein&quot;? Or does it mean &quot;phenotypically different&quot;, so that (say) different pieces of tissue within the same organ behave observably differently?</p>\n<p>I realize that it may still be an open research question whether subcase (a) or (b) holds within either case.</p>\n","text":"Wikipedia defines \"somatic mosaicism\" (https://en.wikipedia.org/wiki/Mosaic_(genetics)#Somatic_mosaicism) to\n\n\n\n\n\n\n\noccur when the somatic cells of the body are of more than one genotype. In the more common mosaics, different genotypes arise from a single fertilized egg cell, due to mitotic errors at first or later cleavages.\n\n\n\n\n\n\n\nWe now know that, at least in the human brain, mitotic mutations are very common, and every neuron in the brain probably has a (slightly) distinct DNA sequence (https://www.scientificamerican.com/article/scientists-surprised-to-find-no-two-neurons-are-genetically-alike/). This would superficially seem to indicate that the phenomenon of somatic mosaicism (as defined literally) is completely ubiquitous and occurs in all mice and humans. But other questions on this site indicate that the concept of a \"genotype\" is more flexible than requiring a literal exact match of DNA sequences. So I want to clarify how the term is used in practice.\n\n\n\n\nWhich of these claims most accurately reflects how the term is used in practice?\n\n\n\n\n\n\"Mosaicism\" refers to any mutation at all, and it's completely ubiquitous in the human (and mouse) brain. It may be \"interesting\" from a phenotypic perspective, or it may not be.\n\n\n\n\n\n1(a). It's also ubiquitous everywhere else in the body.\n\n\n\n\n1(b). Unlike the brain, other organs' cells' mitotic divisions have replication accuracy that is many, many times higher than neurons', so mosaicism remains rare in other organs even under this strict definition. (Also, non-mitotic mutations would have to be very rare. I don't think this subcase holds.)\n\n\n\n\n\n\"Mosaicism\" uses a looser definition of \"more than one genotype\", to mean that different cells' genotypes are \"very\" different.\n\n\n\n\n\n2(a). Mosaicism is much rarer under this more restrictive definition.\n\n\n\n\n2(b). Mosaicism is still ubiquitous in humans, even under this more restrictive definition.\n\n\n\n\nIf case #2 holds, then how can we understand what \"very different\" means in practice? (I know, I know, biologists don't do rigorous definitions. I'm not looking for a rigorous definition; I'm looking for some rough intuition.) Does it maybe mean something like \"a non-synonymous mutation in a gene that codes for a protein\"? Or does it mean \"phenotypically different\", so that (say) different pieces of tissue within the same organ behave observably differently?\n\n\n\n\nI realize that it may still be an open research question whether subcase (a) or (b) holds within either case."},{"context_id":"117993","html":"<p>I would recommend to be careful about binary thinking. We humans seem naturally drawn to binary, but it's just not often a good description of the real world. I might tweak Wikipedia's definition a bit, something like:</p>\n<blockquote>\n<p>&quot;somatic mosaicism&quot; describes genotypic differences in somatic cells of the body.</p>\n</blockquote>\n<p>That is, to emphasize thinking about this as giving a name to observed differences, rather than being a binary condition that is present or not present.</p>\n<p>So yes, genetic differences between somatic cells are common (and certainly not only in the brain), though also many of these differences are inconsequential, see also: <a href=\"https://biology.stackexchange.com/a/117988/27148\">https://biology.stackexchange.com/a/117988/27148</a></p>\n<blockquote>\n<p>how can we understand what &quot;very different&quot; means in practice?</p>\n</blockquote>\n<p>I would expect biologists to use different meanings of &quot;somatic mosaicism&quot; in different contexts. Usually, biologists are going to be studying some phenomenon or mechanism, and since those are almost certainly going to involve some sort of phenotype then that will be the focus.</p>\n<p>I would also argue that mosaicism is as much about what is <em>shared</em> as it is about what is different. It's not just that a mosaic includes cells with different genotypes, but that because these differences are inherited through cell division, you're talking about populations of cells that are more similar to themselves than to another population.</p>\n","text":"I would recommend to be careful about binary thinking. We humans seem naturally drawn to binary, but it's just not often a good description of the real world. I might tweak Wikipedia's definition a bit, something like:\n\n\n\n\n\n\n\n\"somatic mosaicism\" describes genotypic differences in somatic cells of the body.\n\n\n\n\n\n\n\nThat is, to emphasize thinking about this as giving a name to observed differences, rather than being a binary condition that is present or not present.\n\n\n\n\nSo yes, genetic differences between somatic cells are common (and certainly not only in the brain), though also many of these differences are inconsequential, see also: https://biology.stackexchange.com/a/117988/27148 (https://biology.stackexchange.com/a/117988/27148)\n\n\n\n\n\n\n\nhow can we understand what \"very different\" means in practice?\n\n\n\n\n\n\n\nI would expect biologists to use different meanings of \"somatic mosaicism\" in different contexts. Usually, biologists are going to be studying some phenomenon or mechanism, and since those are almost certainly going to involve some sort of phenotype then that will be the focus.\n\n\n\n\nI would also argue that mosaicism is as much about what is shared as it is about what is different. It's not just that a mosaic includes cells with different genotypes, but that because these differences are inherited through cell division, you're talking about populations of cells that are more similar to themselves than to another population."}],"domain":"biology","external_citations":["https://biology.stackexchange.com/a/117988/27148","https://en.wikipedia.org/wiki/Mosaic_(genetics)#Somatic_mosaicism","https://www.scientificamerican.com/article/scientists-surprised-to-find-no-two-neurons-are-genetically-alike/"],"ground_truth_type":"metadata_grounded","group_id":"40a95eca490d80872935be55f978d8fdf50c51e14f9d0f09c120118da504a60a","hard_case_family":["multiple_sources"],"id":"RHM-ff65e5f9e086a2a05b12bb46","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":"tparker","profile_url":"https://biology.stackexchange.com/users/26604/tparker","user_type":"registered"},"created_at":"2025-09-30T18:14:50+00:00","raw_file":"raw/codex_api_v1/e6c4101e2e357aa8c5379bd547ec537e2ae9d3a66d32b72c727e9d2ad82690d6_1790824162028580600_0.json","raw_sha256":"cba09186cd183cf1116bbe2f874d16b08a8bc537baa01c33e34f5c3821229cc5","revision_guid":"57148B93-8F88-436B-B4A6-7F36DCB13FBC","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/57148B93-8F88-436B-B4A6-7F36DCB13FBC/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"tparker","profile_url":"https://biology.stackexchange.com/users/26604/tparker","user_type":"registered"},"created_at":"2025-09-30T18:37:02+00:00","raw_file":"raw/codex_api_v1/e6c4101e2e357aa8c5379bd547ec537e2ae9d3a66d32b72c727e9d2ad82690d6_1790824162028580600_0.json","raw_sha256":"cba09186cd183cf1116bbe2f874d16b08a8bc537baa01c33e34f5c3821229cc5","revision_guid":"09B9300B-97F2-42D9-A6C4-13B9A8E4E693","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/09B9300B-97F2-42D9-A6C4-13B9A8E4E693/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"tparker","profile_url":"https://biology.stackexchange.com/users/26604/tparker","user_type":"registered"},"created_at":"2025-09-30T18:49:48+00:00","raw_file":"raw/codex_api_v1/e6c4101e2e357aa8c5379bd547ec537e2ae9d3a66d32b72c727e9d2ad82690d6_1790824162028580600_0.json","raw_sha256":"cba09186cd183cf1116bbe2f874d16b08a8bc537baa01c33e34f5c3821229cc5","revision_guid":"9620F583-B1E9-4202-AF76-DB8B5C469594","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/9620F583-B1E9-4202-AF76-DB8B5C469594/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Ali Khakbaz","profile_url":"https://biology.stackexchange.com/users/117000/ali-khakbaz","user_type":"registered"},"created_at":"2025-10-01T11:07:33+00:00","raw_file":"raw/codex_api_v1/e6c4101e2e357aa8c5379bd547ec537e2ae9d3a66d32b72c727e9d2ad82690d6_1790824162028580600_0.json","raw_sha256":"cba09186cd183cf1116bbe2f874d16b08a8bc537baa01c33e34f5c3821229cc5","revision_guid":"F99AA262-F949-45FD-9D21-FDF2F0F7A68C","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/F99AA262-F949-45FD-9D21-FDF2F0F7A68C/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-10-01T14:01:39+00:00","raw_file":"raw/codex_api_v1/e6c4101e2e357aa8c5379bd547ec537e2ae9d3a66d32b72c727e9d2ad82690d6_1790824162028580600_0.json","raw_sha256":"cba09186cd183cf1116bbe2f874d16b08a8bc537baa01c33e34f5c3821229cc5","revision_guid":"5D55E511-64FC-4287-973E-0C379419E0CA","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/5D55E511-64FC-4287-973E-0C379419E0CA/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":"117992","source_record_sha256":"ace27d9eba0222d9f4177616fceae987c17955c9c22c65b564f869e82d38fd80","source_url":"https://biology.stackexchange.com/questions/117992/is-somatic-mosaicism-ubiquitious-or-is-it-defined-in-practice-in-a-way-that-mak","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Is somatic mosaicism ubiquitious, or is it defined in practice in a way that makes it more rare?\nWikipedia defines \"somatic mosaicism\" (https://en.wikipedia.org/wiki/Mosaic_(genetics)#Somatic_mosaicism) to\n\n\n\n\n\n\n\noccur when the somatic cells of the body are of more than one genotype. In the more common mosaics, different genotypes arise from a single fertilized egg cell, due to mitotic errors at first or later cleavages.\n\n\n\n\n\n\n\nWe now know that, at least in the human brain, mitotic mutations are very common, and every neuron in the brain probably has a (slightly) distinct DNA sequence (https://www.scientificamerican.com/article/scientists-surprised-to-find-no-two-neurons-are-genetically-alike/). This would superficially seem to indicate that the phenomenon of somatic mosaicism (as defined literally) is completely ubiquitous and occurs in all mice and humans. But other questions on this site indicate that the concept of a \"genotype\" is more flexible than requiring a literal exact match of DNA sequences. So I want to clarify how the term is used in practice.\n\n\n\n\nWhich of these claims most accurately reflects how the term is used in practice?\n\n\n\n\n\n\"Mosaicism\" refers to any mutation at all, and it's completely ubiquitous in the human (and mouse) brain. It may be \"interesting\" from a phenotypic perspective, or it may not be.\n\n\n\n\n\n1(a). It's also ubiquitous everywhere else in the body.\n\n\n\n\n1(b). Unlike the brain, other organs' cells' mitotic divisions have replication accuracy that is many, many times higher than neurons', so mosaicism remains rare in other organs even under this strict definition. (Also, non-mitotic mutations would have to be very rare. I don't think this subcase holds.)\n\n\n\n\n\n\"Mosaicism\" uses a looser definition of \"more than one genotype\", to mean that different cells' genotypes are \"very\" different.\n\n\n\n\n\n2(a). Mosaicism is much rarer under this more restrictive definition.\n\n\n\n\n2(b). Mosaicism is still ubiquitous in humans, even under this more restrictive definition.\n\n\n\n\nIf case #2 holds, then how can we understand what \"very different\" means in practice? (I know, I know, biologists don't do rigorous definitions. I'm not looking for a rigorous definition; I'm looking for some rough intuition.) Does it maybe mean something like \"a non-synonymous mutation in a gene that codes for a protein\"? Or does it mean \"phenotypically different\", so that (say) different pieces of tissue within the same organ behave observably differently?\n\n\n\n\nI realize that it may still be an open research question whether subcase (a) or (b) holds within either case.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":117993,"score":5}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Yes, these are known as <a href=\"https://en.wikipedia.org/wiki/Nested_gene\" rel=\"noreferrer\">nested genes</a>, and there are actually several, even in the human genome. A paper I found while answering this question (<a href=\"https://doi.org/10.1128/ec.00143-09\" rel=\"noreferrer\">Kumar, 2009</a>) claims the human genome has 158 nested protein coding genes.</p>\n<p>The most common type of nested gene, <a href=\"https://doi.org/10.1101/gr.2433104\" rel=\"noreferrer\">at least in the human genome</a>, is where one gene is found on the plus strand and another on the minus strand, with the smaller gene being in an intron of the larger one. For example, the human gene LPAR6 is contained entirely within the human gene RB1, but RB1 is on the forward strand and LPAR6 on the reverse. See the <a href=\"https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&amp;lastVirtModeType=default&amp;lastVirtModeExtraState=&amp;virtModeType=default&amp;virtMode=0&amp;nonVirtPosition=&amp;position=chr13%3A48303751%2D48481890&amp;hgsid=3253448463_8qD6NWIOxcvqyxqB99itbgaASxGP\" rel=\"noreferrer\">UCSC genome browser</a>:</p>\n<p><a href=\"https://i.sstatic.net/7Y0zIHeK.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/7Y0zIHeK.png\" alt=\"UCSC browser screenshot\" /></a></p>\n<p>The <a href=\"https://doi.org/10.1128/ec.00143-09\" rel=\"noreferrer\">same article</a> I linked to earlier also describes another kind of nested gene where the smaller gene falls in an exon of the larger one. This is rarer in metazoans, but does exist.</p>\n<p>Finally, microbial genomes seem to have many overlapping genes that share coding sequence. See <a href=\"https://doi.org/10.1101/gr.2433104\" rel=\"noreferrer\">Johnson and Chisholm, 2004</a></p>\n<h3>References</h3>\n<ul>\n<li><a href=\"https://doi.org/10.1128/ec.00143-09\" rel=\"noreferrer\">Kumar A. <em>An overview of nested genes in eukaryotic genomes.</em> Eukaryot Cell. 2009 Sep;8(9):1321-9. doi: 10.1128/EC.00143-09.</a></li>\n<li><a href=\"https://doi.org/10.1101/gr.2433104\" rel=\"noreferrer\">Johnson ZI, Chisholm SW. <em>Properties of overlapping genes are conserved across microbial genomes.</em> Genome Res. 2004 Nov;14(11):2268-72.</a></li>\n<li><a href=\"https://doi.org/10.1186/1471-2164-9-169\" rel=\"noreferrer\">Sanna, C.R., Li, WH. &amp; Zhang, L. Overlapping genes in the human and mouse genomes. BMC Genomics 9, 169 (2008).</a></li>\n</ul>\n","answer_id":118032,"answer_text":"Yes, these are known as nested genes (https://en.wikipedia.org/wiki/Nested_gene), and there are actually several, even in the human genome. A paper I found while answering this question (Kumar, 2009 (https://doi.org/10.1128/ec.00143-09)) claims the human genome has 158 nested protein coding genes.\n\n\n\n\nThe most common type of nested gene, at least in the human genome (https://doi.org/10.1101/gr.2433104), is where one gene is found on the plus strand and another on the minus strand, with the smaller gene being in an intron of the larger one. For example, the human gene LPAR6 is contained entirely within the human gene RB1, but RB1 is on the forward strand and LPAR6 on the reverse. See the UCSC genome browser (https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr13%3A48303751%2D48481890&hgsid=3253448463_8qD6NWIOxcvqyxqB99itbgaASxGP):\n\n\n\n\n[image: UCSC browser screenshot; source: https://i.sstatic.net/7Y0zIHeK.png] (https://i.sstatic.net/7Y0zIHeK.png)\n\n\n\n\nThe same article (https://doi.org/10.1128/ec.00143-09) I linked to earlier also describes another kind of nested gene where the smaller gene falls in an exon of the larger one. This is rarer in metazoans, but does exist.\n\n\n\n\nFinally, microbial genomes seem to have many overlapping genes that share coding sequence. See Johnson and Chisholm, 2004 (https://doi.org/10.1101/gr.2433104)\n\n\n\n\nReferences\n\n\n\n\n\nKumar A. An overview of nested genes in eukaryotic genomes. Eukaryot Cell. 2009 Sep;8(9):1321-9. doi: 10.1128/EC.00143-09. (https://doi.org/10.1128/ec.00143-09)\n\n\n\n\nJohnson ZI, Chisholm SW. Properties of overlapping genes are conserved across microbial genomes. Genome Res. 2004 Nov;14(11):2268-72. (https://doi.org/10.1101/gr.2433104)\n\n\n\n\nSanna, C.R., Li, WH. & Zhang, L. Overlapping genes in the human and mouse genomes. BMC Genomics 9, 169 (2008). (https://doi.org/10.1186/1471-2164-9-169)","answer_url":"https://biology.stackexchange.com/a/118032","author":"terdon","author_url":"https://biology.stackexchange.com/users/1306/terdon","content_license":"CC BY-SA 4.0","created_at":"2025-10-17T16:59:53+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":118030,"revision_attribution":[{"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":"2025-10-17T16:59:53+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"3B928DEA-9C96-4F9D-800F-4EFFA884C8E9","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3B928DEA-9C96-4F9D-800F-4EFFA884C8E9/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":"2025-10-17T20:20:28+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"69780AA4-ED19-4285-AAC7-8D7E37F26FE0","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/69780AA4-ED19-4285-AAC7-8D7E37F26FE0/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":"2025-10-18T21:51:49+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"B811CF31-40A6-4006-92D0-352A738A0C00","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B811CF31-40A6-4006-92D0-352A738A0C00/view-source"}],"score":13},{"answer_html":"<p><strong>Short Answer</strong><br>\nAlthough the definition of the term <em>gene</em> is open to debate, in answer to what I feel is the most likely meaning of the original poster’s question:</p>\n<p>“<strong>Yes</strong>. Cases do exist in which a region of DNA can be transcribed and translated to produce two different proteins in which a part of the amino acid sequence of each is encoded by the same stretch of the DNA.”</p>\n<p>One description of this situation is <em>Overlapping Genes</em>, and a review of such genes is provided in a 2022 <em>Nature</em> review by Wright <em>et al.</em>, entitled <a href=\"https://doi.org/10.1038/s41576-021-00417-w\" rel=\"nofollow noreferrer\">“Overlapping genes in natural and engineered genomes”</a>.</p>\n<p><strong>Complexity of the question</strong><br>\nThere are a number of complicating factors in considering overlapping genes in general, only some of which apply to this situation:</p>\n<ul>\n<li>Prokaryotes or Eukaryotes? — these differ in their RNA transcripts and their translation</li>\n<li>Same or different mRNAs producing the two proteins?</li>\n<li>Same or different direction for the gene (i.e. DNA strand transcribed)</li>\n<li>If same mRNA, is same reading frame used?</li>\n<li>Overlap of protein-encoding regions of mRNA or  overlap with untranslated region of mRNA?</li>\n</ul>\n<p>The review by Wright <em>et al.</em> includes a figure illustrating some of these possibilities, a modified section of which I reproduce below. (It also makes a distinction between overlapping and nested genes.) The poster’s question is clearly framed in terms of (a) in the figure, so I shall focus on that initially.</p>\n<p><a href=\"https://i.sstatic.net/IIFGGJWk.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/IIFGGJWk.png\" alt=\"Types of gene overlap and nesting\" /></a></p>\n<p><strong>Why are examples of gene overlap uncommon?</strong><br>\nThe information that such overlaps can occur is of much less value than knowing what problems lead them to being uncommon and how these problems are overcome. The key point is that there are specific signals for initiating and translating part of the mRNA into protein — in effect, ‘rules’ for where the protein starts and stops. <em>Overlapping protein products translated from the same mRNA would require the rules to be broken</em>.</p>\n<p>The problem with overlapping proteins translated in different directions ((c) and (d)) is the unlikelihood that both translations could encode functional proteins, and, even if they did, evolutionary changes in one could have deleterious effects on the other. The same problem is encountered if different reading frames are used to translate a single mRNA in the same direction.</p>\n<p><strong>Overcoming the problems</strong><br>\nFor situation (a) let us simplify by assuming there is a common mRNA for two protein products (always true for prokaryotes, as far as I am aware).</p>\n<p>In most prokaryotes there is a site just 5′ to the initiating AUG codon (RBS or Shine–Dalgarno sequence) to which the small ribosomal subunit binds. In order to have alternative AUG starting codons, as in (a) (or (b)), there would have to be alternative ribosome binding sites, the second within the coding sequence specifying the first protein product. Such dual function is not impossible, but I am unaware of any examples of it.</p>\n<p>In eukaryotes an initiation complex of the small ribosomal subunit and the initiator tRNA normally binds to the 5’ methylated cap of the mRNA and then scans along the mRNA, initiating translation at the first AUG or the first AUG in a ‘suitable context’. The difference between a ‘suitable’ and ‘unsuitable’ context for an initiating AUG is not always clear-cut, and this leads to situations where, for the same mRNA, some ribosomes initiate at the first AUG and others at the second (or subsequent) AUG, leading to different proteins.</p>\n<p><a href=\"https://i.sstatic.net/kEXMhKOb.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/kEXMhKOb.jpg\" alt=\"Alternative AUGs in eukaryotic initiation\" /></a></p>\n<p><a href=\"https://doi.org/10.1534/g3.115.018937\" rel=\"nofollow noreferrer\">Examples in the genome of <em>Drosophila melanogaster</em></a> have been well documented.\nThe two forms of the <em>Drosophila</em> Apoptotic signal-regulating kinase 1 are illustrated below:</p>\n<p><a href=\"https://i.sstatic.net/9kQCvBKN.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/9kQCvBKN.png\" alt=\"Example of alternative inititiation Ask1\" /></a></p>\n<p>It can seen that form B of the protein starts at amino acid 169 of form C, although both terminate at the same position. The nomenclature indicates that the proteins are, in fact, considered as variant products of the same gene, Ask1.</p>\n<p>In this and all the other examples of which I am aware in <em>Drosophila</em> the alternative AUG is in the same reading frame as the first one. Although I have already mentioned the problem if the same stretch of DNA encoded entirely different proteins, there is at least one reported exampl. This involves the human ribosomal protein gene RPL36, and an alternative protein, alt-RPL36, translated from the same transcript.</p>\n<p><a href=\"https://i.sstatic.net/UD6dhazE.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/UD6dhazE.png\" alt=\"RPL36 and alt-RPL36\" /></a></p>\n<p>In this case the abnormal initiation codon, GUG, used to start the alternative protein. The viability of such a situation obviously depends on the biological function of the proteins involved, for which the reader is directed to the <a href=\"https://doi.org/10.1038/s41467-020-20841-6\" rel=\"nofollow noreferrer\">original publication</a>.</p>\n<p>The situation regarding termination of translation is the same for prokaryotes and eukaryotes, and examples of an elongated forms of a protein was first shown in the 70s for small RNA bacteriophages. Examples are also common in eukaryotic single-stranded RNA viruses, although less so in cellular mRNAs. There are two main mechanisms for a ribosome to continue past a termination codon. The first is termed ‘read-through’ in which the termination codon (a ‘leaky’ stop codon) is erroneously recognized by an aminoacyl-tRNA. The second involves ‘frameshift’ — an erroneous (but specific) change of reading frame just before the termination codon. Readthrough and frameshift have been extensively reviewed, e.g. by <a href=\"https://doi.org/10.1111/brv.12657\" rel=\"nofollow noreferrer\">Palemer and LeJeune</a>. An example of readthrough in <em>Drosophila</em> is shown below for a component of a ubiquitin ligase:</p>\n<p><a href=\"https://i.sstatic.net/V0lLbcrt.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/V0lLbcrt.png\" alt=\"Readthrough example in Drosophila\" /></a></p>\n<p>[‘X’ indicates an unknown amino acid inserted at the stop codon.]</p>\n<p><strong>A Final Example</strong><br>\nI managed to find a gene or genes to illustrate three of the four cases in the initial figure. This is <em>Syn</em>, the <em>Drosophila</em> gene for synapsin:</p>\n<p><a href=\"https://i.sstatic.net/iVAI5JAj.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/iVAI5JAj.png\" alt=\"Drosophila Synapsins\" /></a></p>\n<p>Protein Syn-PE is the product using the first AUG and stop codon, whereas Syn-PF (from the same transcript) is produced by skipping both of these, and is thus an example of (a). Syn-PD is the longest protein, produced by reading through the first stop codon, so it nests within it Syn-PA, produced by skipping the first AUG. This is an example of (b). Syn-PA is actually produced from a different (terminally truncated) transcript, but this would not appear to contribute to the type of protein produced.</p>\n<p>The gene, <em>Syn</em>, contains another gene, <em>Timp</em>, in the opposite direction. The coding region of the latter (composed of several exons) is contained entirely within an intron of Syn — an example of (d)</p>\n<p><a href=\"https://i.sstatic.net/E4BaU9uZ.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/E4BaU9uZ.png\" alt=\"Syn / Timp gene overlap\" /></a></p>\n<p>The protein-coding regions of the RNA transcripts in the diagram are indicated in orange.</p>\n","answer_id":118041,"answer_text":"Short Answer\n\nAlthough the definition of the term gene is open to debate, in answer to what I feel is the most likely meaning of the original poster’s question:\n\n\n\n\n“Yes. Cases do exist in which a region of DNA can be transcribed and translated to produce two different proteins in which a part of the amino acid sequence of each is encoded by the same stretch of the DNA.”\n\n\n\n\nOne description of this situation is Overlapping Genes, and a review of such genes is provided in a 2022 Nature review by Wright et al., entitled “Overlapping genes in natural and engineered genomes” (https://doi.org/10.1038/s41576-021-00417-w).\n\n\n\n\nComplexity of the question\n\nThere are a number of complicating factors in considering overlapping genes in general, only some of which apply to this situation:\n\n\n\n\n\nProkaryotes or Eukaryotes? — these differ in their RNA transcripts and their translation\n\n\n\n\nSame or different mRNAs producing the two proteins?\n\n\n\n\nSame or different direction for the gene (i.e. DNA strand transcribed)\n\n\n\n\nIf same mRNA, is same reading frame used?\n\n\n\n\nOverlap of protein-encoding regions of mRNA or  overlap with untranslated region of mRNA?\n\n\n\n\n\nThe review by Wright et al. includes a figure illustrating some of these possibilities, a modified section of which I reproduce below. (It also makes a distinction between overlapping and nested genes.) The poster’s question is clearly framed in terms of (a) in the figure, so I shall focus on that initially.\n\n\n\n\n[image: Types of gene overlap and nesting; source: https://i.sstatic.net/IIFGGJWk.png] (https://i.sstatic.net/IIFGGJWk.png)\n\n\n\n\nWhy are examples of gene overlap uncommon?\n\nThe information that such overlaps can occur is of much less value than knowing what problems lead them to being uncommon and how these problems are overcome. The key point is that there are specific signals for initiating and translating part of the mRNA into protein — in effect, ‘rules’ for where the protein starts and stops. Overlapping protein products translated from the same mRNA would require the rules to be broken.\n\n\n\n\nThe problem with overlapping proteins translated in different directions ((c) and (d)) is the unlikelihood that both translations could encode functional proteins, and, even if they did, evolutionary changes in one could have deleterious effects on the other. The same problem is encountered if different reading frames are used to translate a single mRNA in the same direction.\n\n\n\n\nOvercoming the problems\n\nFor situation (a) let us simplify by assuming there is a common mRNA for two protein products (always true for prokaryotes, as far as I am aware).\n\n\n\n\nIn most prokaryotes there is a site just 5′ to the initiating AUG codon (RBS or Shine–Dalgarno sequence) to which the small ribosomal subunit binds. In order to have alternative AUG starting codons, as in (a) (or (b)), there would have to be alternative ribosome binding sites, the second within the coding sequence specifying the first protein product. Such dual function is not impossible, but I am unaware of any examples of it.\n\n\n\n\nIn eukaryotes an initiation complex of the small ribosomal subunit and the initiator tRNA normally binds to the 5’ methylated cap of the mRNA and then scans along the mRNA, initiating translation at the first AUG or the first AUG in a ‘suitable context’. The difference between a ‘suitable’ and ‘unsuitable’ context for an initiating AUG is not always clear-cut, and this leads to situations where, for the same mRNA, some ribosomes initiate at the first AUG and others at the second (or subsequent) AUG, leading to different proteins.\n\n\n\n\n[image: Alternative AUGs in eukaryotic initiation; source: https://i.sstatic.net/kEXMhKOb.jpg] (https://i.sstatic.net/kEXMhKOb.jpg)\n\n\n\n\nExamples in the genome of Drosophila melanogaster (https://doi.org/10.1534/g3.115.018937) have been well documented.\nThe two forms of the Drosophila Apoptotic signal-regulating kinase 1 are illustrated below:\n\n\n\n\n[image: Example of alternative inititiation Ask1; source: https://i.sstatic.net/9kQCvBKN.png] (https://i.sstatic.net/9kQCvBKN.png)\n\n\n\n\nIt can seen that form B of the protein starts at amino acid 169 of form C, although both terminate at the same position. The nomenclature indicates that the proteins are, in fact, considered as variant products of the same gene, Ask1.\n\n\n\n\nIn this and all the other examples of which I am aware in Drosophila the alternative AUG is in the same reading frame as the first one. Although I have already mentioned the problem if the same stretch of DNA encoded entirely different proteins, there is at least one reported exampl. This involves the human ribosomal protein gene RPL36, and an alternative protein, alt-RPL36, translated from the same transcript.\n\n\n\n\n[image: RPL36 and alt-RPL36; source: https://i.sstatic.net/UD6dhazE.png] (https://i.sstatic.net/UD6dhazE.png)\n\n\n\n\nIn this case the abnormal initiation codon, GUG, used to start the alternative protein. The viability of such a situation obviously depends on the biological function of the proteins involved, for which the reader is directed to the original publication (https://doi.org/10.1038/s41467-020-20841-6).\n\n\n\n\nThe situation regarding termination of translation is the same for prokaryotes and eukaryotes, and examples of an elongated forms of a protein was first shown in the 70s for small RNA bacteriophages. Examples are also common in eukaryotic single-stranded RNA viruses, although less so in cellular mRNAs. There are two main mechanisms for a ribosome to continue past a termination codon. The first is termed ‘read-through’ in which the termination codon (a ‘leaky’ stop codon) is erroneously recognized by an aminoacyl-tRNA. The second involves ‘frameshift’ — an erroneous (but specific) change of reading frame just before the termination codon. Readthrough and frameshift have been extensively reviewed, e.g. by Palemer and LeJeune (https://doi.org/10.1111/brv.12657). An example of readthrough in Drosophila is shown below for a component of a ubiquitin ligase:\n\n\n\n\n[image: Readthrough example in Drosophila; source: https://i.sstatic.net/V0lLbcrt.png] (https://i.sstatic.net/V0lLbcrt.png)\n\n\n\n\n[‘X’ indicates an unknown amino acid inserted at the stop codon.]\n\n\n\n\nA Final Example\n\nI managed to find a gene or genes to illustrate three of the four cases in the initial figure. This is Syn, the Drosophila gene for synapsin:\n\n\n\n\n[image: Drosophila Synapsins; source: https://i.sstatic.net/iVAI5JAj.png] (https://i.sstatic.net/iVAI5JAj.png)\n\n\n\n\nProtein Syn-PE is the product using the first AUG and stop codon, whereas Syn-PF (from the same transcript) is produced by skipping both of these, and is thus an example of (a). Syn-PD is the longest protein, produced by reading through the first stop codon, so it nests within it Syn-PA, produced by skipping the first AUG. This is an example of (b). Syn-PA is actually produced from a different (terminally truncated) transcript, but this would not appear to contribute to the type of protein produced.\n\n\n\n\nThe gene, Syn, contains another gene, Timp, in the opposite direction. The coding region of the latter (composed of several exons) is contained entirely within an intron of Syn — an example of (d)\n\n\n\n\n[image: Syn / Timp gene overlap; source: https://i.sstatic.net/E4BaU9uZ.png] (https://i.sstatic.net/E4BaU9uZ.png)\n\n\n\n\nThe protein-coding regions of the RNA transcripts in the diagram are indicated in orange.","answer_url":"https://biology.stackexchange.com/a/118041","author":"David","author_url":"https://biology.stackexchange.com/users/22057/david","content_license":"CC BY-SA 4.0","created_at":"2025-10-22T14:58:28+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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Can there be two different genes in which, for example, the first starts at nt 10 and ends at nt 40 and the second starts at nt 30 and ends at nt 60? (Thus they will include the same section of the genome from nt 30 to nt 40) Or do all genes occupy exclusive sections of a genome?</p>\n","text":"Suppose you have a sequence of 130 nucleotides (nt) in a genome. Can there be two different genes in which, for example, the first starts at nt 10 and ends at nt 40 and the second starts at nt 30 and ends at nt 60? (Thus they will include the same section of the genome from nt 30 to nt 40) Or do all genes occupy exclusive sections of a genome?"},{"context_id":"118032","html":"<p>Yes, these are known as <a href=\"https://en.wikipedia.org/wiki/Nested_gene\" rel=\"noreferrer\">nested genes</a>, and there are actually several, even in the human genome. A paper I found while answering this question (<a href=\"https://doi.org/10.1128/ec.00143-09\" rel=\"noreferrer\">Kumar, 2009</a>) claims the human genome has 158 nested protein coding genes.</p>\n<p>The most common type of nested gene, <a href=\"https://doi.org/10.1101/gr.2433104\" rel=\"noreferrer\">at least in the human genome</a>, is where one gene is found on the plus strand and another on the minus strand, with the smaller gene being in an intron of the larger one. For example, the human gene LPAR6 is contained entirely within the human gene RB1, but RB1 is on the forward strand and LPAR6 on the reverse. See the <a href=\"https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&amp;lastVirtModeType=default&amp;lastVirtModeExtraState=&amp;virtModeType=default&amp;virtMode=0&amp;nonVirtPosition=&amp;position=chr13%3A48303751%2D48481890&amp;hgsid=3253448463_8qD6NWIOxcvqyxqB99itbgaASxGP\" rel=\"noreferrer\">UCSC genome browser</a>:</p>\n<p><a href=\"https://i.sstatic.net/7Y0zIHeK.png\" rel=\"noreferrer\"><img src=\"https://i.sstatic.net/7Y0zIHeK.png\" alt=\"UCSC browser screenshot\" /></a></p>\n<p>The <a href=\"https://doi.org/10.1128/ec.00143-09\" rel=\"noreferrer\">same article</a> I linked to earlier also describes another kind of nested gene where the smaller gene falls in an exon of the larger one. This is rarer in metazoans, but does exist.</p>\n<p>Finally, microbial genomes seem to have many overlapping genes that share coding sequence. See <a href=\"https://doi.org/10.1101/gr.2433104\" rel=\"noreferrer\">Johnson and Chisholm, 2004</a></p>\n<h3>References</h3>\n<ul>\n<li><a href=\"https://doi.org/10.1128/ec.00143-09\" rel=\"noreferrer\">Kumar A. <em>An overview of nested genes in eukaryotic genomes.</em> Eukaryot Cell. 2009 Sep;8(9):1321-9. doi: 10.1128/EC.00143-09.</a></li>\n<li><a href=\"https://doi.org/10.1101/gr.2433104\" rel=\"noreferrer\">Johnson ZI, Chisholm SW. <em>Properties of overlapping genes are conserved across microbial genomes.</em> Genome Res. 2004 Nov;14(11):2268-72.</a></li>\n<li><a href=\"https://doi.org/10.1186/1471-2164-9-169\" rel=\"noreferrer\">Sanna, C.R., Li, WH. &amp; Zhang, L. Overlapping genes in the human and mouse genomes. BMC Genomics 9, 169 (2008).</a></li>\n</ul>\n","text":"Yes, these are known as nested genes (https://en.wikipedia.org/wiki/Nested_gene), and there are actually several, even in the human genome. A paper I found while answering this question (Kumar, 2009 (https://doi.org/10.1128/ec.00143-09)) claims the human genome has 158 nested protein coding genes.\n\n\n\n\nThe most common type of nested gene, at least in the human genome (https://doi.org/10.1101/gr.2433104), is where one gene is found on the plus strand and another on the minus strand, with the smaller gene being in an intron of the larger one. For example, the human gene LPAR6 is contained entirely within the human gene RB1, but RB1 is on the forward strand and LPAR6 on the reverse. See the UCSC genome browser (https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr13%3A48303751%2D48481890&hgsid=3253448463_8qD6NWIOxcvqyxqB99itbgaASxGP):\n\n\n\n\n[image: UCSC browser screenshot; source: https://i.sstatic.net/7Y0zIHeK.png] (https://i.sstatic.net/7Y0zIHeK.png)\n\n\n\n\nThe same article (https://doi.org/10.1128/ec.00143-09) I linked to earlier also describes another kind of nested gene where the smaller gene falls in an exon of the larger one. This is rarer in metazoans, but does exist.\n\n\n\n\nFinally, microbial genomes seem to have many overlapping genes that share coding sequence. See Johnson and Chisholm, 2004 (https://doi.org/10.1101/gr.2433104)\n\n\n\n\nReferences\n\n\n\n\n\nKumar A. An overview of nested genes in eukaryotic genomes. Eukaryot Cell. 2009 Sep;8(9):1321-9. doi: 10.1128/EC.00143-09. (https://doi.org/10.1128/ec.00143-09)\n\n\n\n\nJohnson ZI, Chisholm SW. Properties of overlapping genes are conserved across microbial genomes. Genome Res. 2004 Nov;14(11):2268-72. (https://doi.org/10.1101/gr.2433104)\n\n\n\n\nSanna, C.R., Li, WH. & Zhang, L. Overlapping genes in the human and mouse genomes. BMC Genomics 9, 169 (2008). (https://doi.org/10.1186/1471-2164-9-169)"},{"context_id":"118041","html":"<p><strong>Short Answer</strong><br>\nAlthough the definition of the term <em>gene</em> is open to debate, in answer to what I feel is the most likely meaning of the original poster’s question:</p>\n<p>“<strong>Yes</strong>. Cases do exist in which a region of DNA can be transcribed and translated to produce two different proteins in which a part of the amino acid sequence of each is encoded by the same stretch of the DNA.”</p>\n<p>One description of this situation is <em>Overlapping Genes</em>, and a review of such genes is provided in a 2022 <em>Nature</em> review by Wright <em>et al.</em>, entitled <a href=\"https://doi.org/10.1038/s41576-021-00417-w\" rel=\"nofollow noreferrer\">“Overlapping genes in natural and engineered genomes”</a>.</p>\n<p><strong>Complexity of the question</strong><br>\nThere are a number of complicating factors in considering overlapping genes in general, only some of which apply to this situation:</p>\n<ul>\n<li>Prokaryotes or Eukaryotes? — these differ in their RNA transcripts and their translation</li>\n<li>Same or different mRNAs producing the two proteins?</li>\n<li>Same or different direction for the gene (i.e. DNA strand transcribed)</li>\n<li>If same mRNA, is same reading frame used?</li>\n<li>Overlap of protein-encoding regions of mRNA or  overlap with untranslated region of mRNA?</li>\n</ul>\n<p>The review by Wright <em>et al.</em> includes a figure illustrating some of these possibilities, a modified section of which I reproduce below. (It also makes a distinction between overlapping and nested genes.) The poster’s question is clearly framed in terms of (a) in the figure, so I shall focus on that initially.</p>\n<p><a href=\"https://i.sstatic.net/IIFGGJWk.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/IIFGGJWk.png\" alt=\"Types of gene overlap and nesting\" /></a></p>\n<p><strong>Why are examples of gene overlap uncommon?</strong><br>\nThe information that such overlaps can occur is of much less value than knowing what problems lead them to being uncommon and how these problems are overcome. The key point is that there are specific signals for initiating and translating part of the mRNA into protein — in effect, ‘rules’ for where the protein starts and stops. <em>Overlapping protein products translated from the same mRNA would require the rules to be broken</em>.</p>\n<p>The problem with overlapping proteins translated in different directions ((c) and (d)) is the unlikelihood that both translations could encode functional proteins, and, even if they did, evolutionary changes in one could have deleterious effects on the other. The same problem is encountered if different reading frames are used to translate a single mRNA in the same direction.</p>\n<p><strong>Overcoming the problems</strong><br>\nFor situation (a) let us simplify by assuming there is a common mRNA for two protein products (always true for prokaryotes, as far as I am aware).</p>\n<p>In most prokaryotes there is a site just 5′ to the initiating AUG codon (RBS or Shine–Dalgarno sequence) to which the small ribosomal subunit binds. In order to have alternative AUG starting codons, as in (a) (or (b)), there would have to be alternative ribosome binding sites, the second within the coding sequence specifying the first protein product. Such dual function is not impossible, but I am unaware of any examples of it.</p>\n<p>In eukaryotes an initiation complex of the small ribosomal subunit and the initiator tRNA normally binds to the 5’ methylated cap of the mRNA and then scans along the mRNA, initiating translation at the first AUG or the first AUG in a ‘suitable context’. The difference between a ‘suitable’ and ‘unsuitable’ context for an initiating AUG is not always clear-cut, and this leads to situations where, for the same mRNA, some ribosomes initiate at the first AUG and others at the second (or subsequent) AUG, leading to different proteins.</p>\n<p><a href=\"https://i.sstatic.net/kEXMhKOb.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/kEXMhKOb.jpg\" alt=\"Alternative AUGs in eukaryotic initiation\" /></a></p>\n<p><a href=\"https://doi.org/10.1534/g3.115.018937\" rel=\"nofollow noreferrer\">Examples in the genome of <em>Drosophila melanogaster</em></a> have been well documented.\nThe two forms of the <em>Drosophila</em> Apoptotic signal-regulating kinase 1 are illustrated below:</p>\n<p><a href=\"https://i.sstatic.net/9kQCvBKN.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/9kQCvBKN.png\" alt=\"Example of alternative inititiation Ask1\" /></a></p>\n<p>It can seen that form B of the protein starts at amino acid 169 of form C, although both terminate at the same position. The nomenclature indicates that the proteins are, in fact, considered as variant products of the same gene, Ask1.</p>\n<p>In this and all the other examples of which I am aware in <em>Drosophila</em> the alternative AUG is in the same reading frame as the first one. Although I have already mentioned the problem if the same stretch of DNA encoded entirely different proteins, there is at least one reported exampl. This involves the human ribosomal protein gene RPL36, and an alternative protein, alt-RPL36, translated from the same transcript.</p>\n<p><a href=\"https://i.sstatic.net/UD6dhazE.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/UD6dhazE.png\" alt=\"RPL36 and alt-RPL36\" /></a></p>\n<p>In this case the abnormal initiation codon, GUG, used to start the alternative protein. The viability of such a situation obviously depends on the biological function of the proteins involved, for which the reader is directed to the <a href=\"https://doi.org/10.1038/s41467-020-20841-6\" rel=\"nofollow noreferrer\">original publication</a>.</p>\n<p>The situation regarding termination of translation is the same for prokaryotes and eukaryotes, and examples of an elongated forms of a protein was first shown in the 70s for small RNA bacteriophages. Examples are also common in eukaryotic single-stranded RNA viruses, although less so in cellular mRNAs. There are two main mechanisms for a ribosome to continue past a termination codon. The first is termed ‘read-through’ in which the termination codon (a ‘leaky’ stop codon) is erroneously recognized by an aminoacyl-tRNA. The second involves ‘frameshift’ — an erroneous (but specific) change of reading frame just before the termination codon. Readthrough and frameshift have been extensively reviewed, e.g. by <a href=\"https://doi.org/10.1111/brv.12657\" rel=\"nofollow noreferrer\">Palemer and LeJeune</a>. An example of readthrough in <em>Drosophila</em> is shown below for a component of a ubiquitin ligase:</p>\n<p><a href=\"https://i.sstatic.net/V0lLbcrt.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/V0lLbcrt.png\" alt=\"Readthrough example in Drosophila\" /></a></p>\n<p>[‘X’ indicates an unknown amino acid inserted at the stop codon.]</p>\n<p><strong>A Final Example</strong><br>\nI managed to find a gene or genes to illustrate three of the four cases in the initial figure. This is <em>Syn</em>, the <em>Drosophila</em> gene for synapsin:</p>\n<p><a href=\"https://i.sstatic.net/iVAI5JAj.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/iVAI5JAj.png\" alt=\"Drosophila Synapsins\" /></a></p>\n<p>Protein Syn-PE is the product using the first AUG and stop codon, whereas Syn-PF (from the same transcript) is produced by skipping both of these, and is thus an example of (a). Syn-PD is the longest protein, produced by reading through the first stop codon, so it nests within it Syn-PA, produced by skipping the first AUG. This is an example of (b). Syn-PA is actually produced from a different (terminally truncated) transcript, but this would not appear to contribute to the type of protein produced.</p>\n<p>The gene, <em>Syn</em>, contains another gene, <em>Timp</em>, in the opposite direction. The coding region of the latter (composed of several exons) is contained entirely within an intron of Syn — an example of (d)</p>\n<p><a href=\"https://i.sstatic.net/E4BaU9uZ.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/E4BaU9uZ.png\" alt=\"Syn / Timp gene overlap\" /></a></p>\n<p>The protein-coding regions of the RNA transcripts in the diagram are indicated in orange.</p>\n","text":"Short Answer\n\nAlthough the definition of the term gene is open to debate, in answer to what I feel is the most likely meaning of the original poster’s question:\n\n\n\n\n“Yes. Cases do exist in which a region of DNA can be transcribed and translated to produce two different proteins in which a part of the amino acid sequence of each is encoded by the same stretch of the DNA.”\n\n\n\n\nOne description of this situation is Overlapping Genes, and a review of such genes is provided in a 2022 Nature review by Wright et al., entitled “Overlapping genes in natural and engineered genomes” (https://doi.org/10.1038/s41576-021-00417-w).\n\n\n\n\nComplexity of the question\n\nThere are a number of complicating factors in considering overlapping genes in general, only some of which apply to this situation:\n\n\n\n\n\nProkaryotes or Eukaryotes? — these differ in their RNA transcripts and their translation\n\n\n\n\nSame or different mRNAs producing the two proteins?\n\n\n\n\nSame or different direction for the gene (i.e. DNA strand transcribed)\n\n\n\n\nIf same mRNA, is same reading frame used?\n\n\n\n\nOverlap of protein-encoding regions of mRNA or  overlap with untranslated region of mRNA?\n\n\n\n\n\nThe review by Wright et al. includes a figure illustrating some of these possibilities, a modified section of which I reproduce below. (It also makes a distinction between overlapping and nested genes.) The poster’s question is clearly framed in terms of (a) in the figure, so I shall focus on that initially.\n\n\n\n\n[image: Types of gene overlap and nesting; source: https://i.sstatic.net/IIFGGJWk.png] (https://i.sstatic.net/IIFGGJWk.png)\n\n\n\n\nWhy are examples of gene overlap uncommon?\n\nThe information that such overlaps can occur is of much less value than knowing what problems lead them to being uncommon and how these problems are overcome. The key point is that there are specific signals for initiating and translating part of the mRNA into protein — in effect, ‘rules’ for where the protein starts and stops. Overlapping protein products translated from the same mRNA would require the rules to be broken.\n\n\n\n\nThe problem with overlapping proteins translated in different directions ((c) and (d)) is the unlikelihood that both translations could encode functional proteins, and, even if they did, evolutionary changes in one could have deleterious effects on the other. The same problem is encountered if different reading frames are used to translate a single mRNA in the same direction.\n\n\n\n\nOvercoming the problems\n\nFor situation (a) let us simplify by assuming there is a common mRNA for two protein products (always true for prokaryotes, as far as I am aware).\n\n\n\n\nIn most prokaryotes there is a site just 5′ to the initiating AUG codon (RBS or Shine–Dalgarno sequence) to which the small ribosomal subunit binds. In order to have alternative AUG starting codons, as in (a) (or (b)), there would have to be alternative ribosome binding sites, the second within the coding sequence specifying the first protein product. Such dual function is not impossible, but I am unaware of any examples of it.\n\n\n\n\nIn eukaryotes an initiation complex of the small ribosomal subunit and the initiator tRNA normally binds to the 5’ methylated cap of the mRNA and then scans along the mRNA, initiating translation at the first AUG or the first AUG in a ‘suitable context’. The difference between a ‘suitable’ and ‘unsuitable’ context for an initiating AUG is not always clear-cut, and this leads to situations where, for the same mRNA, some ribosomes initiate at the first AUG and others at the second (or subsequent) AUG, leading to different proteins.\n\n\n\n\n[image: Alternative AUGs in eukaryotic initiation; source: https://i.sstatic.net/kEXMhKOb.jpg] (https://i.sstatic.net/kEXMhKOb.jpg)\n\n\n\n\nExamples in the genome of Drosophila melanogaster (https://doi.org/10.1534/g3.115.018937) have been well documented.\nThe two forms of the Drosophila Apoptotic signal-regulating kinase 1 are illustrated below:\n\n\n\n\n[image: Example of alternative inititiation Ask1; source: https://i.sstatic.net/9kQCvBKN.png] (https://i.sstatic.net/9kQCvBKN.png)\n\n\n\n\nIt can seen that form B of the protein starts at amino acid 169 of form C, although both terminate at the same position. The nomenclature indicates that the proteins are, in fact, considered as variant products of the same gene, Ask1.\n\n\n\n\nIn this and all the other examples of which I am aware in Drosophila the alternative AUG is in the same reading frame as the first one. Although I have already mentioned the problem if the same stretch of DNA encoded entirely different proteins, there is at least one reported exampl. This involves the human ribosomal protein gene RPL36, and an alternative protein, alt-RPL36, translated from the same transcript.\n\n\n\n\n[image: RPL36 and alt-RPL36; source: https://i.sstatic.net/UD6dhazE.png] (https://i.sstatic.net/UD6dhazE.png)\n\n\n\n\nIn this case the abnormal initiation codon, GUG, used to start the alternative protein. The viability of such a situation obviously depends on the biological function of the proteins involved, for which the reader is directed to the original publication (https://doi.org/10.1038/s41467-020-20841-6).\n\n\n\n\nThe situation regarding termination of translation is the same for prokaryotes and eukaryotes, and examples of an elongated forms of a protein was first shown in the 70s for small RNA bacteriophages. Examples are also common in eukaryotic single-stranded RNA viruses, although less so in cellular mRNAs. There are two main mechanisms for a ribosome to continue past a termination codon. The first is termed ‘read-through’ in which the termination codon (a ‘leaky’ stop codon) is erroneously recognized by an aminoacyl-tRNA. The second involves ‘frameshift’ — an erroneous (but specific) change of reading frame just before the termination codon. Readthrough and frameshift have been extensively reviewed, e.g. by Palemer and LeJeune (https://doi.org/10.1111/brv.12657). An example of readthrough in Drosophila is shown below for a component of a ubiquitin ligase:\n\n\n\n\n[image: Readthrough example in Drosophila; source: https://i.sstatic.net/V0lLbcrt.png] (https://i.sstatic.net/V0lLbcrt.png)\n\n\n\n\n[‘X’ indicates an unknown amino acid inserted at the stop codon.]\n\n\n\n\nA Final Example\n\nI managed to find a gene or genes to illustrate three of the four cases in the initial figure. This is Syn, the Drosophila gene for synapsin:\n\n\n\n\n[image: Drosophila Synapsins; source: https://i.sstatic.net/iVAI5JAj.png] (https://i.sstatic.net/iVAI5JAj.png)\n\n\n\n\nProtein Syn-PE is the product using the first AUG and stop codon, whereas Syn-PF (from the same transcript) is produced by skipping both of these, and is thus an example of (a). Syn-PD is the longest protein, produced by reading through the first stop codon, so it nests within it Syn-PA, produced by skipping the first AUG. This is an example of (b). Syn-PA is actually produced from a different (terminally truncated) transcript, but this would not appear to contribute to the type of protein produced.\n\n\n\n\nThe gene, Syn, contains another gene, Timp, in the opposite direction. The coding region of the latter (composed of several exons) is contained entirely within an intron of Syn — an example of (d)\n\n\n\n\n[image: Syn / Timp gene overlap; source: https://i.sstatic.net/E4BaU9uZ.png] (https://i.sstatic.net/E4BaU9uZ.png)\n\n\n\n\nThe protein-coding regions of the RNA transcripts in the diagram are indicated in orange."}],"domain":"biology","external_citations":["https://doi.org/10.1038/s41467-020-20841-6","https://doi.org/10.1038/s41576-021-00417-w","https://doi.org/10.1101/gr.2433104","https://doi.org/10.1111/brv.12657","https://doi.org/10.1128/ec.00143-09","https://doi.org/10.1186/1471-2164-9-169","https://doi.org/10.1534/g3.115.018937","https://en.wikipedia.org/wiki/Nested_gene","https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr13%3A48303751%2D48481890&hgsid=3253448463_8qD6NWIOxcvqyxqB99itbgaASxGP","https://i.sstatic.net/7Y0zIHeK.png","https://i.sstatic.net/9kQCvBKN.png","https://i.sstatic.net/E4BaU9uZ.png","https://i.sstatic.net/IIFGGJWk.png","https://i.sstatic.net/UD6dhazE.png","https://i.sstatic.net/V0lLbcrt.png","https://i.sstatic.net/iVAI5JAj.png","https://i.sstatic.net/kEXMhKOb.jpg"],"ground_truth_type":"metadata_grounded","group_id":"dda9d77613efcc6dfcced317b2ea09aca332a974ae0e4a8bc6393458eb7fa101","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy","multiple_answer_candidates"],"id":"RHM-86cbd79ac82776ab0d3bca08","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":"Root Groves","profile_url":"https://biology.stackexchange.com/users/78184/root-groves","user_type":"registered"},"created_at":"2025-10-17T13:36:28+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"2423E323-9CBE-4587-B6E3-DACB2CCAB2D1","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2423E323-9CBE-4587-B6E3-DACB2CCAB2D1/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":"2025-10-17T13:46:29+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"CE9187C3-9651-49B6-8BD3-ABEF518DE2AD","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/CE9187C3-9651-49B6-8BD3-ABEF518DE2AD/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Root Groves","profile_url":"https://biology.stackexchange.com/users/78184/root-groves","user_type":"registered"},"created_at":"2025-10-17T13:47:02+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"3800C50E-6A9A-46B0-9F31-ACF3AAFFC50D","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/3800C50E-6A9A-46B0-9F31-ACF3AAFFC50D/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":"2025-10-17T13:54:23+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"7ABBD05C-D2B2-4E97-B5A8-52627FCD0027","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/7ABBD05C-D2B2-4E97-B5A8-52627FCD0027/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-10-17T21:45:44+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"E4A90C5D-E6B8-4587-9603-8846C699C392","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/E4A90C5D-E6B8-4587-9603-8846C699C392/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":"2025-10-18T18:36:42+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"1534053C-3D62-4C59-A6FB-D404C1E4A596","revision_number":5,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/1534053C-3D62-4C59-A6FB-D404C1E4A596/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":"118030","source_record_sha256":"ba075df8fdafa87e1dd3c2f76048e4fa471a84d48bafd24f379110679981c456","source_url":"https://biology.stackexchange.com/questions/118030/can-genes-overlap","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Can genes overlap?\nSuppose you have a sequence of 130 nucleotides (nt) in a genome. Can there be two different genes in which, for example, the first starts at nt 10 and ends at nt 40 and the second starts at nt 30 and ends at nt 60? (Thus they will include the same section of the genome from nt 30 to nt 40) Or do all genes occupy exclusive sections of a genome?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":118032,"score":13},{"answer_id":118041,"score":4}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":118040,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Looks to me like a <a href=\"https://en.wikipedia.org/wiki/Abies_balsamea\" rel=\"noreferrer\">balsam fir</a> which is native to your area. Wikipedia's description:</p>\n<blockquote>\n<p>Balsam fir is a small to medium-size evergreen tree typically 14–20 metres (46–66 ft) tall, occasionally reaching a height of 27 metres (89 ft). The narrow conic crown consists of dense, dark-green leaves. The bark on young trees is smooth, grey, and with resin blisters (which tend to spray when ruptured), becoming rough and fissured or scaly on old trees. The leaves are flat and needle-like, 15 to 30 mm (5⁄8 to 1+1⁄8 in) long, dark green above often with a small patch of stomata near the tip, and two white stomatal bands below, and a slightly notched tip. They are arranged spirally on the shoot, but with the leaf bases twisted so that the leaves appear to be in two more-or-less horizontal rows on either side of the shoot. The needles become shorter and thicker the higher they are on the tree. The seed cones are erect, 40 to 80 mm (1+1⁄2 to 3+1⁄4 in) long, dark purple, ripening brown and disintegrating to release the winged seeds in September.</p>\n</blockquote>\n<p>Some other pages with images like yours:</p>\n<p><a href=\"https://landscapeplants.oregonstate.edu/plants/abies-balsamea\" rel=\"noreferrer\">https://landscapeplants.oregonstate.edu/plants/abies-balsamea</a></p>\n<p><a href=\"https://gobotany.nativeplanttrust.org/species/abies/balsamea/\" rel=\"noreferrer\">https://gobotany.nativeplanttrust.org/species/abies/balsamea/</a></p>\n<p><a href=\"https://naturalresources.extension.iastate.edu/forestry/iowa_trees/trees/balsam_fir.html\" rel=\"noreferrer\">https://naturalresources.extension.iastate.edu/forestry/iowa_trees/trees/balsam_fir.html</a></p>\n<p>They are popular as Christmas decorations; the maturing cones are characteristically purplish.</p>\n","answer_id":118040,"answer_text":"Looks to me like a balsam fir (https://en.wikipedia.org/wiki/Abies_balsamea) which is native to your area. Wikipedia's description:\n\n\n\n\n\n\n\nBalsam fir is a small to medium-size evergreen tree typically 14–20 metres (46–66 ft) tall, occasionally reaching a height of 27 metres (89 ft). The narrow conic crown consists of dense, dark-green leaves. The bark on young trees is smooth, grey, and with resin blisters (which tend to spray when ruptured), becoming rough and fissured or scaly on old trees. The leaves are flat and needle-like, 15 to 30 mm (5⁄8 to 1+1⁄8 in) long, dark green above often with a small patch of stomata near the tip, and two white stomatal bands below, and a slightly notched tip. They are arranged spirally on the shoot, but with the leaf bases twisted so that the leaves appear to be in two more-or-less horizontal rows on either side of the shoot. The needles become shorter and thicker the higher they are on the tree. The seed cones are erect, 40 to 80 mm (1+1⁄2 to 3+1⁄4 in) long, dark purple, ripening brown and disintegrating to release the winged seeds in September.\n\n\n\n\n\n\n\nSome other pages with images like yours:\n\n\n\n\nhttps://landscapeplants.oregonstate.edu/plants/abies-balsamea (https://landscapeplants.oregonstate.edu/plants/abies-balsamea)\n\n\n\n\nhttps://gobotany.nativeplanttrust.org/species/abies/balsamea/ (https://gobotany.nativeplanttrust.org/species/abies/balsamea/)\n\n\n\n\nhttps://naturalresources.extension.iastate.edu/forestry/iowa_trees/trees/balsam_fir.html (https://naturalresources.extension.iastate.edu/forestry/iowa_trees/trees/balsam_fir.html)\n\n\n\n\nThey are popular as Christmas decorations; the maturing cones are characteristically purplish.","answer_url":"https://biology.stackexchange.com/a/118040","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2025-10-20T19:38:58+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":118039,"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":"2025-10-20T19:38:58+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"6C6C87F4-3907-4F49-AA34-E4A88081B195","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/6C6C87F4-3907-4F49-AA34-E4A88081B195/view-source"}],"score":9}],"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":"2025-10-20T16:32:06+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"8AAA4560-D0AC-4B37-9C1A-02E943CC2954","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8AAA4560-D0AC-4B37-9C1A-02E943CC2954/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":"2025-10-20T19:29:38+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"28F1B702-9CC6-499D-8FA6-FB295A79C30E","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/28F1B702-9CC6-499D-8FA6-FB295A79C30E/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2025-10-21T00:33:20+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"CDCA09FC-44D4-4B9E-B89E-73B388D163F5","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/CDCA09FC-44D4-4B9E-B89E-73B388D163F5/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":"2025-10-21T20:47:24+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"2A0BB428-4BB9-438B-84DE-64425A068269","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/2A0BB428-4BB9-438B-84DE-64425A068269/view-source"}],"url":"https://biology.stackexchange.com/questions/118039/coniferous-tree-with-flat-needle-pattern"},{"author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","context_id":"118040","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":"2025-10-20T19:38:58+00:00","raw_file":"raw/codex_api_v1/c1f1c77b4be84acc978369dace8896d84167a5ca52eb6711a00d4b338d7f0104_1790824159864978900_0.json","raw_sha256":"5798821fb87997611f2dd8389abcef2303f9edc567f4cd87a06a697319e695cd","revision_guid":"6C6C87F4-3907-4F49-AA34-E4A88081B195","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/6C6C87F4-3907-4F49-AA34-E4A88081B195/view-source"}],"url":"https://biology.stackexchange.com/a/118040"}],"contexts":[{"context_id":"question","html":"<p>What species of tree is this? Is it a fir?</p>\n<ul>\n<li>Site: The edge of a rocky, elevated clearing</li>\n<li>Location: Near Sharbot Lake, Ontario, Canada</li>\n<li>Mid October, 2025</li>\n<li>Flat needle pattern; approx. 1-inch needles, purple buds</li>\n<li>Unlikely to be ornamental; vacant, unused, rural lot</li>\n</ul>\n<p><a href=\"https://i.sstatic.net/pB12Vv5f.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/pB12Vv5f.jpg\" alt=\"enter image description here\" /></a></p>\n<p><a href=\"https://i.sstatic.net/3GSk0q4l.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/3GSk0q4l.png\" alt=\"enter image description here\" /></a></p>\n<p><a href=\"https://i.sstatic.net/pBF66onf.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/pBF66onf.jpg\" alt=\"enter image description here\" /></a></p>\n<p><a href=\"https://i.sstatic.net/4h7pgbpL.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/4h7pgbpL.jpg\" alt=\"enter image description here\" /></a></p>\n<p><a href=\"https://i.sstatic.net/ElmRokZP.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/ElmRokZP.jpg\" alt=\"enter image description here\" /></a></p>\n<p><a href=\"https://i.sstatic.net/cWKyOPug.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/cWKyOPug.jpg\" alt=\"enter image description here\" /></a></p>\n","text":"What species of tree is this? Is it a fir?\n\n\n\n\n\nSite: The edge of a rocky, elevated clearing\n\n\n\n\nLocation: Near Sharbot Lake, Ontario, Canada\n\n\n\n\nMid October, 2025\n\n\n\n\nFlat needle pattern; approx. 1-inch needles, purple buds\n\n\n\n\nUnlikely to be ornamental; vacant, unused, rural lot\n\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/pB12Vv5f.jpg] (https://i.sstatic.net/pB12Vv5f.jpg)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/3GSk0q4l.png] (https://i.sstatic.net/3GSk0q4l.png)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/pBF66onf.jpg] (https://i.sstatic.net/pBF66onf.jpg)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/4h7pgbpL.jpg] (https://i.sstatic.net/4h7pgbpL.jpg)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/ElmRokZP.jpg] (https://i.sstatic.net/ElmRokZP.jpg)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/cWKyOPug.jpg] (https://i.sstatic.net/cWKyOPug.jpg)"},{"context_id":"118040","html":"<p>Looks to me like a <a href=\"https://en.wikipedia.org/wiki/Abies_balsamea\" rel=\"noreferrer\">balsam fir</a> which is native to your area. Wikipedia's description:</p>\n<blockquote>\n<p>Balsam fir is a small to medium-size evergreen tree typically 14–20 metres (46–66 ft) tall, occasionally reaching a height of 27 metres (89 ft). The narrow conic crown consists of dense, dark-green leaves. The bark on young trees is smooth, grey, and with resin blisters (which tend to spray when ruptured), becoming rough and fissured or scaly on old trees. The leaves are flat and needle-like, 15 to 30 mm (5⁄8 to 1+1⁄8 in) long, dark green above often with a small patch of stomata near the tip, and two white stomatal bands below, and a slightly notched tip. They are arranged spirally on the shoot, but with the leaf bases twisted so that the leaves appear to be in two more-or-less horizontal rows on either side of the shoot. The needles become shorter and thicker the higher they are on the tree. The seed cones are erect, 40 to 80 mm (1+1⁄2 to 3+1⁄4 in) long, dark purple, ripening brown and disintegrating to release the winged seeds in September.</p>\n</blockquote>\n<p>Some other pages with images like yours:</p>\n<p><a href=\"https://landscapeplants.oregonstate.edu/plants/abies-balsamea\" rel=\"noreferrer\">https://landscapeplants.oregonstate.edu/plants/abies-balsamea</a></p>\n<p><a href=\"https://gobotany.nativeplanttrust.org/species/abies/balsamea/\" rel=\"noreferrer\">https://gobotany.nativeplanttrust.org/species/abies/balsamea/</a></p>\n<p><a href=\"https://naturalresources.extension.iastate.edu/forestry/iowa_trees/trees/balsam_fir.html\" rel=\"noreferrer\">https://naturalresources.extension.iastate.edu/forestry/iowa_trees/trees/balsam_fir.html</a></p>\n<p>They are popular as Christmas decorations; the maturing cones are characteristically purplish.</p>\n","text":"Looks to me like a balsam fir (https://en.wikipedia.org/wiki/Abies_balsamea) which is native to your area. Wikipedia's description:\n\n\n\n\n\n\n\nBalsam fir is a small to medium-size evergreen tree typically 14–20 metres (46–66 ft) tall, occasionally reaching a height of 27 metres (89 ft). The narrow conic crown consists of dense, dark-green leaves. The bark on young trees is smooth, grey, and with resin blisters (which tend to spray when ruptured), becoming rough and fissured or scaly on old trees. The leaves are flat and needle-like, 15 to 30 mm (5⁄8 to 1+1⁄8 in) long, dark green above often with a small patch of stomata near the tip, and two white stomatal bands below, and a slightly notched tip. They are arranged spirally on the shoot, but with the leaf bases twisted so that the leaves appear to be in two more-or-less horizontal rows on either side of the shoot. The needles become shorter and thicker the higher they are on the tree. The seed cones are erect, 40 to 80 mm (1+1⁄2 to 3+1⁄4 in) long, dark purple, ripening brown and disintegrating to release the winged seeds in September.\n\n\n\n\n\n\n\nSome other pages with images like yours:\n\n\n\n\nhttps://landscapeplants.oregonstate.edu/plants/abies-balsamea (https://landscapeplants.oregonstate.edu/plants/abies-balsamea)\n\n\n\n\nhttps://gobotany.nativeplanttrust.org/species/abies/balsamea/ (https://gobotany.nativeplanttrust.org/species/abies/balsamea/)\n\n\n\n\nhttps://naturalresources.extension.iastate.edu/forestry/iowa_trees/trees/balsam_fir.html (https://naturalresources.extension.iastate.edu/forestry/iowa_trees/trees/balsam_fir.html)\n\n\n\n\nThey are popular as Christmas decorations; the maturing cones are characteristically purplish."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Abies_balsamea","https://gobotany.nativeplanttrust.org/species/abies/balsamea/","https://i.sstatic.net/3GSk0q4l.png","https://i.sstatic.net/4h7pgbpL.jpg","https://i.sstatic.net/ElmRokZP.jpg","https://i.sstatic.net/cWKyOPug.jpg","https://i.sstatic.net/pB12Vv5f.jpg","https://i.sstatic.net/pBF66onf.jpg","https://landscapeplants.oregonstate.edu/plants/abies-balsamea","https://naturalresources.extension.iastate.edu/forestry/iowa_trees/trees/balsam_fir.html"],"ground_truth_type":"metadata_grounded","group_id":"bb5d0bde5007174e9d84693d23f9e9de002bbfb739a7fa7aaa825321f79f308a","hard_case_family":["multiple_sources","citation_heavy"],"id":"RHM-f84bb5355af8d6b8f0fe5b0c","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":"Coniferous tree with flat needle pattern\nWhat species of tree is this? Is it a fir?\n\n\n\n\n\nSite: The edge of a rocky, elevated clearing\n\n\n\n\nLocation: Near Sharbot Lake, Ontario, Canada\n\n\n\n\nMid October, 2025\n\n\n\n\nFlat needle pattern; approx. 1-inch needles, purple buds\n\n\n\n\nUnlikely to be ornamental; vacant, unused, rural lot\n\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/pB12Vv5f.jpg] (https://i.sstatic.net/pB12Vv5f.jpg)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/3GSk0q4l.png] (https://i.sstatic.net/3GSk0q4l.png)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/pBF66onf.jpg] (https://i.sstatic.net/pBF66onf.jpg)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/4h7pgbpL.jpg] (https://i.sstatic.net/4h7pgbpL.jpg)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/ElmRokZP.jpg] (https://i.sstatic.net/ElmRokZP.jpg)\n\n\n\n\n[image: enter image description here; source: https://i.sstatic.net/cWKyOPug.jpg] (https://i.sstatic.net/cWKyOPug.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":118040,"score":9}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I don't totally understand how you're phrasing your questions. After skimming the second link this is how I would explain it. (I recommend if youre having trouble picturing this buy one of these <a href=\"https://www.target.com/p/swimways-elite-spring-float-papasan-pool-lounger/-/A-92245283#lnk=sametab\" rel=\"nofollow noreferrer\">https://www.target.com/p/swimways-elite-spring-float-papasan-pool-lounger/-/A-92245283#lnk=sametab</a> its a good representation of a biconcave disc that can be deformed)</p>\n<p>The membrane resists planar stretching and compression. &quot;In plane compression and/or stretching deforms both leaflets evenly&quot; so when they are flat you would see being pulled from both ends or compressed at both ends would stretch and compress both leaflets together. When you are bending the energetics is different, the bottom leaflet is undergoing compression because it has to occupy less volume. Meaning it is going to want to go back to its more stable flat conformation.</p>\n<p>The lipid bilayer on its own doesn't do anything to resist forces pulling or pushing on it out of the plane, the resistance by bending is very small and cant make a big enough vector to completely resist and applies force which is where spectrin comes in to pull the membrane back into place.</p>\n<p>The fish net analogy I would imagine is appropriate, and this is why I think you should get the pool floaty especially if you live somewhere warm, The shearing forces deform the plane if you pull on the floaty you will see the inner net become more taught, this is analogous to spectrin resisting a shearing force, it pulls everything in towards the centre, if you pulled on just the fish net it would again pull everything to the centre trying to get back to its biconcave disc shape. I might be miffing the  explanation a little  but this is how I am thinking of it.</p>\n","answer_id":119182,"answer_text":"I don't totally understand how you're phrasing your questions. After skimming the second link this is how I would explain it. (I recommend if youre having trouble picturing this buy one of these https://www.target.com/p/swimways-elite-spring-float-papasan-pool-lounger/-/A-92245283#lnk=sametab (https://www.target.com/p/swimways-elite-spring-float-papasan-pool-lounger/-/A-92245283#lnk=sametab) its a good representation of a biconcave disc that can be deformed)\n\n\n\n\nThe membrane resists planar stretching and compression. \"In plane compression and/or stretching deforms both leaflets evenly\" so when they are flat you would see being pulled from both ends or compressed at both ends would stretch and compress both leaflets together. When you are bending the energetics is different, the bottom leaflet is undergoing compression because it has to occupy less volume. Meaning it is going to want to go back to its more stable flat conformation.\n\n\n\n\nThe lipid bilayer on its own doesn't do anything to resist forces pulling or pushing on it out of the plane, the resistance by bending is very small and cant make a big enough vector to completely resist and applies force which is where spectrin comes in to pull the membrane back into place.\n\n\n\n\nThe fish net analogy I would imagine is appropriate, and this is why I think you should get the pool floaty especially if you live somewhere warm, The shearing forces deform the plane if you pull on the floaty you will see the inner net become more taught, this is analogous to spectrin resisting a shearing force, it pulls everything in towards the centre, if you pulled on just the fish net it would again pull everything to the centre trying to get back to its biconcave disc shape. I might be miffing the  explanation a little  but this is how I am thinking of it.","answer_url":"https://biology.stackexchange.com/a/119182","author":"John Saunders","author_url":"https://biology.stackexchange.com/users/115927/john-saunders","content_license":"CC BY-SA 4.0","created_at":"2025-12-14T22:34:04+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":118180,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"John Saunders","profile_url":"https://biology.stackexchange.com/users/115927/john-saunders","user_type":"registered"},"created_at":"2025-12-14T22:34:04+00:00","raw_file":"raw/codex_api_v1/758108496d7e56a3cf6614dffa5104a8870c129dcf518abbe860f55a089c6a12_1790824171594894000_0.json","raw_sha256":"5e5d792a6c484fda48193064d730da32774df13fc12222582feb4605d4472664","revision_guid":"DE1222A2-6E9C-4905-9206-EBBEFA9FE1BA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DE1222A2-6E9C-4905-9206-EBBEFA9FE1BA/view-source"}],"score":3}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Gene-ius","author_url":"https://biology.stackexchange.com/users/114588/gene-ius","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Gene-ius","profile_url":"https://biology.stackexchange.com/users/114588/gene-ius","user_type":"registered"},"created_at":"2025-12-12T14:02:54+00:00","raw_file":"raw/codex_api_v1/758108496d7e56a3cf6614dffa5104a8870c129dcf518abbe860f55a089c6a12_1790824171594894000_0.json","raw_sha256":"5e5d792a6c484fda48193064d730da32774df13fc12222582feb4605d4472664","revision_guid":"0C98BAC9-BF6F-4A56-9439-BC19BFF87F01","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0C98BAC9-BF6F-4A56-9439-BC19BFF87F01/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":"2025-12-13T17:24:37+00:00","raw_file":"raw/codex_api_v1/758108496d7e56a3cf6614dffa5104a8870c129dcf518abbe860f55a089c6a12_1790824171594894000_0.json","raw_sha256":"5e5d792a6c484fda48193064d730da32774df13fc12222582feb4605d4472664","revision_guid":"B19BDEE5-F87D-4E57-B8C3-34FC94A6CA0C","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B19BDEE5-F87D-4E57-B8C3-34FC94A6CA0C/view-source"}],"url":"https://biology.stackexchange.com/questions/118180/how-do-plasma-membrane-and-spectrin-net-contribute-to-bending-shearing-resista"},{"author":"John Saunders","author_url":"https://biology.stackexchange.com/users/115927/john-saunders","content_license":"CC BY-SA 4.0","context_id":"119182","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"John Saunders","profile_url":"https://biology.stackexchange.com/users/115927/john-saunders","user_type":"registered"},"created_at":"2025-12-14T22:34:04+00:00","raw_file":"raw/codex_api_v1/758108496d7e56a3cf6614dffa5104a8870c129dcf518abbe860f55a089c6a12_1790824171594894000_0.json","raw_sha256":"5e5d792a6c484fda48193064d730da32774df13fc12222582feb4605d4472664","revision_guid":"DE1222A2-6E9C-4905-9206-EBBEFA9FE1BA","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DE1222A2-6E9C-4905-9206-EBBEFA9FE1BA/view-source"}],"url":"https://biology.stackexchange.com/a/119182"}],"contexts":[{"context_id":"question","html":"<p>I was trying to understand the pathology of Hereditary Spherocytosis (from Robbins).</p>\n<p>So obviously it led to me trying to understand the contribution of cytoskeleton and memberane to RBCs shear and bending stiffness.</p>\n<p>After reading a few articles like these\n<a href=\"https://www.researchgate.net/publication/303026350_Measuring_shape_fluctuations_in_biological_membranes\" rel=\"nofollow noreferrer\">Measuring shape fluctuations in biological membranes</a><br>\n<a href=\"https://www.frontiersin.org/journals/physiology/articles/10.3389/fphys.2022.953257/full\" rel=\"nofollow noreferrer\">Structural and mechanical properties of the red blood cell’s cytoplasmic membrane seen through the lens of biophysics</a></p>\n<p>I understand that plasma membrane contributes to bending resistance and spectrin network to shearing resistance.</p>\n<p>I don't have sufficient knowledge of biophysics(not my field) and most of the papers used a lot more physics than just high school level so I couldn't understand it. <strong>I am looking for an intuitive explanation for the mechanism of RBC stability/deformability</strong></p>\n<h2>Questions</h2>\n<ol>\n<li>Lipid bilayer is said to resist stretching(hydrophobic tails exposed) and conpression(hydrophilic and hydrophobic parts come closer). <strong>Why does it have high bending resistance?</strong></li>\n<li>Lipid bilayer is said to have zero shearing resistance. I can see a rectangular sheet of lipid bilayer slide on each other easily. <strong>But RBC is biconcave disc, so upper leaflet can slide on lower leaflet but at the edges(where membrane bends), wouldn't there be compression/stretching which it resists leading ultimately to shear resistance?</strong></li>\n<li>Spectrin network has no bending resistance but high shear resistance. Some call it analogus to a fishing net and some to an iron cage. <strong>If it like an iron cage, it should resist both bending and shearing.  If it's like a fishing net, it should have neither?</strong></li>\n</ol>\n","text":"I was trying to understand the pathology of Hereditary Spherocytosis (from Robbins).\n\n\n\n\nSo obviously it led to me trying to understand the contribution of cytoskeleton and memberane to RBCs shear and bending stiffness.\n\n\n\n\nAfter reading a few articles like these\nMeasuring shape fluctuations in biological membranes (https://www.researchgate.net/publication/303026350_Measuring_shape_fluctuations_in_biological_membranes)\n\nStructural and mechanical properties of the red blood cell’s cytoplasmic membrane seen through the lens of biophysics (https://www.frontiersin.org/journals/physiology/articles/10.3389/fphys.2022.953257/full)\n\n\n\n\nI understand that plasma membrane contributes to bending resistance and spectrin network to shearing resistance.\n\n\n\n\nI don't have sufficient knowledge of biophysics(not my field) and most of the papers used a lot more physics than just high school level so I couldn't understand it. I am looking for an intuitive explanation for the mechanism of RBC stability/deformability\n\n\n\n\nQuestions\n\n\n\n\n\nLipid bilayer is said to resist stretching(hydrophobic tails exposed) and conpression(hydrophilic and hydrophobic parts come closer). Why does it have high bending resistance?\n\n\n\n\nLipid bilayer is said to have zero shearing resistance. I can see a rectangular sheet of lipid bilayer slide on each other easily. But RBC is biconcave disc, so upper leaflet can slide on lower leaflet but at the edges(where membrane bends), wouldn't there be compression/stretching which it resists leading ultimately to shear resistance?\n\n\n\n\nSpectrin network has no bending resistance but high shear resistance. Some call it analogus to a fishing net and some to an iron cage. If it like an iron cage, it should resist both bending and shearing.  If it's like a fishing net, it should have neither?"},{"context_id":"119182","html":"<p>I don't totally understand how you're phrasing your questions. After skimming the second link this is how I would explain it. (I recommend if youre having trouble picturing this buy one of these <a href=\"https://www.target.com/p/swimways-elite-spring-float-papasan-pool-lounger/-/A-92245283#lnk=sametab\" rel=\"nofollow noreferrer\">https://www.target.com/p/swimways-elite-spring-float-papasan-pool-lounger/-/A-92245283#lnk=sametab</a> its a good representation of a biconcave disc that can be deformed)</p>\n<p>The membrane resists planar stretching and compression. &quot;In plane compression and/or stretching deforms both leaflets evenly&quot; so when they are flat you would see being pulled from both ends or compressed at both ends would stretch and compress both leaflets together. When you are bending the energetics is different, the bottom leaflet is undergoing compression because it has to occupy less volume. Meaning it is going to want to go back to its more stable flat conformation.</p>\n<p>The lipid bilayer on its own doesn't do anything to resist forces pulling or pushing on it out of the plane, the resistance by bending is very small and cant make a big enough vector to completely resist and applies force which is where spectrin comes in to pull the membrane back into place.</p>\n<p>The fish net analogy I would imagine is appropriate, and this is why I think you should get the pool floaty especially if you live somewhere warm, The shearing forces deform the plane if you pull on the floaty you will see the inner net become more taught, this is analogous to spectrin resisting a shearing force, it pulls everything in towards the centre, if you pulled on just the fish net it would again pull everything to the centre trying to get back to its biconcave disc shape. I might be miffing the  explanation a little  but this is how I am thinking of it.</p>\n","text":"I don't totally understand how you're phrasing your questions. After skimming the second link this is how I would explain it. (I recommend if youre having trouble picturing this buy one of these https://www.target.com/p/swimways-elite-spring-float-papasan-pool-lounger/-/A-92245283#lnk=sametab (https://www.target.com/p/swimways-elite-spring-float-papasan-pool-lounger/-/A-92245283#lnk=sametab) its a good representation of a biconcave disc that can be deformed)\n\n\n\n\nThe membrane resists planar stretching and compression. \"In plane compression and/or stretching deforms both leaflets evenly\" so when they are flat you would see being pulled from both ends or compressed at both ends would stretch and compress both leaflets together. When you are bending the energetics is different, the bottom leaflet is undergoing compression because it has to occupy less volume. Meaning it is going to want to go back to its more stable flat conformation.\n\n\n\n\nThe lipid bilayer on its own doesn't do anything to resist forces pulling or pushing on it out of the plane, the resistance by bending is very small and cant make a big enough vector to completely resist and applies force which is where spectrin comes in to pull the membrane back into place.\n\n\n\n\nThe fish net analogy I would imagine is appropriate, and this is why I think you should get the pool floaty especially if you live somewhere warm, The shearing forces deform the plane if you pull on the floaty you will see the inner net become more taught, this is analogous to spectrin resisting a shearing force, it pulls everything in towards the centre, if you pulled on just the fish net it would again pull everything to the centre trying to get back to its biconcave disc shape. I might be miffing the  explanation a little  but this is how I am thinking of it."}],"domain":"biology","external_citations":["https://www.frontiersin.org/journals/physiology/articles/10.3389/fphys.2022.953257/full","https://www.researchgate.net/publication/303026350_Measuring_shape_fluctuations_in_biological_membranes","https://www.target.com/p/swimways-elite-spring-float-papasan-pool-lounger/-/A-92245283#lnk=sametab"],"ground_truth_type":"metadata_grounded","group_id":"5076092ba4f49b2225bd2b51e39d7d95ea3c8e38d30a9b61629e52eca8f53ed1","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-883348df8b7e6fea426ff3df","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":"Gene-ius","profile_url":"https://biology.stackexchange.com/users/114588/gene-ius","user_type":"registered"},"created_at":"2025-12-12T14:02:54+00:00","raw_file":"raw/codex_api_v1/758108496d7e56a3cf6614dffa5104a8870c129dcf518abbe860f55a089c6a12_1790824171594894000_0.json","raw_sha256":"5e5d792a6c484fda48193064d730da32774df13fc12222582feb4605d4472664","revision_guid":"0C98BAC9-BF6F-4A56-9439-BC19BFF87F01","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/0C98BAC9-BF6F-4A56-9439-BC19BFF87F01/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":"2025-12-13T17:24:37+00:00","raw_file":"raw/codex_api_v1/758108496d7e56a3cf6614dffa5104a8870c129dcf518abbe860f55a089c6a12_1790824171594894000_0.json","raw_sha256":"5e5d792a6c484fda48193064d730da32774df13fc12222582feb4605d4472664","revision_guid":"B19BDEE5-F87D-4E57-B8C3-34FC94A6CA0C","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B19BDEE5-F87D-4E57-B8C3-34FC94A6CA0C/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":"118180","source_record_sha256":"4ffd34f2c5629e803a03e3a7c96267be9a22be69dcfb29ab07f5070926c69b76","source_url":"https://biology.stackexchange.com/questions/118180/how-do-plasma-membrane-and-spectrin-net-contribute-to-bending-shearing-resista","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How do plasma membrane and spectrin net contribute to bending & shearing resistance of Red Blood Cells (intuitive explanation)?\nI was trying to understand the pathology of Hereditary Spherocytosis (from Robbins).\n\n\n\n\nSo obviously it led to me trying to understand the contribution of cytoskeleton and memberane to RBCs shear and bending stiffness.\n\n\n\n\nAfter reading a few articles like these\nMeasuring shape fluctuations in biological membranes (https://www.researchgate.net/publication/303026350_Measuring_shape_fluctuations_in_biological_membranes)\n\nStructural and mechanical properties of the red blood cell’s cytoplasmic membrane seen through the lens of biophysics (https://www.frontiersin.org/journals/physiology/articles/10.3389/fphys.2022.953257/full)\n\n\n\n\nI understand that plasma membrane contributes to bending resistance and spectrin network to shearing resistance.\n\n\n\n\nI don't have sufficient knowledge of biophysics(not my field) and most of the papers used a lot more physics than just high school level so I couldn't understand it. I am looking for an intuitive explanation for the mechanism of RBC stability/deformability\n\n\n\n\nQuestions\n\n\n\n\n\nLipid bilayer is said to resist stretching(hydrophobic tails exposed) and conpression(hydrophilic and hydrophobic parts come closer). Why does it have high bending resistance?\n\n\n\n\nLipid bilayer is said to have zero shearing resistance. I can see a rectangular sheet of lipid bilayer slide on each other easily. But RBC is biconcave disc, so upper leaflet can slide on lower leaflet but at the edges(where membrane bends), wouldn't there be compression/stretching which it resists leading ultimately to shear resistance?\n\n\n\n\nSpectrin network has no bending resistance but high shear resistance. Some call it analogus to a fishing net and some to an iron cage. If it like an iron cage, it should resist both bending and shearing.  If it's like a fishing net, it should have neither?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":119182,"score":3}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":119282,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>This is a quite relevant question in breeding in general and has to do with &quot;response to selection&quot;. This is a part of quantitative genetics that tries to mathematically explain how do populations change when they are selected upon. The most basic way to understand this is the &quot;breeders equation&quot;:</p>\n<p><span class=\"math-container\">$R = h^2 \\times S$</span></p>\n<p>Where:</p>\n<ul>\n<li><span class=\"math-container\">$R$</span> is response to selection (expected new mean)</li>\n<li><span class=\"math-container\">$h^2$</span> is heritability (in your example this is 1, i.e. the observed phenotypic variation is totally determined by genetic variation)</li>\n<li><span class=\"math-container\">$S$</span> is selection differential (in your case this is 190cm - 170cm)</li>\n</ul>\n<p>This equation predicts the new population mean given the <a href=\"https://vsni.co.uk/narrow-sense-heritability/\" rel=\"nofollow noreferrer\">(narrow sense) heritability</a>. In essence, it just means that the new population mean is a result of the selected parents AND how genetic your trait is. In your example, because heritability is 1 (i.e. no other effects but a polygenic trait determine the phenotype), your <strong>new population mean should be 190cm (not 180cm).</strong></p>\n<p>But your question has more to do about &quot;stability&quot; of the new mean. This has two aspects to it: the stability of the mean across generations, and the final <strong>variance</strong> of your new population.</p>\n<p>Firstly, the mean is &quot;stable&quot; from gen 1, meaning that if you would randomly reproduce the individuals of the tall population with 190cm of average height; you would get a new population with 190cm of average height.</p>\n<p>Second, the population variability is reduced every time you select. This is because &quot;bad alelles&quot; are being eliminated through selection, thus less alleles means less variation. The exact formulas that dictate this reduction are a bit convoluted, although this is the main shape they take:</p>\n<p><span class=\"math-container\">$\\sigma_{A1} = (1 - k\\times h^2) \\sigma_{A0}$</span></p>\n<p>Where <span class=\"math-container\">$k$</span> is a normalised selection intensity index, and <span class=\"math-container\">$\\sigma_{A0}, \\sigma_{A1}$</span> are the original and generation 1 genetic variances. In essence this just shows that the harder you select the more variance you loose.</p>\n<p>To sum up, the mean is stable from generation 1. Whether your population will still vary depends on how strongly you have selected. In any case, very strong selection leads to all sorts of issues, especially in animals (because inbreeding is bad). Complex topic!</p>\n<p>Some resources for you:</p>\n<ul>\n<li><a href=\"https://www.edge.org/response-detail/27199\" rel=\"nofollow noreferrer\">Easy understanding of breeders equation</a></li>\n<li><a href=\"https://iastate.pressbooks.pub/quantitativegenetics/chapter/selection-response/\" rel=\"nofollow noreferrer\">Complete Response to Selection theory (pretty dense)</a></li>\n<li>Check the intro of this article for a good explanation of <a href=\"https://www.nature.com/articles/s41437-021-00411-2\" rel=\"nofollow noreferrer\">reduction of genetic variance due to selection</a></li>\n</ul>\n","answer_id":119282,"answer_text":"This is a quite relevant question in breeding in general and has to do with \"response to selection\". This is a part of quantitative genetics that tries to mathematically explain how do populations change when they are selected upon. The most basic way to understand this is the \"breeders equation\":\n\n\n\n\n$R = h^2 \\times S$\n\n\n\n\nWhere:\n\n\n\n\n\n$R$ is response to selection (expected new mean)\n\n\n\n\n$h^2$ is heritability (in your example this is 1, i.e. the observed phenotypic variation is totally determined by genetic variation)\n\n\n\n\n$S$ is selection differential (in your case this is 190cm - 170cm)\n\n\n\n\n\nThis equation predicts the new population mean given the (narrow sense) heritability (https://vsni.co.uk/narrow-sense-heritability/). In essence, it just means that the new population mean is a result of the selected parents AND how genetic your trait is. In your example, because heritability is 1 (i.e. no other effects but a polygenic trait determine the phenotype), your new population mean should be 190cm (not 180cm).\n\n\n\n\nBut your question has more to do about \"stability\" of the new mean. This has two aspects to it: the stability of the mean across generations, and the final variance of your new population.\n\n\n\n\nFirstly, the mean is \"stable\" from gen 1, meaning that if you would randomly reproduce the individuals of the tall population with 190cm of average height; you would get a new population with 190cm of average height.\n\n\n\n\nSecond, the population variability is reduced every time you select. This is because \"bad alelles\" are being eliminated through selection, thus less alleles means less variation. The exact formulas that dictate this reduction are a bit convoluted, although this is the main shape they take:\n\n\n\n\n$\\sigma_{A1} = (1 - k\\times h^2) \\sigma_{A0}$\n\n\n\n\nWhere $k$ is a normalised selection intensity index, and $\\sigma_{A0}, \\sigma_{A1}$ are the original and generation 1 genetic variances. In essence this just shows that the harder you select the more variance you loose.\n\n\n\n\nTo sum up, the mean is stable from generation 1. Whether your population will still vary depends on how strongly you have selected. In any case, very strong selection leads to all sorts of issues, especially in animals (because inbreeding is bad). Complex topic!\n\n\n\n\nSome resources for you:\n\n\n\n\n\nEasy understanding of breeders equation (https://www.edge.org/response-detail/27199)\n\n\n\n\nComplete Response to Selection theory (pretty dense) (https://iastate.pressbooks.pub/quantitativegenetics/chapter/selection-response/)\n\n\n\n\nCheck the intro of this article for a good explanation of reduction of genetic variance due to selection (https://www.nature.com/articles/s41437-021-00411-2)","answer_url":"https://biology.stackexchange.com/a/119282","author":"Athe","author_url":"https://biology.stackexchange.com/users/17385/athe","content_license":"CC BY-SA 4.0","created_at":"2026-01-26T10:00:49+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":119273,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Athe","profile_url":"https://biology.stackexchange.com/users/17385/athe","user_type":"registered"},"created_at":"2026-01-26T10:00:49+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"582C5091-F80B-4986-930A-8C03DD081447","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/582C5091-F80B-4986-930A-8C03DD081447/view-source"}],"score":3},{"answer_html":"<p>Assuming there isn't any environmental influence from the parents and simple non-interacting traits, all you have is regression to the mean, then it only takes 1 generation.</p>\n<p>But, your story setup is a bit weird if &quot;environment for each generation is the same&quot; is taken too literally, such that all of the 10 cm SD is genetic and there is no environmental variation. If there's literally no environmental variation, there is no &quot;noise&quot;, and there is no regression to the mean; Athe's answer assumes this. I'll instead assume that what you meant is that the <em>extent of environmental variation (noise) is constant from generation to generation and is random</em>, rather than that the environmental variation is zero.</p>\n<p><strong>Regression to the mean is a feature of selection bias on <em>noise in the data</em>.</strong> Consider a population with mean height 170 cm, no genetic variation, but some environmental variation resulting in SD 10 cm.</p>\n<p>If you only breed individuals that are &gt;190cm (that is, in the extreme of height from this population), the next generation will still have mean 170 cm and SD 10 cm.</p>\n<p>Remember, there's no genetic variation in this scenario; individuals that are taller than the mean are only taller by random chance. That's why you get regression to the mean: you have a bias (you chose from the tallest individuals) that's not based on anything heritable.</p>\n<p>The same is true if part of the difference is heritable and part is not.</p>\n<p>The problem a breeder faces is not taking multiple generations for regression to the mean to end, the problem is <em>sample size</em>. If you breed two individuals and get 4 offspring, your confidence interval is going to be approximately <span class=\"math-container\">$+/- \\{\\frac{2 \\times 10cm}{\\sqrt{4}}\\} = +/- 10 cm$</span> from whatever you estimate. So, if you select some 190 cm individuals, who really have &quot;180 cm&quot; of genetic height (that is, if you breed them and their offspring to an infinite population you'd get to a mean of 180 cm) and the other 10 cm was noise, the population mean of their offspring will be 180 cm, but in a finite sample sometimes you'll estimate 175 or 185 cm.</p>\n<p>In summary, repeating: <strong>regression to the mean is a feature of selection bias on <em>noise in the data</em>.</strong> - therefore, if the 'noise' is independent generation to generation, then noise in one generation can't influence the next, so there's no further for the mean to regress.</p>\n","answer_id":119283,"answer_text":"Assuming there isn't any environmental influence from the parents and simple non-interacting traits, all you have is regression to the mean, then it only takes 1 generation.\n\n\n\n\nBut, your story setup is a bit weird if \"environment for each generation is the same\" is taken too literally, such that all of the 10 cm SD is genetic and there is no environmental variation. If there's literally no environmental variation, there is no \"noise\", and there is no regression to the mean; Athe's answer assumes this. I'll instead assume that what you meant is that the extent of environmental variation (noise) is constant from generation to generation and is random, rather than that the environmental variation is zero.\n\n\n\n\nRegression to the mean is a feature of selection bias on noise in the data. Consider a population with mean height 170 cm, no genetic variation, but some environmental variation resulting in SD 10 cm.\n\n\n\n\nIf you only breed individuals that are >190cm (that is, in the extreme of height from this population), the next generation will still have mean 170 cm and SD 10 cm.\n\n\n\n\nRemember, there's no genetic variation in this scenario; individuals that are taller than the mean are only taller by random chance. That's why you get regression to the mean: you have a bias (you chose from the tallest individuals) that's not based on anything heritable.\n\n\n\n\nThe same is true if part of the difference is heritable and part is not.\n\n\n\n\nThe problem a breeder faces is not taking multiple generations for regression to the mean to end, the problem is sample size. If you breed two individuals and get 4 offspring, your confidence interval is going to be approximately $+/- \\{\\frac{2 \\times 10cm}{\\sqrt{4}}\\} = +/- 10 cm$ from whatever you estimate. So, if you select some 190 cm individuals, who really have \"180 cm\" of genetic height (that is, if you breed them and their offspring to an infinite population you'd get to a mean of 180 cm) and the other 10 cm was noise, the population mean of their offspring will be 180 cm, but in a finite sample sometimes you'll estimate 175 or 185 cm.\n\n\n\n\nIn summary, repeating: regression to the mean is a feature of selection bias on noise in the data. - therefore, if the 'noise' is independent generation to generation, then noise in one generation can't influence the next, so there's no further for the mean to regress.","answer_url":"https://biology.stackexchange.com/a/119283","author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","created_at":"2026-01-26T15:09:14+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":119273,"revision_attribution":[{"content_license":"CC BY-SA 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4.0","contributor":{"display_name":"Athe","profile_url":"https://biology.stackexchange.com/users/17385/athe","user_type":"registered"},"created_at":"2026-01-26T10:00:49+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"582C5091-F80B-4986-930A-8C03DD081447","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/582C5091-F80B-4986-930A-8C03DD081447/view-source"}],"url":"https://biology.stackexchange.com/a/119282"},{"author":"Bryan Krause","author_url":"https://biology.stackexchange.com/users/27148/bryan-krause","content_license":"CC BY-SA 4.0","context_id":"119283","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":"2026-01-26T15:09:14+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"B5D7B6BC-59B1-4DC9-920D-6BBA3C50C2B7","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B5D7B6BC-59B1-4DC9-920D-6BBA3C50C2B7/view-source"},{"content_license":"CC BY-SA 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and the postulated <strong>std of height is 10cm</strong>. Background assumption: The environment for each generation is the same, there are no famines, nutrition stays the same, no endocrinal changes like difference in exposure to certain hormones, etc.</p>\n<p>Now you take those with height <strong>exactly</strong> above 2stds above the mean (height 190cm) and let them mingle. Call these individuals part of generation 1. Their offspring, the second generation, will have a mean somewhere in between 170cm and 190cm, let's say 180cm. Is this new mean in generation 2 already stable, i.e. would the offspring of parents taken from this second generation with mean 180cm have a mean of 180cm as well or would the regression to the mean continue to the mean of the base population, which was 100? In other words, after how many generations of selective breeding can the breeder be sure that he has achieved a new mean for the relevant trait?</p>\n","text":"Take any polygenic trait whose phenotypic expression in todays first world countries mostly depends on genetics, e.g. height.\n\n\n\n\nExample: Base population has mean height of 170cm in both men and women (Yes, I know this is not true but I want to keep it simple) and the postulated std of height is 10cm. Background assumption: The environment for each generation is the same, there are no famines, nutrition stays the same, no endocrinal changes like difference in exposure to certain hormones, etc.\n\n\n\n\nNow you take those with height exactly above 2stds above the mean (height 190cm) and let them mingle. Call these individuals part of generation 1. Their offspring, the second generation, will have a mean somewhere in between 170cm and 190cm, let's say 180cm. Is this new mean in generation 2 already stable, i.e. would the offspring of parents taken from this second generation with mean 180cm have a mean of 180cm as well or would the regression to the mean continue to the mean of the base population, which was 100? In other words, after how many generations of selective breeding can the breeder be sure that he has achieved a new mean for the relevant trait?"},{"context_id":"119282","html":"<p>This is a quite relevant question in breeding in general and has to do with &quot;response to selection&quot;. This is a part of quantitative genetics that tries to mathematically explain how do populations change when they are selected upon. The most basic way to understand this is the &quot;breeders equation&quot;:</p>\n<p><span class=\"math-container\">$R = h^2 \\times S$</span></p>\n<p>Where:</p>\n<ul>\n<li><span class=\"math-container\">$R$</span> is response to selection (expected new mean)</li>\n<li><span class=\"math-container\">$h^2$</span> is heritability (in your example this is 1, i.e. the observed phenotypic variation is totally determined by genetic variation)</li>\n<li><span class=\"math-container\">$S$</span> is selection differential (in your case this is 190cm - 170cm)</li>\n</ul>\n<p>This equation predicts the new population mean given the <a href=\"https://vsni.co.uk/narrow-sense-heritability/\" rel=\"nofollow noreferrer\">(narrow sense) heritability</a>. In essence, it just means that the new population mean is a result of the selected parents AND how genetic your trait is. In your example, because heritability is 1 (i.e. no other effects but a polygenic trait determine the phenotype), your <strong>new population mean should be 190cm (not 180cm).</strong></p>\n<p>But your question has more to do about &quot;stability&quot; of the new mean. This has two aspects to it: the stability of the mean across generations, and the final <strong>variance</strong> of your new population.</p>\n<p>Firstly, the mean is &quot;stable&quot; from gen 1, meaning that if you would randomly reproduce the individuals of the tall population with 190cm of average height; you would get a new population with 190cm of average height.</p>\n<p>Second, the population variability is reduced every time you select. This is because &quot;bad alelles&quot; are being eliminated through selection, thus less alleles means less variation. The exact formulas that dictate this reduction are a bit convoluted, although this is the main shape they take:</p>\n<p><span class=\"math-container\">$\\sigma_{A1} = (1 - k\\times h^2) \\sigma_{A0}$</span></p>\n<p>Where <span class=\"math-container\">$k$</span> is a normalised selection intensity index, and <span class=\"math-container\">$\\sigma_{A0}, \\sigma_{A1}$</span> are the original and generation 1 genetic variances. In essence this just shows that the harder you select the more variance you loose.</p>\n<p>To sum up, the mean is stable from generation 1. Whether your population will still vary depends on how strongly you have selected. In any case, very strong selection leads to all sorts of issues, especially in animals (because inbreeding is bad). Complex topic!</p>\n<p>Some resources for you:</p>\n<ul>\n<li><a href=\"https://www.edge.org/response-detail/27199\" rel=\"nofollow noreferrer\">Easy understanding of breeders equation</a></li>\n<li><a href=\"https://iastate.pressbooks.pub/quantitativegenetics/chapter/selection-response/\" rel=\"nofollow noreferrer\">Complete Response to Selection theory (pretty dense)</a></li>\n<li>Check the intro of this article for a good explanation of <a href=\"https://www.nature.com/articles/s41437-021-00411-2\" rel=\"nofollow noreferrer\">reduction of genetic variance due to selection</a></li>\n</ul>\n","text":"This is a quite relevant question in breeding in general and has to do with \"response to selection\". This is a part of quantitative genetics that tries to mathematically explain how do populations change when they are selected upon. The most basic way to understand this is the \"breeders equation\":\n\n\n\n\n$R = h^2 \\times S$\n\n\n\n\nWhere:\n\n\n\n\n\n$R$ is response to selection (expected new mean)\n\n\n\n\n$h^2$ is heritability (in your example this is 1, i.e. the observed phenotypic variation is totally determined by genetic variation)\n\n\n\n\n$S$ is selection differential (in your case this is 190cm - 170cm)\n\n\n\n\n\nThis equation predicts the new population mean given the (narrow sense) heritability (https://vsni.co.uk/narrow-sense-heritability/). In essence, it just means that the new population mean is a result of the selected parents AND how genetic your trait is. In your example, because heritability is 1 (i.e. no other effects but a polygenic trait determine the phenotype), your new population mean should be 190cm (not 180cm).\n\n\n\n\nBut your question has more to do about \"stability\" of the new mean. This has two aspects to it: the stability of the mean across generations, and the final variance of your new population.\n\n\n\n\nFirstly, the mean is \"stable\" from gen 1, meaning that if you would randomly reproduce the individuals of the tall population with 190cm of average height; you would get a new population with 190cm of average height.\n\n\n\n\nSecond, the population variability is reduced every time you select. This is because \"bad alelles\" are being eliminated through selection, thus less alleles means less variation. The exact formulas that dictate this reduction are a bit convoluted, although this is the main shape they take:\n\n\n\n\n$\\sigma_{A1} = (1 - k\\times h^2) \\sigma_{A0}$\n\n\n\n\nWhere $k$ is a normalised selection intensity index, and $\\sigma_{A0}, \\sigma_{A1}$ are the original and generation 1 genetic variances. In essence this just shows that the harder you select the more variance you loose.\n\n\n\n\nTo sum up, the mean is stable from generation 1. Whether your population will still vary depends on how strongly you have selected. In any case, very strong selection leads to all sorts of issues, especially in animals (because inbreeding is bad). Complex topic!\n\n\n\n\nSome resources for you:\n\n\n\n\n\nEasy understanding of breeders equation (https://www.edge.org/response-detail/27199)\n\n\n\n\nComplete Response to Selection theory (pretty dense) (https://iastate.pressbooks.pub/quantitativegenetics/chapter/selection-response/)\n\n\n\n\nCheck the intro of this article for a good explanation of reduction of genetic variance due to selection (https://www.nature.com/articles/s41437-021-00411-2)"},{"context_id":"119283","html":"<p>Assuming there isn't any environmental influence from the parents and simple non-interacting traits, all you have is regression to the mean, then it only takes 1 generation.</p>\n<p>But, your story setup is a bit weird if &quot;environment for each generation is the same&quot; is taken too literally, such that all of the 10 cm SD is genetic and there is no environmental variation. If there's literally no environmental variation, there is no &quot;noise&quot;, and there is no regression to the mean; Athe's answer assumes this. I'll instead assume that what you meant is that the <em>extent of environmental variation (noise) is constant from generation to generation and is random</em>, rather than that the environmental variation is zero.</p>\n<p><strong>Regression to the mean is a feature of selection bias on <em>noise in the data</em>.</strong> Consider a population with mean height 170 cm, no genetic variation, but some environmental variation resulting in SD 10 cm.</p>\n<p>If you only breed individuals that are &gt;190cm (that is, in the extreme of height from this population), the next generation will still have mean 170 cm and SD 10 cm.</p>\n<p>Remember, there's no genetic variation in this scenario; individuals that are taller than the mean are only taller by random chance. That's why you get regression to the mean: you have a bias (you chose from the tallest individuals) that's not based on anything heritable.</p>\n<p>The same is true if part of the difference is heritable and part is not.</p>\n<p>The problem a breeder faces is not taking multiple generations for regression to the mean to end, the problem is <em>sample size</em>. If you breed two individuals and get 4 offspring, your confidence interval is going to be approximately <span class=\"math-container\">$+/- \\{\\frac{2 \\times 10cm}{\\sqrt{4}}\\} = +/- 10 cm$</span> from whatever you estimate. So, if you select some 190 cm individuals, who really have &quot;180 cm&quot; of genetic height (that is, if you breed them and their offspring to an infinite population you'd get to a mean of 180 cm) and the other 10 cm was noise, the population mean of their offspring will be 180 cm, but in a finite sample sometimes you'll estimate 175 or 185 cm.</p>\n<p>In summary, repeating: <strong>regression to the mean is a feature of selection bias on <em>noise in the data</em>.</strong> - therefore, if the 'noise' is independent generation to generation, then noise in one generation can't influence the next, so there's no further for the mean to regress.</p>\n","text":"Assuming there isn't any environmental influence from the parents and simple non-interacting traits, all you have is regression to the mean, then it only takes 1 generation.\n\n\n\n\nBut, your story setup is a bit weird if \"environment for each generation is the same\" is taken too literally, such that all of the 10 cm SD is genetic and there is no environmental variation. If there's literally no environmental variation, there is no \"noise\", and there is no regression to the mean; Athe's answer assumes this. I'll instead assume that what you meant is that the extent of environmental variation (noise) is constant from generation to generation and is random, rather than that the environmental variation is zero.\n\n\n\n\nRegression to the mean is a feature of selection bias on noise in the data. Consider a population with mean height 170 cm, no genetic variation, but some environmental variation resulting in SD 10 cm.\n\n\n\n\nIf you only breed individuals that are >190cm (that is, in the extreme of height from this population), the next generation will still have mean 170 cm and SD 10 cm.\n\n\n\n\nRemember, there's no genetic variation in this scenario; individuals that are taller than the mean are only taller by random chance. That's why you get regression to the mean: you have a bias (you chose from the tallest individuals) that's not based on anything heritable.\n\n\n\n\nThe same is true if part of the difference is heritable and part is not.\n\n\n\n\nThe problem a breeder faces is not taking multiple generations for regression to the mean to end, the problem is sample size. If you breed two individuals and get 4 offspring, your confidence interval is going to be approximately $+/- \\{\\frac{2 \\times 10cm}{\\sqrt{4}}\\} = +/- 10 cm$ from whatever you estimate. So, if you select some 190 cm individuals, who really have \"180 cm\" of genetic height (that is, if you breed them and their offspring to an infinite population you'd get to a mean of 180 cm) and the other 10 cm was noise, the population mean of their offspring will be 180 cm, but in a finite sample sometimes you'll estimate 175 or 185 cm.\n\n\n\n\nIn summary, repeating: regression to the mean is a feature of selection bias on noise in the data. - therefore, if the 'noise' is independent generation to generation, then noise in one generation can't influence the next, so there's no further for the mean to regress."}],"domain":"biology","external_citations":["https://iastate.pressbooks.pub/quantitativegenetics/chapter/selection-response/","https://vsni.co.uk/narrow-sense-heritability/","https://www.edge.org/response-detail/27199","https://www.nature.com/articles/s41437-021-00411-2"],"ground_truth_type":"metadata_grounded","group_id":"105b9cd1a1562f9a9d8d43e9dfcce069a236676ced0a2b66a56ea042bb3225a8","hard_case_family":["multiple_sources","multiple_answer_candidates"],"id":"RHM-a97139377cdee89e5b74dd95","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":"Maximilian","profile_url":"https://biology.stackexchange.com/users/65161/maximilian","user_type":"registered"},"created_at":"2026-01-24T00:46:29+00:00","raw_file":"raw/codex_api_v1/91e75308ae5d4e2adbc966eeaa33ee31183f3dcee03ede8f8105b7c8973deeb6_1790824169436990200_0.json","raw_sha256":"4ecc6c39f2269357dfd5478f8b88ef2f2e3d1b91841927b9ef870a736f612c14","revision_guid":"8143F66F-D940-4438-B6B5-15072E325F75","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/8143F66F-D940-4438-B6B5-15072E325F75/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":"119273","source_record_sha256":"0fe59c163a100d93d2806fbecd0dc3cf0efc6a28c779b69af0ac06bff6cdf871","source_url":"https://biology.stackexchange.com/questions/119273/when-does-regression-to-the-mean-stop-after-how-many-generations-is-a-new-mean","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"When does regression to the mean stop? After how many generations is a new mean reached?\nTake any polygenic trait whose phenotypic expression in todays first world countries mostly depends on genetics, e.g. height.\n\n\n\n\nExample: Base population has mean height of 170cm in both men and women (Yes, I know this is not true but I want to keep it simple) and the postulated std of height is 10cm. Background assumption: The environment for each generation is the same, there are no famines, nutrition stays the same, no endocrinal changes like difference in exposure to certain hormones, etc.\n\n\n\n\nNow you take those with height exactly above 2stds above the mean (height 190cm) and let them mingle. Call these individuals part of generation 1. Their offspring, the second generation, will have a mean somewhere in between 170cm and 190cm, let's say 180cm. Is this new mean in generation 2 already stable, i.e. would the offspring of parents taken from this second generation with mean 180cm have a mean of 180cm as well or would the regression to the mean continue to the mean of the base population, which was 100? In other words, after how many generations of selective breeding can the breeder be sure that he has achieved a new mean for the relevant trait?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":119282,"score":3},{"answer_id":119283,"score":3}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Flightless birds evolved from flight-capable ancestors, who, as you say, lost the trait for flexible femurs as they emerged from therapod dinosaurs.<br />\nIt seems that inflexible femurs did not pose negative consequences for birds that lost the ability to fly, so therefore there was no <a href=\"https://en.wikipedia.org/wiki/Evolutionary_pressure\" rel=\"nofollow noreferrer\">selection pressure</a> in favor of regaining flexible femurs.</p>\n","answer_id":119318,"answer_text":"Flightless birds evolved from flight-capable ancestors, who, as you say, lost the trait for flexible femurs as they emerged from therapod dinosaurs.\n\nIt seems that inflexible femurs did not pose negative consequences for birds that lost the ability to fly, so therefore there was no selection pressure (https://en.wikipedia.org/wiki/Evolutionary_pressure) in favor of regaining flexible femurs.","answer_url":"https://biology.stackexchange.com/a/119318","author":"William","author_url":"https://biology.stackexchange.com/users/124114/william","content_license":"CC BY-SA 4.0","created_at":"2026-02-10T05:22:19+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":119317,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"William","profile_url":"https://biology.stackexchange.com/users/124114/william","user_type":"registered"},"created_at":"2026-02-10T05:22:19+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"D1752533-D5F5-40E3-887E-55A391F2566A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D1752533-D5F5-40E3-887E-55A391F2566A/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"William","profile_url":"https://biology.stackexchange.com/users/124114/william","user_type":"registered"},"created_at":"2026-02-10T11:33:26+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"D7F89275-CCF0-4C9A-B037-1F4C3C2AF9B0","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D7F89275-CCF0-4C9A-B037-1F4C3C2AF9B0/view-source"}],"score":-2}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Craig Morrison","author_url":"https://biology.stackexchange.com/users/76118/craig-morrison","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Craig Morrison","profile_url":"https://biology.stackexchange.com/users/76118/craig-morrison","user_type":"registered"},"created_at":"2026-02-09T22:02:50+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"60A8135D-BAB2-4A40-805E-8A609FF239B0","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/60A8135D-BAB2-4A40-805E-8A609FF239B0/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Craig Morrison","profile_url":"https://biology.stackexchange.com/users/76118/craig-morrison","user_type":"registered"},"created_at":"2026-02-10T19:53:50+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"B65DB2F1-B38D-4877-956A-E23BFAFF64CA","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B65DB2F1-B38D-4877-956A-E23BFAFF64CA/view-source"}],"url":"https://biology.stackexchange.com/questions/119317/are-birds-prevented-from-having-flexible-femurs"},{"author":"William","author_url":"https://biology.stackexchange.com/users/124114/william","content_license":"CC BY-SA 4.0","context_id":"119318","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"William","profile_url":"https://biology.stackexchange.com/users/124114/william","user_type":"registered"},"created_at":"2026-02-10T05:22:19+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"D1752533-D5F5-40E3-887E-55A391F2566A","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D1752533-D5F5-40E3-887E-55A391F2566A/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"William","profile_url":"https://biology.stackexchange.com/users/124114/william","user_type":"registered"},"created_at":"2026-02-10T11:33:26+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"D7F89275-CCF0-4C9A-B037-1F4C3C2AF9B0","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D7F89275-CCF0-4C9A-B037-1F4C3C2AF9B0/view-source"}],"url":"https://biology.stackexchange.com/a/119318"}],"contexts":[{"context_id":"question","html":"<p>The femurs in birds seem to be very limited in movement, something that I always understood as a necessary sacrifice to minimize weight for flight. However, flightless birds such as ostriches also seem to have a limited range of movement in their femurs, and to my knowledge there isn't any bird with a mobile femur. Non-avian therapods in contrast hav more mobile femurs, so it is not as if having mobile femurs are detrimental to a large bipedal animal. Why is this the case in flightless birds? Does the structure of their hips necessarily prevent a wider range of motion for their hip-joint in a way that makes selection for a mobile femur impractical/unlikely?</p>\n","text":"The femurs in birds seem to be very limited in movement, something that I always understood as a necessary sacrifice to minimize weight for flight. However, flightless birds such as ostriches also seem to have a limited range of movement in their femurs, and to my knowledge there isn't any bird with a mobile femur. Non-avian therapods in contrast hav more mobile femurs, so it is not as if having mobile femurs are detrimental to a large bipedal animal. Why is this the case in flightless birds? Does the structure of their hips necessarily prevent a wider range of motion for their hip-joint in a way that makes selection for a mobile femur impractical/unlikely?"},{"context_id":"119318","html":"<p>Flightless birds evolved from flight-capable ancestors, who, as you say, lost the trait for flexible femurs as they emerged from therapod dinosaurs.<br />\nIt seems that inflexible femurs did not pose negative consequences for birds that lost the ability to fly, so therefore there was no <a href=\"https://en.wikipedia.org/wiki/Evolutionary_pressure\" rel=\"nofollow noreferrer\">selection pressure</a> in favor of regaining flexible femurs.</p>\n","text":"Flightless birds evolved from flight-capable ancestors, who, as you say, lost the trait for flexible femurs as they emerged from therapod dinosaurs.\n\nIt seems that inflexible femurs did not pose negative consequences for birds that lost the ability to fly, so therefore there was no selection pressure (https://en.wikipedia.org/wiki/Evolutionary_pressure) in favor of regaining flexible femurs."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Evolutionary_pressure"],"ground_truth_type":"metadata_grounded","group_id":"648bd58cce407233f5e73250f0ea25c2896a6d330b24349e3f324b5e210264ef","hard_case_family":["no_accepted_answer"],"id":"RHM-9bc639df07132fc0e3e12772","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":"Craig Morrison","profile_url":"https://biology.stackexchange.com/users/76118/craig-morrison","user_type":"registered"},"created_at":"2026-02-09T22:02:50+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"60A8135D-BAB2-4A40-805E-8A609FF239B0","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/60A8135D-BAB2-4A40-805E-8A609FF239B0/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Craig Morrison","profile_url":"https://biology.stackexchange.com/users/76118/craig-morrison","user_type":"registered"},"created_at":"2026-02-10T19:53:50+00:00","raw_file":"raw/codex_api_v1/8e952f166349d197ca438d4c6da0a6ceb83001adf6bf53b79021f6f47dbac9ed_1790824167246505200_0.json","raw_sha256":"e4bf5a8cf72ab19ae92569b60006ce309cee9bb0a51afc54be5e3a597306b0a8","revision_guid":"B65DB2F1-B38D-4877-956A-E23BFAFF64CA","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/B65DB2F1-B38D-4877-956A-E23BFAFF64CA/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":"119317","source_record_sha256":"a0dba01cd3bb91b1bb538c97067235bb3bc48d715b2fe4ec0e51fdaf0e1ff739","source_url":"https://biology.stackexchange.com/questions/119317/are-birds-prevented-from-having-flexible-femurs","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Are birds prevented from having flexible femurs?\nThe femurs in birds seem to be very limited in movement, something that I always understood as a necessary sacrifice to minimize weight for flight. However, flightless birds such as ostriches also seem to have a limited range of movement in their femurs, and to my knowledge there isn't any bird with a mobile femur. Non-avian therapods in contrast hav more mobile femurs, so it is not as if having mobile femurs are detrimental to a large bipedal animal. Why is this the case in flightless birds? Does the structure of their hips necessarily prevent a wider range of motion for their hip-joint in a way that makes selection for a mobile femur impractical/unlikely?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":119318,"score":-2}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Not surprisingly, it's <em>Populus deltoides</em> (Eastern cottonwood). <a href=\"https://en.wikipedia.org/wiki/Populus_deltoides\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/Populus_deltoides</a></p>\n<p><a href=\"https://i.sstatic.net/UiY3TzED.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/UiY3TzED.png\" alt=\"cottonwood foliage\" /></a> By Laurent Bélanger - Own work, CC BY-SA 4.0, <a href=\"https://commons.wikimedia.org/w/index.php?curid=42013972\" rel=\"nofollow noreferrer\">https://commons.wikimedia.org/w/index.php?curid=42013972</a></p>\n<p><a href=\"https://i.sstatic.net/Ti5KXFJj.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/Ti5KXFJj.png\" alt=\"cottonwood fluff\" /></a> By EnLorax G. Edward Johnson - Own work, CC BY 3.0, <a href=\"https://commons.wikimedia.org/w/index.php?curid=6837577\" rel=\"nofollow noreferrer\">https://commons.wikimedia.org/w/index.php?curid=6837577</a></p>\n","answer_id":119570,"answer_text":"Not surprisingly, it's Populus deltoides (Eastern cottonwood). https://en.wikipedia.org/wiki/Populus_deltoides (https://en.wikipedia.org/wiki/Populus_deltoides)\n\n\n\n\n[image: cottonwood foliage; source: https://i.sstatic.net/UiY3TzED.png] (https://i.sstatic.net/UiY3TzED.png) By Laurent Bélanger - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=42013972 (https://commons.wikimedia.org/w/index.php?curid=42013972)\n\n\n\n\n[image: cottonwood fluff; source: https://i.sstatic.net/Ti5KXFJj.png] (https://i.sstatic.net/Ti5KXFJj.png) By EnLorax G. Edward Johnson - Own work, CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=6837577 (https://commons.wikimedia.org/w/index.php?curid=6837577)","answer_url":"https://biology.stackexchange.com/a/119570","author":"Ben Bolker","author_url":"https://biology.stackexchange.com/users/25523/ben-bolker","content_license":"CC BY-SA 4.0","created_at":"2026-07-02T23:58:39+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":119529,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Ben Bolker","profile_url":"https://biology.stackexchange.com/users/25523/ben-bolker","user_type":"registered"},"created_at":"2026-07-02T23:58:39+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"DA029020-D4AF-4871-9C0B-553397378BDB","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DA029020-D4AF-4871-9C0B-553397378BDB/view-source"}],"score":4}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"E Tam","author_url":"https://biology.stackexchange.com/users/5149/e-tam","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"E Tam","profile_url":"https://biology.stackexchange.com/users/5149/e-tam","user_type":"registered"},"created_at":"2026-06-05T16:27:51+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"6264C67C-A249-4936-BD8E-4D3A2A50C34B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/6264C67C-A249-4936-BD8E-4D3A2A50C34B/view-source"}],"url":"https://biology.stackexchange.com/questions/119529/identifing-tall-tree-with-cotton-like-seeds"},{"author":"Ben Bolker","author_url":"https://biology.stackexchange.com/users/25523/ben-bolker","content_license":"CC BY-SA 4.0","context_id":"119570","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Ben Bolker","profile_url":"https://biology.stackexchange.com/users/25523/ben-bolker","user_type":"registered"},"created_at":"2026-07-02T23:58:39+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"DA029020-D4AF-4871-9C0B-553397378BDB","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/DA029020-D4AF-4871-9C0B-553397378BDB/view-source"}],"url":"https://biology.stackexchange.com/a/119570"}],"contexts":[{"context_id":"question","html":"<p>I live in a suburb of Boston, Massachusetts. I recently noticed a whole bunch of cotton-like seeds floating in the air around this one area. I did a little investigating and found a branch covered in the same type of fluffy seeds. Looking up, I saw a <strong>really</strong> tall tree. Looking carefully I could see white patches in its branches that are almost certainly more seeds.</p>\n<p>I took a few pictures. One is of the tree with a nearby telephone poll for scale. The other two are of the branch that fell of in a storm.\n<a href=\"https://i.sstatic.net/kEDfDSJb.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/kEDfDSJb.jpg\" alt=\"Tree\" /></a>\n<a href=\"https://i.sstatic.net/FyxRWJfV.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/FyxRWJfV.jpg\" alt=\"Branch\" /></a>\n<a href=\"https://i.sstatic.net/jk3BZSFd.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/jk3BZSFd.jpg\" alt=\"Leaves\" /></a></p>\n","text":"I live in a suburb of Boston, Massachusetts. I recently noticed a whole bunch of cotton-like seeds floating in the air around this one area. I did a little investigating and found a branch covered in the same type of fluffy seeds. Looking up, I saw a really tall tree. Looking carefully I could see white patches in its branches that are almost certainly more seeds.\n\n\n\n\nI took a few pictures. One is of the tree with a nearby telephone poll for scale. The other two are of the branch that fell of in a storm.\n[image: Tree; source: https://i.sstatic.net/kEDfDSJb.jpg] (https://i.sstatic.net/kEDfDSJb.jpg)\n[image: Branch; source: https://i.sstatic.net/FyxRWJfV.jpg] (https://i.sstatic.net/FyxRWJfV.jpg)\n[image: Leaves; source: https://i.sstatic.net/jk3BZSFd.jpg] (https://i.sstatic.net/jk3BZSFd.jpg)"},{"context_id":"119570","html":"<p>Not surprisingly, it's <em>Populus deltoides</em> (Eastern cottonwood). <a href=\"https://en.wikipedia.org/wiki/Populus_deltoides\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/Populus_deltoides</a></p>\n<p><a href=\"https://i.sstatic.net/UiY3TzED.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/UiY3TzED.png\" alt=\"cottonwood foliage\" /></a> By Laurent Bélanger - Own work, CC BY-SA 4.0, <a href=\"https://commons.wikimedia.org/w/index.php?curid=42013972\" rel=\"nofollow noreferrer\">https://commons.wikimedia.org/w/index.php?curid=42013972</a></p>\n<p><a href=\"https://i.sstatic.net/Ti5KXFJj.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/Ti5KXFJj.png\" alt=\"cottonwood fluff\" /></a> By EnLorax G. Edward Johnson - Own work, CC BY 3.0, <a href=\"https://commons.wikimedia.org/w/index.php?curid=6837577\" rel=\"nofollow noreferrer\">https://commons.wikimedia.org/w/index.php?curid=6837577</a></p>\n","text":"Not surprisingly, it's Populus deltoides (Eastern cottonwood). https://en.wikipedia.org/wiki/Populus_deltoides (https://en.wikipedia.org/wiki/Populus_deltoides)\n\n\n\n\n[image: cottonwood foliage; source: https://i.sstatic.net/UiY3TzED.png] (https://i.sstatic.net/UiY3TzED.png) By Laurent Bélanger - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=42013972 (https://commons.wikimedia.org/w/index.php?curid=42013972)\n\n\n\n\n[image: cottonwood fluff; source: https://i.sstatic.net/Ti5KXFJj.png] (https://i.sstatic.net/Ti5KXFJj.png) By EnLorax G. Edward Johnson - Own work, CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=6837577 (https://commons.wikimedia.org/w/index.php?curid=6837577)"}],"domain":"biology","external_citations":["https://commons.wikimedia.org/w/index.php?curid=42013972","https://commons.wikimedia.org/w/index.php?curid=6837577","https://en.wikipedia.org/wiki/Populus_deltoides","https://i.sstatic.net/FyxRWJfV.jpg","https://i.sstatic.net/Ti5KXFJj.png","https://i.sstatic.net/UiY3TzED.png","https://i.sstatic.net/jk3BZSFd.jpg","https://i.sstatic.net/kEDfDSJb.jpg"],"ground_truth_type":"metadata_grounded","group_id":"66bf03017813df49ae5d3bb4dffa766f7573d9296f0a191733b19ec6635ae157","hard_case_family":["no_accepted_answer","multiple_sources","citation_heavy"],"id":"RHM-61c4c8519e7c0bed3c9b2556","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":"E Tam","profile_url":"https://biology.stackexchange.com/users/5149/e-tam","user_type":"registered"},"created_at":"2026-06-05T16:27:51+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"6264C67C-A249-4936-BD8E-4D3A2A50C34B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/6264C67C-A249-4936-BD8E-4D3A2A50C34B/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":"119529","source_record_sha256":"52943889c4099f6d0ade9a8b491a7272d2015d7533812feb10c5d498a28b7555","source_url":"https://biology.stackexchange.com/questions/119529/identifing-tall-tree-with-cotton-like-seeds","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Identifing Tall Tree with Cotton-Like Seeds\nI live in a suburb of Boston, Massachusetts. I recently noticed a whole bunch of cotton-like seeds floating in the air around this one area. I did a little investigating and found a branch covered in the same type of fluffy seeds. Looking up, I saw a really tall tree. Looking carefully I could see white patches in its branches that are almost certainly more seeds.\n\n\n\n\nI took a few pictures. One is of the tree with a nearby telephone poll for scale. The other two are of the branch that fell of in a storm.\n[image: Tree; source: https://i.sstatic.net/kEDfDSJb.jpg] (https://i.sstatic.net/kEDfDSJb.jpg)\n[image: Branch; source: https://i.sstatic.net/FyxRWJfV.jpg] (https://i.sstatic.net/FyxRWJfV.jpg)\n[image: Leaves; source: https://i.sstatic.net/jk3BZSFd.jpg] (https://i.sstatic.net/jk3BZSFd.jpg)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":119570,"score":4}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":119650,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>There is any of a number of reasons why a plant part might grow “into darkness”—not least of all being mere luck (think of a length of ivy losing its “footing” and simply drooping into the shade).</p>\n<p>With vines in particular, many have a thigmotropic response which allows them twine and grow in any of a number of directions—including in the opposite direction of light, at least for a time—so that they better establish themselves on whatever they happen to be climbing up</p>\n","answer_id":119649,"answer_text":"There is any of a number of reasons why a plant part might grow “into darkness”—not least of all being mere luck (think of a length of ivy losing its “footing” and simply drooping into the shade).\n\n\n\n\nWith vines in particular, many have a thigmotropic response which allows them twine and grow in any of a number of directions—including in the opposite direction of light, at least for a time—so that they better establish themselves on whatever they happen to be climbing up","answer_url":"https://biology.stackexchange.com/a/119649","author":"resplaine","author_url":"https://biology.stackexchange.com/users/50862/resplaine","content_license":"CC BY-SA 4.0","created_at":"2026-08-14T02:03:26+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":119639,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"resplaine","profile_url":"https://biology.stackexchange.com/users/50862/resplaine","user_type":"registered"},"created_at":"2026-08-14T02:03:26+00:00","raw_file":"raw/codex_api_v1/05a07ac5b899aedc4a355e74e14372bb9f5c68880d960b52e1cb7db2e69e21a7_1790824192733506600_0.json","raw_sha256":"a95113893b680d2f015d30e681bff685c192aae637f6399ca4974513858f935d","revision_guid":"11B71C23-425D-41F2-9E62-541E660D139B","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/11B71C23-425D-41F2-9E62-541E660D139B/view-source"},{"content_license":null,"contributor":{"display_name":"terdon","profile_url":"https://biology.stackexchange.com/users/1306/terdon","user_type":"moderator"},"created_at":"2026-08-14T16:12:11+00:00","raw_file":"raw/codex_api_v1/05a07ac5b899aedc4a355e74e14372bb9f5c68880d960b52e1cb7db2e69e21a7_1790824192733506600_0.json","raw_sha256":"a95113893b680d2f015d30e681bff685c192aae637f6399ca4974513858f935d","revision_guid":"7A09E73B-7D91-458E-81C8-47471B5F9D3C","revision_number":null,"revision_type":"vote_based","revision_url":"https://biology.stackexchange.com/revisions/7A09E73B-7D91-458E-81C8-47471B5F9D3C/view-source"}],"score":0},{"answer_html":"<p>Positive phototropism isn't a &quot;every single plant or bit of plant does this&quot; rule. Negative phototropism is a well observed phenomenon in plants, particularly in roots. In addition, there are other movements that are independent of light or other such tropisms. These are termed <a href=\"https://en.wikipedia.org/wiki/Nastic_movements\" rel=\"nofollow noreferrer\">nastic movements</a>. Charles and Francis Darwin (Him of the <em>Origin of Species</em> and his son) wrote a long treatise on movements in plants in the late 1800's called <em>The Power of Movement in Plants</em><sup>1</sup>, which you can read for free at <a href=\"https://www.gutenberg.org/ebooks/5605\" rel=\"nofollow noreferrer\">Project Gutenberg</a>.</p>\n<p>In the case of many creepers and vines, the plants start on the forest floor and must reach the canopy. They are generally not capable of self support to any great extent, so must climb a tree or other object that reaches the canopy. To do this they must &quot;search&quot; for something to climb, using nastic movements to do something called circumnutation (moving in an approximate circular motion), which allow them to move around and find the nearest vertical surface to climb on. Once found, thigmotropism (touch sensitivity) causes the shoots to coil and attach to the surface. This movement is independent of light and will by random chance always reach regions that are darker than others. I think, but haven't put the effort in to find the references, that there may be a negative phototropism at play here too - the stem/trunk of a tree will be darker than the edges around the canopy, but the climbing plant will need to reach that dark trunk to be able to climb.</p>\n<p>Circumnutation also allows movement through and between crowded spaces on the forest floor and between branches when higher up. The Darwins, in their above mentioned book, performed some experiments that looked at this motion and found that the movement of stolons between stems of plants was facilitated in plants that were capable of larger circumnutation than in smaller circumnutation. This circumnutation was, however in response to light, so the stolons were growing towards a light source along a horizontal surface.</p>\n<p>I think in your case, what you are seeing is a product of the two things I talked about in the previous two paragraphs. Basically, the plants are searching for ways to grow, and sometimes this will involve going through regions that are dark.</p>\n<p>Ref:</p>\n<ol>\n<li>.Darwin, C. &amp; Darwin, F. (1880) The Power of Movement in Plants (John Murray, London).</li>\n</ol>\n","answer_id":119650,"answer_text":"Positive phototropism isn't a \"every single plant or bit of plant does this\" rule. Negative phototropism is a well observed phenomenon in plants, particularly in roots. In addition, there are other movements that are independent of light or other such tropisms. These are termed nastic movements (https://en.wikipedia.org/wiki/Nastic_movements). Charles and Francis Darwin (Him of the Origin of Species and his son) wrote a long treatise on movements in plants in the late 1800's called The Power of Movement in Plants1, which you can read for free at Project Gutenberg (https://www.gutenberg.org/ebooks/5605).\n\n\n\n\nIn the case of many creepers and vines, the plants start on the forest floor and must reach the canopy. They are generally not capable of self support to any great extent, so must climb a tree or other object that reaches the canopy. To do this they must \"search\" for something to climb, using nastic movements to do something called circumnutation (moving in an approximate circular motion), which allow them to move around and find the nearest vertical surface to climb on. Once found, thigmotropism (touch sensitivity) causes the shoots to coil and attach to the surface. This movement is independent of light and will by random chance always reach regions that are darker than others. I think, but haven't put the effort in to find the references, that there may be a negative phototropism at play here too - the stem/trunk of a tree will be darker than the edges around the canopy, but the climbing plant will need to reach that dark trunk to be able to climb.\n\n\n\n\nCircumnutation also allows movement through and between crowded spaces on the forest floor and between branches when higher up. The Darwins, in their above mentioned book, performed some experiments that looked at this motion and found that the movement of stolons between stems of plants was facilitated in plants that were capable of larger circumnutation than in smaller circumnutation. This circumnutation was, however in response to light, so the stolons were growing towards a light source along a horizontal surface.\n\n\n\n\nI think in your case, what you are seeing is a product of the two things I talked about in the previous two paragraphs. Basically, the plants are searching for ways to grow, and sometimes this will involve going through regions that are dark.\n\n\n\n\nRef:\n\n\n\n\n\n.Darwin, C. & Darwin, F. (1880) The Power of Movement in Plants (John Murray, London).","answer_url":"https://biology.stackexchange.com/a/119650","author":"bob1","author_url":"https://biology.stackexchange.com/users/65284/bob1","content_license":"CC BY-SA 4.0","created_at":"2026-08-14T02:56:23+00:00","is_accepted":true,"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 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side of a different shed (I'm in the Northern Hemisphere).  Some of the shoots insist on growing in between the planks into the shed instead of staying out in sunshine.  I find that I have to continually tease the new shoots out from in between the planks.  They are light green after I've teased them out.  They change to the normal green colour after being in sunshine for a while.</p>\n<p>Question: Is there any reason for the plant to favour growing towards darkness?</p>\n<p><img src=\"https://i.sstatic.net/k9UTdIb8.jpg\" alt=\"Plant growing into shed\" /></p>\n<p><img src=\"https://i.sstatic.net/VCbEMvQt.jpg\" alt=\"Plant pulled out\" /></p>\n","text":"I always thought plants grew towards sunlight.\n\n\n\n\nIncident 1: Yesterday, I found about 3ft of ivy growing inside my shed, which has no windows.\n\n\n\n\nIncident 2: I've got a creeper growing on the south facing side of a different shed (I'm in the Northern Hemisphere).  Some of the shoots insist on growing in between the planks into the shed instead of staying out in sunshine.  I find that I have to continually tease the new shoots out from in between the planks.  They are light green after I've teased them out.  They change to the normal green colour after being in sunshine for a while.\n\n\n\n\nQuestion: Is there any reason for the plant to favour growing towards darkness?\n\n\n\n\n[image: Plant growing into shed; source: https://i.sstatic.net/k9UTdIb8.jpg]\n\n\n\n\n[image: Plant pulled out; source: https://i.sstatic.net/VCbEMvQt.jpg]"},{"context_id":"119649","html":"<p>There is any of a number of reasons why a plant part might grow “into darkness”—not least of all being mere luck (think of a length of ivy losing its “footing” and simply drooping into the shade).</p>\n<p>With vines in particular, many have a thigmotropic response which allows them twine and grow in any of a number of directions—including in the opposite direction of light, at least for a time—so that they better establish themselves on whatever they happen to be climbing up</p>\n","text":"There is any of a number of reasons why a plant part might grow “into darkness”—not least of all being mere luck (think of a length of ivy losing its “footing” and simply drooping into the shade).\n\n\n\n\nWith vines in particular, many have a thigmotropic response which allows them twine and grow in any of a number of directions—including in the opposite direction of light, at least for a time—so that they better establish themselves on whatever they happen to be climbing up"},{"context_id":"119650","html":"<p>Positive phototropism isn't a &quot;every single plant or bit of plant does this&quot; rule. Negative phototropism is a well observed phenomenon in plants, particularly in roots. In addition, there are other movements that are independent of light or other such tropisms. These are termed <a href=\"https://en.wikipedia.org/wiki/Nastic_movements\" rel=\"nofollow noreferrer\">nastic movements</a>. Charles and Francis Darwin (Him of the <em>Origin of Species</em> and his son) wrote a long treatise on movements in plants in the late 1800's called <em>The Power of Movement in Plants</em><sup>1</sup>, which you can read for free at <a href=\"https://www.gutenberg.org/ebooks/5605\" rel=\"nofollow noreferrer\">Project Gutenberg</a>.</p>\n<p>In the case of many creepers and vines, the plants start on the forest floor and must reach the canopy. They are generally not capable of self support to any great extent, so must climb a tree or other object that reaches the canopy. To do this they must &quot;search&quot; for something to climb, using nastic movements to do something called circumnutation (moving in an approximate circular motion), which allow them to move around and find the nearest vertical surface to climb on. Once found, thigmotropism (touch sensitivity) causes the shoots to coil and attach to the surface. This movement is independent of light and will by random chance always reach regions that are darker than others. I think, but haven't put the effort in to find the references, that there may be a negative phototropism at play here too - the stem/trunk of a tree will be darker than the edges around the canopy, but the climbing plant will need to reach that dark trunk to be able to climb.</p>\n<p>Circumnutation also allows movement through and between crowded spaces on the forest floor and between branches when higher up. The Darwins, in their above mentioned book, performed some experiments that looked at this motion and found that the movement of stolons between stems of plants was facilitated in plants that were capable of larger circumnutation than in smaller circumnutation. This circumnutation was, however in response to light, so the stolons were growing towards a light source along a horizontal surface.</p>\n<p>I think in your case, what you are seeing is a product of the two things I talked about in the previous two paragraphs. Basically, the plants are searching for ways to grow, and sometimes this will involve going through regions that are dark.</p>\n<p>Ref:</p>\n<ol>\n<li>.Darwin, C. &amp; Darwin, F. (1880) The Power of Movement in Plants (John Murray, London).</li>\n</ol>\n","text":"Positive phototropism isn't a \"every single plant or bit of plant does this\" rule. Negative phototropism is a well observed phenomenon in plants, particularly in roots. In addition, there are other movements that are independent of light or other such tropisms. These are termed nastic movements (https://en.wikipedia.org/wiki/Nastic_movements). Charles and Francis Darwin (Him of the Origin of Species and his son) wrote a long treatise on movements in plants in the late 1800's called The Power of Movement in Plants1, which you can read for free at Project Gutenberg (https://www.gutenberg.org/ebooks/5605).\n\n\n\n\nIn the case of many creepers and vines, the plants start on the forest floor and must reach the canopy. They are generally not capable of self support to any great extent, so must climb a tree or other object that reaches the canopy. To do this they must \"search\" for something to climb, using nastic movements to do something called circumnutation (moving in an approximate circular motion), which allow them to move around and find the nearest vertical surface to climb on. Once found, thigmotropism (touch sensitivity) causes the shoots to coil and attach to the surface. This movement is independent of light and will by random chance always reach regions that are darker than others. I think, but haven't put the effort in to find the references, that there may be a negative phototropism at play here too - the stem/trunk of a tree will be darker than the edges around the canopy, but the climbing plant will need to reach that dark trunk to be able to climb.\n\n\n\n\nCircumnutation also allows movement through and between crowded spaces on the forest floor and between branches when higher up. The Darwins, in their above mentioned book, performed some experiments that looked at this motion and found that the movement of stolons between stems of plants was facilitated in plants that were capable of larger circumnutation than in smaller circumnutation. This circumnutation was, however in response to light, so the stolons were growing towards a light source along a horizontal surface.\n\n\n\n\nI think in your case, what you are seeing is a product of the two things I talked about in the previous two paragraphs. Basically, the plants are searching for ways to grow, and sometimes this will involve going through regions that are dark.\n\n\n\n\nRef:\n\n\n\n\n\n.Darwin, C. & Darwin, F. (1880) The Power of Movement in Plants (John Murray, London)."}],"domain":"biology","external_citations":["https://en.wikipedia.org/wiki/Nastic_movements","https://www.gutenberg.org/ebooks/5605"],"ground_truth_type":"metadata_grounded","group_id":"6def3f01a087100555d8db1e739c867899873d63bfb19a1391b583166a816922","hard_case_family":["multiple_sources","multiple_answer_candidates"],"id":"RHM-6eb7736a7f56587ac86c19ac","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":"cup","profile_url":"https://biology.stackexchange.com/users/8410/cup","user_type":"registered"},"created_at":"2026-08-11T16:23:35+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"50D5D8FD-D62B-48F3-81F6-8E3C14847D57","revision_number":1,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/50D5D8FD-D62B-48F3-81F6-8E3C14847D57/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"cup","profile_url":"https://biology.stackexchange.com/users/8410/cup","user_type":"registered"},"created_at":"2026-08-16T16:57:11+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"D1F2C3A2-258C-48F3-9B89-720620044F6C","revision_number":2,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/D1F2C3A2-258C-48F3-9B89-720620044F6C/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"cup","profile_url":"https://biology.stackexchange.com/users/8410/cup","user_type":"registered"},"created_at":"2026-08-16T17:02:42+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"5200E264-E125-4962-B857-2E6951A43F8F","revision_number":3,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/5200E264-E125-4962-B857-2E6951A43F8F/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"cup","profile_url":"https://biology.stackexchange.com/users/8410/cup","user_type":"registered"},"created_at":"2026-08-16T17:09:20+00:00","raw_file":"raw/codex_api_v1/30edb57b578064458be0726e8f438b6e87f6be83f37b063b5f6097379fca514d_1790824174828155600_0.json","raw_sha256":"88f86163c238074f8177d1ef634208b9e49a1f4e659b8032dd7e5061bf358244","revision_guid":"45E36358-81FD-4C82-A1E9-C7FC6E7D1E79","revision_number":4,"revision_type":"single_user","revision_url":"https://biology.stackexchange.com/revisions/45E36358-81FD-4C82-A1E9-C7FC6E7D1E79/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":"119639","source_record_sha256":"00c28c2f1cf288ccc2fff16a891d2139c6aa9419e94c3e8c7aceffa2ebee4065","source_url":"https://biology.stackexchange.com/questions/119639/plants-sending-shoots-into-darkness","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Plants sending shoots into darkness\nI always thought plants grew towards sunlight.\n\n\n\n\nIncident 1: Yesterday, I found about 3ft of ivy growing inside my shed, which has no windows.\n\n\n\n\nIncident 2: I've got a creeper growing on the south facing side of a different shed (I'm in the Northern Hemisphere).  Some of the shoots insist on growing in between the planks into the shed instead of staying out in sunshine.  I find that I have to continually tease the new shoots out from in between the planks.  They are light green after I've teased them out.  They change to the normal green colour after being in sunshine for a while.\n\n\n\n\nQuestion: Is there any reason for the plant to favour growing towards darkness?\n\n\n\n\n[image: Plant growing into shed; source: https://i.sstatic.net/k9UTdIb8.jpg]\n\n\n\n\n[image: Plant pulled out; source: https://i.sstatic.net/VCbEMvQt.jpg]","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":119649,"score":0},{"answer_id":119650,"score":4}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>If you run a plain Gibbs on a classic mixture model, you face the paradox that the Markov chain is uniformly ergodic (because the latent space is finite and hence compact) AND usually fails to switch between modes, i.e. does not exhibit label switching. This is the point we make in the <a href=\"https://www.jstor.org/stable/2669477?searchText=celeux%20hurn%20robert&amp;searchUri=%2Faction%2FdoBasicSearch%3FQuery%3Dceleux%2Bhurn%2Brobert%26so%3Drel%26efqs%3DeyJjdHkiOlsiYW05MWNtNWhiQT09Il19&amp;ab_segments=0%2Fbasic_search_gsv2%2Fcontrol&amp;refreqid=fastly-default%3A0dc4861d75073d6e1d8fc9756aa699a8\" rel=\"noreferrer\">2000 JASA paper with Gilles Celeux and Merilee Hurn</a>.</p>\n<p>The literature has now expanded with several solutions for ensuring the label switching property by:</p>\n<ul>\n<li>randomly shuffling the labels at each iteration, à la Früwirth-Schnatter</li>\n<li>inserting tempering steps between each iteration, à la Neal</li>\n<li>avoiding the latent variable simulation (as we suggest in our paper)</li>\n<li>using the point process representation of the mixture parameters, à la Green</li>\n<li>using a sequential approach where new labels appear with new observations, à la Chopin</li>\n</ul>\n<p>These perspectives are discussed in our edited book\n<a href=\"https://www.routledge.com/Handbook-of-Mixture-Analysis/Fruhwirth-Schnatter-Celeux-Robert/p/book/9780367732066\" rel=\"noreferrer\">Handbook of Mixture Analysis</a></p>\n","answer_id":676884,"answer_text":"If you run a plain Gibbs on a classic mixture model, you face the paradox that the Markov chain is uniformly ergodic (because the latent space is finite and hence compact) AND usually fails to switch between modes, i.e. does not exhibit label switching. This is the point we make in the 2000 JASA paper with Gilles Celeux and Merilee Hurn (https://www.jstor.org/stable/2669477?searchText=celeux%20hurn%20robert&searchUri=%2Faction%2FdoBasicSearch%3FQuery%3Dceleux%2Bhurn%2Brobert%26so%3Drel%26efqs%3DeyJjdHkiOlsiYW05MWNtNWhiQT09Il19&ab_segments=0%2Fbasic_search_gsv2%2Fcontrol&refreqid=fastly-default%3A0dc4861d75073d6e1d8fc9756aa699a8).\n\n\n\n\nThe literature has now expanded with several solutions for ensuring the label switching property by:\n\n\n\n\n\nrandomly shuffling the labels at each iteration, à la Früwirth-Schnatter\n\n\n\n\ninserting tempering steps between each iteration, à la Neal\n\n\n\n\navoiding the latent variable simulation (as we suggest in our paper)\n\n\n\n\nusing the point process representation of the mixture parameters, à la Green\n\n\n\n\nusing a sequential approach where new labels appear with new observations, à la Chopin\n\n\n\n\n\nThese perspectives are discussed in our edited book\nHandbook of Mixture Analysis (https://www.routledge.com/Handbook-of-Mixture-Analysis/Fruhwirth-Schnatter-Celeux-Robert/p/book/9780367732066)","answer_url":"https://stats.stackexchange.com/a/676884","author":"Xi'an","author_url":"https://stats.stackexchange.com/users/7224/xian","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-08-15T20:39:37+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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Cox","profile_url":"https://stats.stackexchange.com/users/22047/nick-cox","user_type":"registered"},"created_at":"2026-08-16T08:08:52+00:00","raw_file":"raw/codex_api_v1/01ff643b5e725b2402c38de261074c3bef3326820f24db4342e17e318353268e_1790825246205492400_0.json","raw_sha256":"a0521ae83c8630be00a12499e9aaa253069e57a5e0ff902fea3e9b8e7acb810f","revision_guid":"835E1857-6F7B-4983-806C-8B86C7B28C02","revision_number":2,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/835E1857-6F7B-4983-806C-8B86C7B28C02/view-source"}],"url":"https://stats.stackexchange.com/a/676884"}],"contexts":[{"context_id":"question","html":"<p>Let's say you have a classic mixture model and you want to use a Gibbs sampler over the parameters and the latent variable. How do you deal with your sampler getting stuck at a single node?</p>\n","text":"Let's say you have a classic mixture model and you want to use a Gibbs sampler over the parameters and the latent variable. How do you deal with your sampler getting stuck at a single node?"},{"context_id":"676884","html":"<p>If you run a plain Gibbs on a classic mixture model, you face the paradox that the Markov chain is uniformly ergodic (because the latent space is finite and hence compact) AND usually fails to switch between modes, i.e. does not exhibit label switching. This is the point we make in the <a href=\"https://www.jstor.org/stable/2669477?searchText=celeux%20hurn%20robert&amp;searchUri=%2Faction%2FdoBasicSearch%3FQuery%3Dceleux%2Bhurn%2Brobert%26so%3Drel%26efqs%3DeyJjdHkiOlsiYW05MWNtNWhiQT09Il19&amp;ab_segments=0%2Fbasic_search_gsv2%2Fcontrol&amp;refreqid=fastly-default%3A0dc4861d75073d6e1d8fc9756aa699a8\" rel=\"noreferrer\">2000 JASA paper with Gilles Celeux and Merilee Hurn</a>.</p>\n<p>The literature has now expanded with several solutions for ensuring the label switching property by:</p>\n<ul>\n<li>randomly shuffling the labels at each iteration, à la Früwirth-Schnatter</li>\n<li>inserting tempering steps between each iteration, à la Neal</li>\n<li>avoiding the latent variable simulation (as we suggest in our paper)</li>\n<li>using the point process representation of the mixture parameters, à la Green</li>\n<li>using a sequential approach where new labels appear with new observations, à la Chopin</li>\n</ul>\n<p>These perspectives are discussed in our edited book\n<a href=\"https://www.routledge.com/Handbook-of-Mixture-Analysis/Fruhwirth-Schnatter-Celeux-Robert/p/book/9780367732066\" rel=\"noreferrer\">Handbook of Mixture Analysis</a></p>\n","text":"If you run a plain Gibbs on a classic mixture model, you face the paradox that the Markov chain is uniformly ergodic (because the latent space is finite and hence compact) AND usually fails to switch between modes, i.e. does not exhibit label switching. This is the point we make in the 2000 JASA paper with Gilles Celeux and Merilee Hurn (https://www.jstor.org/stable/2669477?searchText=celeux%20hurn%20robert&searchUri=%2Faction%2FdoBasicSearch%3FQuery%3Dceleux%2Bhurn%2Brobert%26so%3Drel%26efqs%3DeyJjdHkiOlsiYW05MWNtNWhiQT09Il19&ab_segments=0%2Fbasic_search_gsv2%2Fcontrol&refreqid=fastly-default%3A0dc4861d75073d6e1d8fc9756aa699a8).\n\n\n\n\nThe literature has now expanded with several solutions for ensuring the label switching property by:\n\n\n\n\n\nrandomly shuffling the labels at each iteration, à la Früwirth-Schnatter\n\n\n\n\ninserting tempering steps between each iteration, à la Neal\n\n\n\n\navoiding the latent variable simulation (as we suggest in our paper)\n\n\n\n\nusing the point process representation of the mixture parameters, à la Green\n\n\n\n\nusing a sequential approach where new labels appear with new observations, à la Chopin\n\n\n\n\n\nThese perspectives are discussed in our edited book\nHandbook of Mixture Analysis (https://www.routledge.com/Handbook-of-Mixture-Analysis/Fruhwirth-Schnatter-Celeux-Robert/p/book/9780367732066)"}],"domain":"statistics","external_citations":["https://www.jstor.org/stable/2669477?searchText=celeux%20hurn%20robert&searchUri=%2Faction%2FdoBasicSearch%3FQuery%3Dceleux%2Bhurn%2Brobert%26so%3Drel%26efqs%3DeyJjdHkiOlsiYW05MWNtNWhiQT09Il19&ab_segments=0%2Fbasic_search_gsv2%2Fcontrol&refreqid=fastly-default%3A0dc4861d75073d6e1d8fc9756aa699a8","https://www.routledge.com/Handbook-of-Mixture-Analysis/Fruhwirth-Schnatter-Celeux-Robert/p/book/9780367732066"],"ground_truth_type":"metadata_grounded","group_id":"b09547d85e12cf2a89f5cd15e1f1bc3ba5c56ef8d4862475c25d204fca21220f","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-24ef75d89d0fae76a16d4402","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":"5 d","profile_url":"https://stats.stackexchange.com/users/515521/5-d","user_type":"registered"},"created_at":"2026-08-15T12:45:58+00:00","raw_file":"raw/codex_api_v1/01ff643b5e725b2402c38de261074c3bef3326820f24db4342e17e318353268e_1790825246205492400_0.json","raw_sha256":"a0521ae83c8630be00a12499e9aaa253069e57a5e0ff902fea3e9b8e7acb810f","revision_guid":"82BC8558-016A-4705-A5FD-57942444684B","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/82BC8558-016A-4705-A5FD-57942444684B/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Nick Cox","profile_url":"https://stats.stackexchange.com/users/22047/nick-cox","user_type":"registered"},"created_at":"2026-08-15T18:07:14+00:00","raw_file":"raw/codex_api_v1/01ff643b5e725b2402c38de261074c3bef3326820f24db4342e17e318353268e_1790825246205492400_0.json","raw_sha256":"a0521ae83c8630be00a12499e9aaa253069e57a5e0ff902fea3e9b8e7acb810f","revision_guid":"001C88C1-DF6C-4863-973A-9A264F1A2C79","revision_number":2,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/001C88C1-DF6C-4863-973A-9A264F1A2C79/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-08-16T08:56:04+00:00","raw_file":"raw/codex_api_v1/01ff643b5e725b2402c38de261074c3bef3326820f24db4342e17e318353268e_1790825246205492400_0.json","raw_sha256":"a0521ae83c8630be00a12499e9aaa253069e57a5e0ff902fea3e9b8e7acb810f","revision_guid":"51FF7245-F5D9-4250-AECD-11ED7475CAA3","revision_number":null,"revision_type":"vote_based","revision_url":"https://stats.stackexchange.com/revisions/51FF7245-F5D9-4250-AECD-11ED7475CAA3/view-source"},{"content_license":null,"contributor":{"display_name":"kjetil b halvorsen","profile_url":"https://stats.stackexchange.com/users/11887/kjetil-b-halvorsen","user_type":"moderator"},"created_at":"2026-08-16T21:02:28+00:00","raw_file":"raw/codex_api_v1/01ff643b5e725b2402c38de261074c3bef3326820f24db4342e17e318353268e_1790825246205492400_0.json","raw_sha256":"a0521ae83c8630be00a12499e9aaa253069e57a5e0ff902fea3e9b8e7acb810f","revision_guid":"1124C47B-8496-4670-BAD8-1A5DA7F237F6","revision_number":3,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/1124C47B-8496-4670-BAD8-1A5DA7F237F6/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:676879","source_record_sha256":"1120ba1f9b4e4f389dc4515c85140a74f15fdff101be64b1206c3e9f42da4e1e","source_url":"https://stats.stackexchange.com/questions/676879/how-does-one-deal-with-the-gibbs-sampler-being-stuck-in-a-node-when-we-consider","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How does one deal with the Gibbs sampler being stuck in a node when we consider a mixture model\nLet's say you have a classic mixture model and you want to use a Gibbs sampler over the parameters and the latent variable. How do you deal with your sampler getting stuck at a single node?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":676884,"score":11}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>A few thoughts:</p>\n<blockquote>\n<p>My coauthor ... does want a specific cutoff that we call good, excellent etc.</p>\n</blockquote>\n<p>This probably isn't a useful goal. What presumably matters is whether the differences in annotation will matter in clinical practice. For example, minor disagreements about which individual pixels belong in a region of interest (ROI) wouldn't be expected to have much practical effect. Differences in overall annotations of ROI (e.g., tumor versus normal) would matter a lot. It's not clear that any choice of arbitrary &quot;cutoffs&quot; would capture the practical importance of the differences. The practical difference is what presumably will matter most to your audience.</p>\n<blockquote>\n<p>... I calculated the Jaccard index...</p>\n</blockquote>\n<p>Think carefully about whether that's the appropriate measure for inter-rater reliability. That won't take into account the agreement that would be expected just by chance. The <a href=\"https://en.wikipedia.org/wiki/Inter-rater_reliability\" rel=\"nofollow noreferrer\">Wikipedia entry</a> explains:</p>\n<blockquote>\n<p>When the number of categories being used is small (e.g. 2 or 3), the likelihood for 2 raters to agree by pure chance increases dramatically.</p>\n</blockquote>\n<p>You only have 2 categories. The Wikipedia entry describes several measures that adjust for chance agreement. <a href=\"https://en.wikipedia.org/wiki/Inter-rater_reliability#Kappa_statistics\" rel=\"nofollow noreferrer\">Kappa statistics</a> would probably be better choices.</p>\n<blockquote>\n<p>The &quot;ground truth&quot; is the human annotations...</p>\n</blockquote>\n<p>As the 2 humans don't always agree, you don't really have a &quot;ground truth.&quot; You might get closer to a &quot;ground truth&quot; if you had 3 human raters and used the majority vote for each assessment.</p>\n","answer_id":676929,"answer_text":"A few thoughts:\n\n\n\n\n\n\n\nMy coauthor ... does want a specific cutoff that we call good, excellent etc.\n\n\n\n\n\n\n\nThis probably isn't a useful goal. What presumably matters is whether the differences in annotation will matter in clinical practice. For example, minor disagreements about which individual pixels belong in a region of interest (ROI) wouldn't be expected to have much practical effect. Differences in overall annotations of ROI (e.g., tumor versus normal) would matter a lot. It's not clear that any choice of arbitrary \"cutoffs\" would capture the practical importance of the differences. The practical difference is what presumably will matter most to your audience.\n\n\n\n\n\n\n\n... I calculated the Jaccard index...\n\n\n\n\n\n\n\nThink carefully about whether that's the appropriate measure for inter-rater reliability. That won't take into account the agreement that would be expected just by chance. The Wikipedia entry (https://en.wikipedia.org/wiki/Inter-rater_reliability) explains:\n\n\n\n\n\n\n\nWhen the number of categories being used is small (e.g. 2 or 3), the likelihood for 2 raters to agree by pure chance increases dramatically.\n\n\n\n\n\n\n\nYou only have 2 categories. The Wikipedia entry describes several measures that adjust for chance agreement. Kappa statistics (https://en.wikipedia.org/wiki/Inter-rater_reliability#Kappa_statistics) would probably be better choices.\n\n\n\n\n\n\n\nThe \"ground truth\" is the human annotations...\n\n\n\n\n\n\n\nAs the 2 humans don't always agree, you don't really have a \"ground truth.\" You might get closer to a \"ground truth\" if you had 3 human raters and used the majority vote for each assessment.","answer_url":"https://stats.stackexchange.com/a/676929","author":"EdM","author_url":"https://stats.stackexchange.com/users/28500/edm","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-08-21T16:56:04+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":676924,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"EdM","profile_url":"https://stats.stackexchange.com/users/28500/edm","user_type":"registered"},"created_at":"2026-08-21T16:56:04+00:00","raw_file":"raw/codex_api_v1/01ff643b5e725b2402c38de261074c3bef3326820f24db4342e17e318353268e_1790825246205492400_0.json","raw_sha256":"a0521ae83c8630be00a12499e9aaa253069e57a5e0ff902fea3e9b8e7acb810f","revision_guid":"00FF675D-4690-4BD3-BC52-6349CAAC7745","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/00FF675D-4690-4BD3-BC52-6349CAAC7745/view-source"}],"score":2,"updated_at":"2026-08-21T16:56:04+00:00"}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"deee","author_url":"https://stats.stackexchange.com/users/492702/deee","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"deee","profile_url":"https://stats.stackexchange.com/users/492702/deee","user_type":"registered"},"created_at":"2026-08-20T15:23:03+00:00","raw_file":"raw/codex_api_v1/01ff643b5e725b2402c38de261074c3bef3326820f24db4342e17e318353268e_1790825246205492400_0.json","raw_sha256":"a0521ae83c8630be00a12499e9aaa253069e57a5e0ff902fea3e9b8e7acb810f","revision_guid":"F3431DE0-82AE-4630-A45E-E672DDBF5F5A","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/F3431DE0-82AE-4630-A45E-E672DDBF5F5A/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-08-21T22:30:56+00:00","raw_file":"raw/codex_api_v1/01ff643b5e725b2402c38de261074c3bef3326820f24db4342e17e318353268e_1790825246205492400_0.json","raw_sha256":"a0521ae83c8630be00a12499e9aaa253069e57a5e0ff902fea3e9b8e7acb810f","revision_guid":"62C64EA4-AD43-4820-A545-BC23853CCAD6","revision_number":null,"revision_type":"vote_based","revision_url":"https://stats.stackexchange.com/revisions/62C64EA4-AD43-4820-A545-BC23853CCAD6/view-source"}],"url":"https://stats.stackexchange.com/questions/676924/interpretation-of-interrater-reliability-metrics"},{"author":"EdM","author_url":"https://stats.stackexchange.com/users/28500/edm","content_license":"CC BY-SA 4.0","context_id":"676929","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"EdM","profile_url":"https://stats.stackexchange.com/users/28500/edm","user_type":"registered"},"created_at":"2026-08-21T16:56:04+00:00","raw_file":"raw/codex_api_v1/01ff643b5e725b2402c38de261074c3bef3326820f24db4342e17e318353268e_1790825246205492400_0.json","raw_sha256":"a0521ae83c8630be00a12499e9aaa253069e57a5e0ff902fea3e9b8e7acb810f","revision_guid":"00FF675D-4690-4BD3-BC52-6349CAAC7745","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/00FF675D-4690-4BD3-BC52-6349CAAC7745/view-source"}],"url":"https://stats.stackexchange.com/a/676929"}],"contexts":[{"context_id":"question","html":"<p>I'm working on a medical image segmentation problem. I have the source images, automated annotations, and manual annotations from two human raters. The annotations have two formats: predefined regions, and per-pixel annotation.</p>\n<p>For the predefined regions, each rater overlaid a map of 44 semantically meaningful regions onto the source image and annotated each region as True/False. For a given example, there are therefore 44 binary variables that each rater can agree or disagree on.</p>\n<p>For the per-pixel annotation, each rater created a pixel mask to identify the region of interest. For a given example, each rater could therefore agree or disagree on each individual pixel in the image.</p>\n<p>The &quot;ground truth&quot; is the human annotations. The humans don't perfectly agree on their annotations. The nature of the task means that for the per-pixel annotation there's a fair amount of possible disagreement without one rater being &quot;wrong&quot;.</p>\n<p>I want to assess the reliability of my automated annotations. I have calculated some metrics between each pair of raters (rater a to automated, rater b to automated, rater a to rater b). For the predefined regions I calculated the Jaccard index on a per-region basis, and for the per-pixel annotations I calculated the Jaccard index on a per-pixel basis, plus the Normalised Surface Distance.</p>\n<p>As far as I know, there aren't established conventions on what is &quot;good&quot; for these metrics on this task. One of my coauthors is strongly advocating to use ICC thresholds from <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC4913118/#bb0090\" rel=\"nofollow noreferrer\">this paper</a> to interpret those metrics (&lt;0.5 is poor, 0.5 to 0.75 is moderate, 0.75 to 0.9 is good, &gt;0.9 is excellent). I'm unhappy about this because I think ICC is fundamentally different from the metrics we've used.</p>\n<p>My coauthor is happy to use <em>different</em> thresholds if I can find more relevant ones, but does want a specific cutoff that we call good, excellent etc. I can't find any resources for more relevant thresholds.</p>\n<p>Is it reasonable to use these thresholds to interpret Jaccard index and Normalised Surface Distance on an image segmentation task? Is there an established way to decide what &quot;good&quot; agreement is for these metrics?</p>\n","text":"I'm working on a medical image segmentation problem. I have the source images, automated annotations, and manual annotations from two human raters. The annotations have two formats: predefined regions, and per-pixel annotation.\n\n\n\n\nFor the predefined regions, each rater overlaid a map of 44 semantically meaningful regions onto the source image and annotated each region as True/False. For a given example, there are therefore 44 binary variables that each rater can agree or disagree on.\n\n\n\n\nFor the per-pixel annotation, each rater created a pixel mask to identify the region of interest. For a given example, each rater could therefore agree or disagree on each individual pixel in the image.\n\n\n\n\nThe \"ground truth\" is the human annotations. The humans don't perfectly agree on their annotations. The nature of the task means that for the per-pixel annotation there's a fair amount of possible disagreement without one rater being \"wrong\".\n\n\n\n\nI want to assess the reliability of my automated annotations. I have calculated some metrics between each pair of raters (rater a to automated, rater b to automated, rater a to rater b). For the predefined regions I calculated the Jaccard index on a per-region basis, and for the per-pixel annotations I calculated the Jaccard index on a per-pixel basis, plus the Normalised Surface Distance.\n\n\n\n\nAs far as I know, there aren't established conventions on what is \"good\" for these metrics on this task. One of my coauthors is strongly advocating to use ICC thresholds from this paper (https://pmc.ncbi.nlm.nih.gov/articles/PMC4913118/#bb0090) to interpret those metrics (<0.5 is poor, 0.5 to 0.75 is moderate, 0.75 to 0.9 is good, >0.9 is excellent). I'm unhappy about this because I think ICC is fundamentally different from the metrics we've used.\n\n\n\n\nMy coauthor is happy to use different thresholds if I can find more relevant ones, but does want a specific cutoff that we call good, excellent etc. I can't find any resources for more relevant thresholds.\n\n\n\n\nIs it reasonable to use these thresholds to interpret Jaccard index and Normalised Surface Distance on an image segmentation task? Is there an established way to decide what \"good\" agreement is for these metrics?"},{"context_id":"676929","html":"<p>A few thoughts:</p>\n<blockquote>\n<p>My coauthor ... does want a specific cutoff that we call good, excellent etc.</p>\n</blockquote>\n<p>This probably isn't a useful goal. What presumably matters is whether the differences in annotation will matter in clinical practice. For example, minor disagreements about which individual pixels belong in a region of interest (ROI) wouldn't be expected to have much practical effect. Differences in overall annotations of ROI (e.g., tumor versus normal) would matter a lot. It's not clear that any choice of arbitrary &quot;cutoffs&quot; would capture the practical importance of the differences. The practical difference is what presumably will matter most to your audience.</p>\n<blockquote>\n<p>... I calculated the Jaccard index...</p>\n</blockquote>\n<p>Think carefully about whether that's the appropriate measure for inter-rater reliability. That won't take into account the agreement that would be expected just by chance. The <a href=\"https://en.wikipedia.org/wiki/Inter-rater_reliability\" rel=\"nofollow noreferrer\">Wikipedia entry</a> explains:</p>\n<blockquote>\n<p>When the number of categories being used is small (e.g. 2 or 3), the likelihood for 2 raters to agree by pure chance increases dramatically.</p>\n</blockquote>\n<p>You only have 2 categories. The Wikipedia entry describes several measures that adjust for chance agreement. <a href=\"https://en.wikipedia.org/wiki/Inter-rater_reliability#Kappa_statistics\" rel=\"nofollow noreferrer\">Kappa statistics</a> would probably be better choices.</p>\n<blockquote>\n<p>The &quot;ground truth&quot; is the human annotations...</p>\n</blockquote>\n<p>As the 2 humans don't always agree, you don't really have a &quot;ground truth.&quot; You might get closer to a &quot;ground truth&quot; if you had 3 human raters and used the majority vote for each assessment.</p>\n","text":"A few thoughts:\n\n\n\n\n\n\n\nMy coauthor ... does want a specific cutoff that we call good, excellent etc.\n\n\n\n\n\n\n\nThis probably isn't a useful goal. What presumably matters is whether the differences in annotation will matter in clinical practice. For example, minor disagreements about which individual pixels belong in a region of interest (ROI) wouldn't be expected to have much practical effect. Differences in overall annotations of ROI (e.g., tumor versus normal) would matter a lot. It's not clear that any choice of arbitrary \"cutoffs\" would capture the practical importance of the differences. The practical difference is what presumably will matter most to your audience.\n\n\n\n\n\n\n\n... I calculated the Jaccard index...\n\n\n\n\n\n\n\nThink carefully about whether that's the appropriate measure for inter-rater reliability. That won't take into account the agreement that would be expected just by chance. The Wikipedia entry (https://en.wikipedia.org/wiki/Inter-rater_reliability) explains:\n\n\n\n\n\n\n\nWhen the number of categories being used is small (e.g. 2 or 3), the likelihood for 2 raters to agree by pure chance increases dramatically.\n\n\n\n\n\n\n\nYou only have 2 categories. The Wikipedia entry describes several measures that adjust for chance agreement. Kappa statistics (https://en.wikipedia.org/wiki/Inter-rater_reliability#Kappa_statistics) would probably be better choices.\n\n\n\n\n\n\n\nThe \"ground truth\" is the human annotations...\n\n\n\n\n\n\n\nAs the 2 humans don't always agree, you don't really have a \"ground truth.\" You might get closer to a \"ground truth\" if you had 3 human raters and used the majority vote for each assessment."}],"domain":"statistics","external_citations":["https://en.wikipedia.org/wiki/Inter-rater_reliability","https://en.wikipedia.org/wiki/Inter-rater_reliability#Kappa_statistics","https://pmc.ncbi.nlm.nih.gov/articles/PMC4913118/#bb0090"],"ground_truth_type":"metadata_grounded","group_id":"9c02b73f37a559651cdecc4c01fab342666e662f5ca39617f022675f6fa1bf70","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-c79d86547c98b105936a3c6f","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":"deee","profile_url":"https://stats.stackexchange.com/users/492702/deee","user_type":"registered"},"created_at":"2026-08-20T15:23:03+00:00","raw_file":"raw/codex_api_v1/01ff643b5e725b2402c38de261074c3bef3326820f24db4342e17e318353268e_1790825246205492400_0.json","raw_sha256":"a0521ae83c8630be00a12499e9aaa253069e57a5e0ff902fea3e9b8e7acb810f","revision_guid":"F3431DE0-82AE-4630-A45E-E672DDBF5F5A","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/F3431DE0-82AE-4630-A45E-E672DDBF5F5A/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-08-21T22:30:56+00:00","raw_file":"raw/codex_api_v1/01ff643b5e725b2402c38de261074c3bef3326820f24db4342e17e318353268e_1790825246205492400_0.json","raw_sha256":"a0521ae83c8630be00a12499e9aaa253069e57a5e0ff902fea3e9b8e7acb810f","revision_guid":"62C64EA4-AD43-4820-A545-BC23853CCAD6","revision_number":null,"revision_type":"vote_based","revision_url":"https://stats.stackexchange.com/revisions/62C64EA4-AD43-4820-A545-BC23853CCAD6/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:676924","source_record_sha256":"ed462a9170864223fc565553727e63647b1f1bf26a5e5d383b3ead229bafe856","source_url":"https://stats.stackexchange.com/questions/676924/interpretation-of-interrater-reliability-metrics","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Interpretation of interrater reliability metrics\nI'm working on a medical image segmentation problem. I have the source images, automated annotations, and manual annotations from two human raters. The annotations have two formats: predefined regions, and per-pixel annotation.\n\n\n\n\nFor the predefined regions, each rater overlaid a map of 44 semantically meaningful regions onto the source image and annotated each region as True/False. For a given example, there are therefore 44 binary variables that each rater can agree or disagree on.\n\n\n\n\nFor the per-pixel annotation, each rater created a pixel mask to identify the region of interest. For a given example, each rater could therefore agree or disagree on each individual pixel in the image.\n\n\n\n\nThe \"ground truth\" is the human annotations. The humans don't perfectly agree on their annotations. The nature of the task means that for the per-pixel annotation there's a fair amount of possible disagreement without one rater being \"wrong\".\n\n\n\n\nI want to assess the reliability of my automated annotations. I have calculated some metrics between each pair of raters (rater a to automated, rater b to automated, rater a to rater b). For the predefined regions I calculated the Jaccard index on a per-region basis, and for the per-pixel annotations I calculated the Jaccard index on a per-pixel basis, plus the Normalised Surface Distance.\n\n\n\n\nAs far as I know, there aren't established conventions on what is \"good\" for these metrics on this task. One of my coauthors is strongly advocating to use ICC thresholds from this paper (https://pmc.ncbi.nlm.nih.gov/articles/PMC4913118/#bb0090) to interpret those metrics (<0.5 is poor, 0.5 to 0.75 is moderate, 0.75 to 0.9 is good, >0.9 is excellent). I'm unhappy about this because I think ICC is fundamentally different from the metrics we've used.\n\n\n\n\nMy coauthor is happy to use different thresholds if I can find more relevant ones, but does want a specific cutoff that we call good, excellent etc. I can't find any resources for more relevant thresholds.\n\n\n\n\nIs it reasonable to use these thresholds to interpret Jaccard index and Normalised Surface Distance on an image segmentation task? Is there an established way to decide what \"good\" agreement is for these metrics?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":676929,"score":2}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Welcome to CV. It's not clear why you think there is multicollinearity. That is a relation among independent variables and has nothing to do with the DV. You've only listed one IV. However, collinearity does not affect prediction very much.</p>\n<p>One problem is surely what @RickHass said: Your IV contains your DV. You are then asking &quot;can we predict number of store purchases from number of store purchases&quot;.</p>\n<p>One way around this is to take out &quot;Num store purchases&quot; from the feature set.</p>\n<p>You may have other problems as well. Purchasing data is often highly skewed, and, while regression does not require normal data, it does assume normal error, and that may be violated. You might want to take logs.</p>\n<p>However, if all the numbers of purchases are small (as might be the case for 'big ticket' items) then you might consider a count model.</p>\n<p>I'd consider hiring a statistician.</p>\n","answer_id":677034,"answer_text":"Welcome to CV. It's not clear why you think there is multicollinearity. That is a relation among independent variables and has nothing to do with the DV. You've only listed one IV. However, collinearity does not affect prediction very much.\n\n\n\n\nOne problem is surely what @RickHass said: Your IV contains your DV. You are then asking \"can we predict number of store purchases from number of store purchases\".\n\n\n\n\nOne way around this is to take out \"Num store purchases\" from the feature set.\n\n\n\n\nYou may have other problems as well. Purchasing data is often highly skewed, and, while regression does not require normal data, it does assume normal error, and that may be violated. You might want to take logs.\n\n\n\n\nHowever, if all the numbers of purchases are small (as might be the case for 'big ticket' items) then you might consider a count model.\n\n\n\n\nI'd consider hiring a statistician.","answer_url":"https://stats.stackexchange.com/a/677034","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":"2026-09-01T11:41:58+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":677033,"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":"2026-09-01T11:41:58+00:00","raw_file":"raw/codex_api_v1/84bb317e707465a80f008019404ef1f770e152d74ef692d3b81c48903ec855cc_1790825232001984700_0.json","raw_sha256":"75778d86d5325e15f4b491a748dc70ae6ac6ee98840d584e01ed28416cb71fbe","revision_guid":"D7BDB0E7-7A8C-438F-84B8-BD6B7817B150","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/D7BDB0E7-7A8C-438F-84B8-BD6B7817B150/view-source"}],"score":3,"updated_at":"2026-09-01T11:41:58+00:00"},{"answer_html":"<p>RMSE  = 3.82e-13\n=&gt; Model is getting a perfect score.\n=&gt; Red Flag</p>\n<p>You put Store is the data.\nTotal Purchases =  Store + Web + Catalog\n=&gt; OLS Regressor didn't bother to learn about the customer behavior.\nIt is actually solving an eqn : Store = Total Purchases - Web - Catalog</p>\n<p>Do a quick check on features like MntWines or MntMeatProducts.\nMake sure those totals don't accidentally contain the physical store purchase counts we are trying to predict.</p>\n<p>If We are trying to predict NumStorePurchases (Let's say, how many times a man visited the physical store).</p>\n<p>The danger is that features like MntWines (Total dollars spent on wine) or MntMeatProducts(Total dollars spent on meat) might be acting like a Wines or Meat bought from this physical store receipt.\nThen the machine will cheat saying &quot;He bought wines from this physical store, therefore he went to the physical store.&quot;</p>\n<p>All I am saying is If MntWines includes physical store purchases, we have to drop it. It gives away the answer.\nBut Why am I saying this? Let's say we want to predict the human behavior.<br />\nIf you put this model into the real world to predict what customers will do tomorrow, it will crash.</p>\n<p>Why? Because tomorrow hasn't happened yet. You don't have tomorrow's meat receipts. You only have MntMeatProducts after the target (NumStorePurchases) has already occurred.</p>\n<p>Hence, it will crash.\nIf the correlation is suspiciously high, you must drop that Mnt... feature. It is giving the model a shortcut which we don't want.\nI have tried my best to make you understand. If you still have any  doubt then please leave a comment.</p>\n","answer_id":677069,"answer_text":"RMSE  = 3.82e-13\n=> Model is getting a perfect score.\n=> Red Flag\n\n\n\n\nYou put Store is the data.\nTotal Purchases =  Store + Web + Catalog\n=> OLS Regressor didn't bother to learn about the customer behavior.\nIt is actually solving an eqn : Store = Total Purchases - Web - Catalog\n\n\n\n\nDo a quick check on features like MntWines or MntMeatProducts.\nMake sure those totals don't accidentally contain the physical store purchase counts we are trying to predict.\n\n\n\n\nIf We are trying to predict NumStorePurchases (Let's say, how many times a man visited the physical store).\n\n\n\n\nThe danger is that features like MntWines (Total dollars spent on wine) or MntMeatProducts(Total dollars spent on meat) might be acting like a Wines or Meat bought from this physical store receipt.\nThen the machine will cheat saying \"He bought wines from this physical store, therefore he went to the physical store.\"\n\n\n\n\nAll I am saying is If MntWines includes physical store purchases, we have to drop it. It gives away the answer.\nBut Why am I saying this? Let's say we want to predict the human behavior.\n\nIf you put this model into the real world to predict what customers will do tomorrow, it will crash.\n\n\n\n\nWhy? Because tomorrow hasn't happened yet. You don't have tomorrow's meat receipts. You only have MntMeatProducts after the target (NumStorePurchases) has already occurred.\n\n\n\n\nHence, it will crash.\nIf the correlation is suspiciously high, you must drop that Mnt... feature. It is giving the model a shortcut which we don't want.\nI have tried my best to make you understand. If you still have any  doubt then please leave a comment.","answer_url":"https://stats.stackexchange.com/a/677069","author":"Soudipta Dutta","author_url":"https://stats.stackexchange.com/users/207636/soudipta-dutta","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-09-04T12:10:41+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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Kar","profile_url":"https://stats.stackexchange.com/users/510955/abir-kar","user_type":"registered"},"created_at":"2026-09-03T17:20:40+00:00","raw_file":"raw/codex_api_v1/84bb317e707465a80f008019404ef1f770e152d74ef692d3b81c48903ec855cc_1790825232001984700_0.json","raw_sha256":"75778d86d5325e15f4b491a748dc70ae6ac6ee98840d584e01ed28416cb71fbe","revision_guid":"8EF25545-061A-4014-BC66-7C810301BD57","revision_number":2,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/8EF25545-061A-4014-BC66-7C810301BD57/view-source"}],"url":"https://stats.stackexchange.com/questions/677033/is-removing-multicollinear-variable-necessary-to-get-a-proper-predictive-analysi"},{"author":"Peter Flom","author_url":"https://stats.stackexchange.com/users/686/peter-flom","content_license":"CC BY-SA 4.0","context_id":"677034","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":"2026-09-01T11:41:58+00:00","raw_file":"raw/codex_api_v1/84bb317e707465a80f008019404ef1f770e152d74ef692d3b81c48903ec855cc_1790825232001984700_0.json","raw_sha256":"75778d86d5325e15f4b491a748dc70ae6ac6ee98840d584e01ed28416cb71fbe","revision_guid":"D7BDB0E7-7A8C-438F-84B8-BD6B7817B150","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/D7BDB0E7-7A8C-438F-84B8-BD6B7817B150/view-source"}],"url":"https://stats.stackexchange.com/a/677034"},{"author":"Soudipta Dutta","author_url":"https://stats.stackexchange.com/users/207636/soudipta-dutta","content_license":"CC BY-SA 4.0","context_id":"677069","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Soudipta Dutta","profile_url":"https://stats.stackexchange.com/users/207636/soudipta-dutta","user_type":"registered"},"created_at":"2026-09-04T12:10:41+00:00","raw_file":"raw/codex_api_v1/64ee278f47b21ead17c9e9fc156835d607f15cff0518af0117a527463a68df8a_1790825256327661600_0.json","raw_sha256":"18d894000304f6d836d0b21a9f2f35d37c183b3d25e32a897338c6dff012df04","revision_guid":"8E0BAE17-D514-43DD-8915-7D6D1D11997B","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/8E0BAE17-D514-43DD-8915-7D6D1D11997B/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Soudipta Dutta","profile_url":"https://stats.stackexchange.com/users/207636/soudipta-dutta","user_type":"registered"},"created_at":"2026-09-04T12:17:06+00:00","raw_file":"raw/codex_api_v1/64ee278f47b21ead17c9e9fc156835d607f15cff0518af0117a527463a68df8a_1790825256327661600_0.json","raw_sha256":"18d894000304f6d836d0b21a9f2f35d37c183b3d25e32a897338c6dff012df04","revision_guid":"3ED08E0D-FFB4-4E46-AB7E-8287BD20CF14","revision_number":2,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/3ED08E0D-FFB4-4E46-AB7E-8287BD20CF14/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Soudipta Dutta","profile_url":"https://stats.stackexchange.com/users/207636/soudipta-dutta","user_type":"registered"},"created_at":"2026-09-08T09:35:00+00:00","raw_file":"raw/codex_api_v1/3f959895a29b33d83894e5370d82e1c0cf87f20ac57fa423ebc923738357c657_1790825253957066500_0.json","raw_sha256":"ddd8808039e410ca99f97e2a7f12c307f046c4e5c3e184683bc12f816e6f49fc","revision_guid":"EADD6F80-51D8-488C-90A1-B951DAE79867","revision_number":3,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/EADD6F80-51D8-488C-90A1-B951DAE79867/view-source"}],"url":"https://stats.stackexchange.com/a/677069"}],"contexts":[{"context_id":"question","html":"<p>I am doing a project to understand the predictive viability of different regressors on the dependent variable(<code>NumStorePurchases</code>). In the feature space, we have a feature called <code>Total Purchases</code>- Sum of (<code>NumStorePurchases</code>,<code>WebPurchases</code>,<code>CatalogPurchases</code>) along with other variables <code>Income</code>, <code>Kidhome</code>, <code>Teenhome</code>, <code>Recency</code>, <code>MntWines</code>, <code>MntFruits</code>, <code>MntMeatProducts</code>, <code>MntFishProducts</code>, <code>MntSweetProducts</code>, <code>MntGoldProds</code>, <code>NumDealsPurchases</code>, <code>NumWebPurchases</code>, <code>NumCatalogPurchases</code>, <code>NumStorePurchases</code>, <code>NumWebVisitsMonth</code>, <code>AcceptedCmp3</code>, <code>AcceptedCmp4</code>, <code>AcceptedCmp5</code>, <code>AcceptedCmp1</code>, <code>AcceptedCmp2</code>, <code>Response</code>, <code>Complain</code>, <code>Country</code>. When we are doing an OLS regression by splitting out test-train data by 70-30% &amp; finding out <strong>RMSE(Root Mean Squared Error)</strong>, value is a minuscule number-<code>3.8200863988425333e-13</code>.\nSo, I am little bit skeptical with this number, although according to my understanding Multicollinearity do not impact predictive viability of a model, it's just impact the significance of each regressors.</p>\n<p>Is it somehow impacting the model predictive accuracy or maybe some other factors like <strong>data leakage</strong> can reduce the RMSE as well due to the presence of Y on X(Feature space) itself or maybe this small RMSE value can be possible?</p>\n<p>Looking for your reply community members.</p>\n<p>Thanks.</p>\n","text":"I am doing a project to understand the predictive viability of different regressors on the dependent variable(NumStorePurchases). In the feature space, we have a feature called Total Purchases- Sum of (NumStorePurchases,WebPurchases,CatalogPurchases) along with other variables Income, Kidhome, Teenhome, Recency, MntWines, MntFruits, MntMeatProducts, MntFishProducts, MntSweetProducts, MntGoldProds, NumDealsPurchases, NumWebPurchases, NumCatalogPurchases, NumStorePurchases, NumWebVisitsMonth, AcceptedCmp3, AcceptedCmp4, AcceptedCmp5, AcceptedCmp1, AcceptedCmp2, Response, Complain, Country. When we are doing an OLS regression by splitting out test-train data by 70-30% & finding out RMSE(Root Mean Squared Error), value is a minuscule number-3.8200863988425333e-13.\nSo, I am little bit skeptical with this number, although according to my understanding Multicollinearity do not impact predictive viability of a model, it's just impact the significance of each regressors.\n\n\n\n\nIs it somehow impacting the model predictive accuracy or maybe some other factors like data leakage can reduce the RMSE as well due to the presence of Y on X(Feature space) itself or maybe this small RMSE value can be possible?\n\n\n\n\nLooking for your reply community members.\n\n\n\n\nThanks."},{"context_id":"677034","html":"<p>Welcome to CV. It's not clear why you think there is multicollinearity. That is a relation among independent variables and has nothing to do with the DV. You've only listed one IV. However, collinearity does not affect prediction very much.</p>\n<p>One problem is surely what @RickHass said: Your IV contains your DV. You are then asking &quot;can we predict number of store purchases from number of store purchases&quot;.</p>\n<p>One way around this is to take out &quot;Num store purchases&quot; from the feature set.</p>\n<p>You may have other problems as well. Purchasing data is often highly skewed, and, while regression does not require normal data, it does assume normal error, and that may be violated. You might want to take logs.</p>\n<p>However, if all the numbers of purchases are small (as might be the case for 'big ticket' items) then you might consider a count model.</p>\n<p>I'd consider hiring a statistician.</p>\n","text":"Welcome to CV. It's not clear why you think there is multicollinearity. That is a relation among independent variables and has nothing to do with the DV. You've only listed one IV. However, collinearity does not affect prediction very much.\n\n\n\n\nOne problem is surely what @RickHass said: Your IV contains your DV. You are then asking \"can we predict number of store purchases from number of store purchases\".\n\n\n\n\nOne way around this is to take out \"Num store purchases\" from the feature set.\n\n\n\n\nYou may have other problems as well. Purchasing data is often highly skewed, and, while regression does not require normal data, it does assume normal error, and that may be violated. You might want to take logs.\n\n\n\n\nHowever, if all the numbers of purchases are small (as might be the case for 'big ticket' items) then you might consider a count model.\n\n\n\n\nI'd consider hiring a statistician."},{"context_id":"677069","html":"<p>RMSE  = 3.82e-13\n=&gt; Model is getting a perfect score.\n=&gt; Red Flag</p>\n<p>You put Store is the data.\nTotal Purchases =  Store + Web + Catalog\n=&gt; OLS Regressor didn't bother to learn about the customer behavior.\nIt is actually solving an eqn : Store = Total Purchases - Web - Catalog</p>\n<p>Do a quick check on features like MntWines or MntMeatProducts.\nMake sure those totals don't accidentally contain the physical store purchase counts we are trying to predict.</p>\n<p>If We are trying to predict NumStorePurchases (Let's say, how many times a man visited the physical store).</p>\n<p>The danger is that features like MntWines (Total dollars spent on wine) or MntMeatProducts(Total dollars spent on meat) might be acting like a Wines or Meat bought from this physical store receipt.\nThen the machine will cheat saying &quot;He bought wines from this physical store, therefore he went to the physical store.&quot;</p>\n<p>All I am saying is If MntWines includes physical store purchases, we have to drop it. It gives away the answer.\nBut Why am I saying this? Let's say we want to predict the human behavior.<br />\nIf you put this model into the real world to predict what customers will do tomorrow, it will crash.</p>\n<p>Why? Because tomorrow hasn't happened yet. You don't have tomorrow's meat receipts. You only have MntMeatProducts after the target (NumStorePurchases) has already occurred.</p>\n<p>Hence, it will crash.\nIf the correlation is suspiciously high, you must drop that Mnt... feature. It is giving the model a shortcut which we don't want.\nI have tried my best to make you understand. If you still have any  doubt then please leave a comment.</p>\n","text":"RMSE  = 3.82e-13\n=> Model is getting a perfect score.\n=> Red Flag\n\n\n\n\nYou put Store is the data.\nTotal Purchases =  Store + Web + Catalog\n=> OLS Regressor didn't bother to learn about the customer behavior.\nIt is actually solving an eqn : Store = Total Purchases - Web - Catalog\n\n\n\n\nDo a quick check on features like MntWines or MntMeatProducts.\nMake sure those totals don't accidentally contain the physical store purchase counts we are trying to predict.\n\n\n\n\nIf We are trying to predict NumStorePurchases (Let's say, how many times a man visited the physical store).\n\n\n\n\nThe danger is that features like MntWines (Total dollars spent on wine) or MntMeatProducts(Total dollars spent on meat) might be acting like a Wines or Meat bought from this physical store receipt.\nThen the machine will cheat saying \"He bought wines from this physical store, therefore he went to the physical store.\"\n\n\n\n\nAll I am saying is If MntWines includes physical store purchases, we have to drop it. It gives away the answer.\nBut Why am I saying this? Let's say we want to predict the human behavior.\n\nIf you put this model into the real world to predict what customers will do tomorrow, it will crash.\n\n\n\n\nWhy? Because tomorrow hasn't happened yet. You don't have tomorrow's meat receipts. You only have MntMeatProducts after the target (NumStorePurchases) has already occurred.\n\n\n\n\nHence, it will crash.\nIf the correlation is suspiciously high, you must drop that Mnt... feature. It is giving the model a shortcut which we don't want.\nI have tried my best to make you understand. If you still have any  doubt then please leave a comment."}],"domain":"statistics","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"102b388517cf7d43c2ff8a219530780181161d6f6d6d0c1be3933e0d6558941f","hard_case_family":["no_accepted_answer","multiple_answer_candidates"],"id":"RHM-1643fba7045673fe17fe24f5","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":"Abir Kar","profile_url":"https://stats.stackexchange.com/users/510955/abir-kar","user_type":"registered"},"created_at":"2026-09-01T09:40:16+00:00","raw_file":"raw/codex_api_v1/84bb317e707465a80f008019404ef1f770e152d74ef692d3b81c48903ec855cc_1790825232001984700_0.json","raw_sha256":"75778d86d5325e15f4b491a748dc70ae6ac6ee98840d584e01ed28416cb71fbe","revision_guid":"B8FA9293-7F0F-46F6-96CD-BA3F1590F973","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/B8FA9293-7F0F-46F6-96CD-BA3F1590F973/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Abir Kar","profile_url":"https://stats.stackexchange.com/users/510955/abir-kar","user_type":"registered"},"created_at":"2026-09-03T17:20:40+00:00","raw_file":"raw/codex_api_v1/84bb317e707465a80f008019404ef1f770e152d74ef692d3b81c48903ec855cc_1790825232001984700_0.json","raw_sha256":"75778d86d5325e15f4b491a748dc70ae6ac6ee98840d584e01ed28416cb71fbe","revision_guid":"8EF25545-061A-4014-BC66-7C810301BD57","revision_number":2,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/8EF25545-061A-4014-BC66-7C810301BD57/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:677033","source_record_sha256":"f604576f5a15c005a776215e359b5cdf26831fdfbfc421c80d126bd9b160e224","source_url":"https://stats.stackexchange.com/questions/677033/is-removing-multicollinear-variable-necessary-to-get-a-proper-predictive-analysi","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Is removing multicollinear variable necessary to get a proper predictive analysis of RMSE(Root Mean Squared Error) of OLS regression in test data?\nI am doing a project to understand the predictive viability of different regressors on the dependent variable(NumStorePurchases). In the feature space, we have a feature called Total Purchases- Sum of (NumStorePurchases,WebPurchases,CatalogPurchases) along with other variables Income, Kidhome, Teenhome, Recency, MntWines, MntFruits, MntMeatProducts, MntFishProducts, MntSweetProducts, MntGoldProds, NumDealsPurchases, NumWebPurchases, NumCatalogPurchases, NumStorePurchases, NumWebVisitsMonth, AcceptedCmp3, AcceptedCmp4, AcceptedCmp5, AcceptedCmp1, AcceptedCmp2, Response, Complain, Country. When we are doing an OLS regression by splitting out test-train data by 70-30% & finding out RMSE(Root Mean Squared Error), value is a minuscule number-3.8200863988425333e-13.\nSo, I am little bit skeptical with this number, although according to my understanding Multicollinearity do not impact predictive viability of a model, it's just impact the significance of each regressors.\n\n\n\n\nIs it somehow impacting the model predictive accuracy or maybe some other factors like data leakage can reduce the RMSE as well due to the presence of Y on X(Feature space) itself or maybe this small RMSE value can be possible?\n\n\n\n\nLooking for your reply community members.\n\n\n\n\nThanks.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":677034,"score":3},{"answer_id":677069,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":677132,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>Lasso is not capable of doing that as explained <a href=\"https://hbiostat.org/hdata\" rel=\"noreferrer\">here</a>.  No other simple method can either.  As explained in that link, data reduction (unsupervised learning) is generally a better approach than selection.</p>\n<p>Your sample size is probably not large enough for the data to tell you how to choose <span class=\"math-container\">$\\lambda$</span>.</p>\n<p>If you use any method you like on your dataset, compute a variable importance measure for all candidate features, and bootstrap the importances to obtain 0.95 confidence intervals on each variable's importance, you'll be shocked at the CL widths.  The data do not have sufficient information to tell you how important the features are, and if you can't assess importance you can't do reliable selection.</p>\n<p>Your outcome variable may have a strange distribution.  Consider <a href=\"https://hbiostat.org/ordinal\" rel=\"noreferrer\">semiparametric models</a>.</p>\n","answer_id":677132,"answer_text":"Lasso is not capable of doing that as explained here (https://hbiostat.org/hdata).  No other simple method can either.  As explained in that link, data reduction (unsupervised learning) is generally a better approach than selection.\n\n\n\n\nYour sample size is probably not large enough for the data to tell you how to choose $\\lambda$.\n\n\n\n\nIf you use any method you like on your dataset, compute a variable importance measure for all candidate features, and bootstrap the importances to obtain 0.95 confidence intervals on each variable's importance, you'll be shocked at the CL widths.  The data do not have sufficient information to tell you how important the features are, and if you can't assess importance you can't do reliable selection.\n\n\n\n\nYour outcome variable may have a strange distribution.  Consider semiparametric models (https://hbiostat.org/ordinal).","answer_url":"https://stats.stackexchange.com/a/677132","author":"Frank Harrell","author_url":"https://stats.stackexchange.com/users/4253/frank-harrell","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-09-10T22:55:08+00:00","is_accepted":true,"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":677131,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Frank Harrell","profile_url":"https://stats.stackexchange.com/users/4253/frank-harrell","user_type":"registered"},"created_at":"2026-09-10T22:55:08+00:00","raw_file":"raw/codex_api_v1/3f959895a29b33d83894e5370d82e1c0cf87f20ac57fa423ebc923738357c657_1790825253957066500_0.json","raw_sha256":"ddd8808039e410ca99f97e2a7f12c307f046c4e5c3e184683bc12f816e6f49fc","revision_guid":"B76B8D57-E57B-4CD1-82D8-CCE116B92262","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/B76B8D57-E57B-4CD1-82D8-CCE116B92262/view-source"}],"score":7,"updated_at":"2026-09-10T22:55:08+00:00"},{"answer_html":"<p>You write</p>\n<blockquote>\n<p>For a secondary, exploratory analysis I want to identify which of\nthese screening items and test scores are more strongly associated\nwith the biomarker concentration</p>\n</blockquote>\n<p>If this is an accurate statement of your goal, then you can simply do 50 bivariate regressions and see which is strongest. This doesn't lead to a model, but you question doesn't require one. It doesn't do variable selection but see Frank's post on the inherent difficulties there. You can include parameter estimates and CIs and SEs.</p>\n<p>An alternative is to reduce the number of variables <em>a priori</em> either by something like factor analysis or by substantive knowledge. The types of variables you mention often have high collinearity and you may be able to combine them without much loss of information.</p>\n","answer_id":677133,"answer_text":"You write\n\n\n\n\n\n\n\nFor a secondary, exploratory analysis I want to identify which of\nthese screening items and test scores are more strongly associated\nwith the biomarker concentration\n\n\n\n\n\n\n\nIf this is an accurate statement of your goal, then you can simply do 50 bivariate regressions and see which is strongest. This doesn't lead to a model, but you question doesn't require one. It doesn't do variable selection but see Frank's post on the inherent difficulties there. You can include parameter estimates and CIs and SEs.\n\n\n\n\nAn alternative is to reduce the number of variables a priori either by something like factor analysis or by substantive knowledge. The types of variables you mention often have high collinearity and you may be able to combine them without much loss of information.","answer_url":"https://stats.stackexchange.com/a/677133","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":"2026-09-10T23:06:19+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":677131,"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":"2026-09-10T23:06:19+00:00","raw_file":"raw/codex_api_v1/3f959895a29b33d83894e5370d82e1c0cf87f20ac57fa423ebc923738357c657_1790825253957066500_0.json","raw_sha256":"ddd8808039e410ca99f97e2a7f12c307f046c4e5c3e184683bc12f816e6f49fc","revision_guid":"FAB9DA36-EDCB-41AB-A901-F0B023A8C5FE","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/FAB9DA36-EDCB-41AB-A901-F0B023A8C5FE/view-source"}],"score":2,"updated_at":"2026-09-10T23:06:19+00:00"},{"answer_html":"<p>I think this depends entirely on what you mean by &quot;identify&quot; and &quot;associated&quot;.</p>\n<p>Barring any unrealistic asks (e.g. hoping that LASSO can magically identify truly associated variables, causal or otherwise, in a manner which could generalize to new samples and new populations across time and space), there seems to be some evidence LASSO can identify predictors under some understandable assumptions.</p>\n<p>Simulations from <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC2732298/\" rel=\"nofollow noreferrer\">Genome-wide association analysis by lasso penalized logistic regression</a> seem to suggest that LASSO <em>can</em> correctly identify main effects (and interactions) in large scale scenarios.  The approach seems to do particularly well when:</p>\n<ul>\n<li>The sample size was sufficiently large, and</li>\n<li>Predictors were not strongly correlated.</li>\n</ul>\n<p>Your <span class=\"math-container\">$p/n = 1/2$</span>, whereas they examine <span class=\"math-container\">$p/n$</span> as large as 50 (although their <span class=\"math-container\">$n$</span> is much larger than yours). Now, the approach described is not a 1:1 with your problem.  In particular, this study requires the analyst to choose in advance the number of predictors to retain meaning you can't magically &quot;identify which of these screening items and test scores are more strongly associated with the biomarker concentration&quot;.  Additionally, the approach described in the paper seems to be deficient when predictors are highly correlated.  This is to be expected.</p>\n<p>If you were to use this approach for your stated <span class=\"math-container\">$n$</span> and <span class=\"math-container\">$p$</span>, I would suggest performing similar simulations as described in the linked paper to better understand the operating characteristics of the procedure.  If this sounds like too high a bar to meet, I would suggest avoiding the approach completely (lest you erroneously lend too much credit to the method).</p>\n","answer_id":677134,"answer_text":"I think this depends entirely on what you mean by \"identify\" and \"associated\".\n\n\n\n\nBarring any unrealistic asks (e.g. hoping that LASSO can magically identify truly associated variables, causal or otherwise, in a manner which could generalize to new samples and new populations across time and space), there seems to be some evidence LASSO can identify predictors under some understandable assumptions.\n\n\n\n\nSimulations from Genome-wide association analysis by lasso penalized logistic regression (https://pmc.ncbi.nlm.nih.gov/articles/PMC2732298/) seem to suggest that LASSO can correctly identify main effects (and interactions) in large scale scenarios.  The approach seems to do particularly well when:\n\n\n\n\n\nThe sample size was sufficiently large, and\n\n\n\n\nPredictors were not strongly correlated.\n\n\n\n\n\nYour $p/n = 1/2$, whereas they examine $p/n$ as large as 50 (although their $n$ is much larger than yours). Now, the approach described is not a 1:1 with your problem.  In particular, this study requires the analyst to choose in advance the number of predictors to retain meaning you can't magically \"identify which of these screening items and test scores are more strongly associated with the biomarker concentration\".  Additionally, the approach described in the paper seems to be deficient when predictors are highly correlated.  This is to be expected.\n\n\n\n\nIf you were to use this approach for your stated $n$ and $p$, I would suggest performing similar simulations as described in the linked paper to better understand the operating characteristics of the procedure.  If this sounds like too high a bar to meet, I would suggest avoiding the approach completely (lest you erroneously lend too much credit to the method).","answer_url":"https://stats.stackexchange.com/a/677134","author":"Demetri Pananos","author_url":"https://stats.stackexchange.com/users/111259/demetri-pananos","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-09-11T00:40:00+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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Harrell","profile_url":"https://stats.stackexchange.com/users/4253/frank-harrell","user_type":"registered"},"created_at":"2026-09-10T22:55:08+00:00","raw_file":"raw/codex_api_v1/3f959895a29b33d83894e5370d82e1c0cf87f20ac57fa423ebc923738357c657_1790825253957066500_0.json","raw_sha256":"ddd8808039e410ca99f97e2a7f12c307f046c4e5c3e184683bc12f816e6f49fc","revision_guid":"B76B8D57-E57B-4CD1-82D8-CCE116B92262","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/B76B8D57-E57B-4CD1-82D8-CCE116B92262/view-source"}],"url":"https://stats.stackexchange.com/a/677132"},{"author":"Peter Flom","author_url":"https://stats.stackexchange.com/users/686/peter-flom","content_license":"CC BY-SA 4.0","context_id":"677133","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":"2026-09-10T23:06:19+00:00","raw_file":"raw/codex_api_v1/3f959895a29b33d83894e5370d82e1c0cf87f20ac57fa423ebc923738357c657_1790825253957066500_0.json","raw_sha256":"ddd8808039e410ca99f97e2a7f12c307f046c4e5c3e184683bc12f816e6f49fc","revision_guid":"FAB9DA36-EDCB-41AB-A901-F0B023A8C5FE","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/FAB9DA36-EDCB-41AB-A901-F0B023A8C5FE/view-source"}],"url":"https://stats.stackexchange.com/a/677133"},{"author":"Demetri Pananos","author_url":"https://stats.stackexchange.com/users/111259/demetri-pananos","content_license":"CC BY-SA 4.0","context_id":"677134","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Demetri 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Pananos","profile_url":"https://stats.stackexchange.com/users/111259/demetri-pananos","user_type":"registered"},"created_at":"2026-09-11T00:54:12+00:00","raw_file":"raw/codex_api_v1/3f959895a29b33d83894e5370d82e1c0cf87f20ac57fa423ebc923738357c657_1790825253957066500_0.json","raw_sha256":"ddd8808039e410ca99f97e2a7f12c307f046c4e5c3e184683bc12f816e6f49fc","revision_guid":"061B28DB-0576-4492-97DB-660BD78AF69A","revision_number":3,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/061B28DB-0576-4492-97DB-660BD78AF69A/view-source"}],"url":"https://stats.stackexchange.com/a/677134"}],"contexts":[{"context_id":"question","html":"<p>I have baseline data on 100 participants from an ongoing longitudinal study. At the screening visit each participant answered sociodemographic, clinical and lifestyle questions and completed a cognitive screening battery — more than 50 candidate variables in total. A blood sample drawn at the same visit gives the serum concentration of a protein of interest, which is my (continuous) outcome.</p>\n<p>For a secondary, exploratory analysis I want to identify which of these screening items and test scores are more strongly associated with the biomarker concentration. However, this is not a prediction problem: I am not building a model to apply to new individuals, but trying to establish which of the screening variables are associated with the biomarker.</p>\n<p>Since the number of candidate variables is large relative to the sample size (n/p ≈ 2), an unpenalised model with all variables is not viable and stepwise selection is widely discouraged, so my first thought was LASSO with λ chosen by cross-validation. I am unsure this is defensible: selection at this ratio seems likely to be unstable, and inference on LASSO-selected variables is not valid.</p>\n<ol>\n<li>Is LASSO appropriate when the goal is identifying associated variables rather than predicting new observations?</li>\n<li>With n = 100 and ~50 candidate predictors, is the selected set stable enough to support any substantive association?</li>\n<li>If it is not, what would you recommend instead?</li>\n</ol>\n","text":"I have baseline data on 100 participants from an ongoing longitudinal study. At the screening visit each participant answered sociodemographic, clinical and lifestyle questions and completed a cognitive screening battery — more than 50 candidate variables in total. A blood sample drawn at the same visit gives the serum concentration of a protein of interest, which is my (continuous) outcome.\n\n\n\n\nFor a secondary, exploratory analysis I want to identify which of these screening items and test scores are more strongly associated with the biomarker concentration. However, this is not a prediction problem: I am not building a model to apply to new individuals, but trying to establish which of the screening variables are associated with the biomarker.\n\n\n\n\nSince the number of candidate variables is large relative to the sample size (n/p ≈ 2), an unpenalised model with all variables is not viable and stepwise selection is widely discouraged, so my first thought was LASSO with λ chosen by cross-validation. I am unsure this is defensible: selection at this ratio seems likely to be unstable, and inference on LASSO-selected variables is not valid.\n\n\n\n\n\nIs LASSO appropriate when the goal is identifying associated variables rather than predicting new observations?\n\n\n\n\nWith n = 100 and ~50 candidate predictors, is the selected set stable enough to support any substantive association?\n\n\n\n\nIf it is not, what would you recommend instead?"},{"context_id":"677132","html":"<p>Lasso is not capable of doing that as explained <a href=\"https://hbiostat.org/hdata\" rel=\"noreferrer\">here</a>.  No other simple method can either.  As explained in that link, data reduction (unsupervised learning) is generally a better approach than selection.</p>\n<p>Your sample size is probably not large enough for the data to tell you how to choose <span class=\"math-container\">$\\lambda$</span>.</p>\n<p>If you use any method you like on your dataset, compute a variable importance measure for all candidate features, and bootstrap the importances to obtain 0.95 confidence intervals on each variable's importance, you'll be shocked at the CL widths.  The data do not have sufficient information to tell you how important the features are, and if you can't assess importance you can't do reliable selection.</p>\n<p>Your outcome variable may have a strange distribution.  Consider <a href=\"https://hbiostat.org/ordinal\" rel=\"noreferrer\">semiparametric models</a>.</p>\n","text":"Lasso is not capable of doing that as explained here (https://hbiostat.org/hdata).  No other simple method can either.  As explained in that link, data reduction (unsupervised learning) is generally a better approach than selection.\n\n\n\n\nYour sample size is probably not large enough for the data to tell you how to choose $\\lambda$.\n\n\n\n\nIf you use any method you like on your dataset, compute a variable importance measure for all candidate features, and bootstrap the importances to obtain 0.95 confidence intervals on each variable's importance, you'll be shocked at the CL widths.  The data do not have sufficient information to tell you how important the features are, and if you can't assess importance you can't do reliable selection.\n\n\n\n\nYour outcome variable may have a strange distribution.  Consider semiparametric models (https://hbiostat.org/ordinal)."},{"context_id":"677133","html":"<p>You write</p>\n<blockquote>\n<p>For a secondary, exploratory analysis I want to identify which of\nthese screening items and test scores are more strongly associated\nwith the biomarker concentration</p>\n</blockquote>\n<p>If this is an accurate statement of your goal, then you can simply do 50 bivariate regressions and see which is strongest. This doesn't lead to a model, but you question doesn't require one. It doesn't do variable selection but see Frank's post on the inherent difficulties there. You can include parameter estimates and CIs and SEs.</p>\n<p>An alternative is to reduce the number of variables <em>a priori</em> either by something like factor analysis or by substantive knowledge. The types of variables you mention often have high collinearity and you may be able to combine them without much loss of information.</p>\n","text":"You write\n\n\n\n\n\n\n\nFor a secondary, exploratory analysis I want to identify which of\nthese screening items and test scores are more strongly associated\nwith the biomarker concentration\n\n\n\n\n\n\n\nIf this is an accurate statement of your goal, then you can simply do 50 bivariate regressions and see which is strongest. This doesn't lead to a model, but you question doesn't require one. It doesn't do variable selection but see Frank's post on the inherent difficulties there. You can include parameter estimates and CIs and SEs.\n\n\n\n\nAn alternative is to reduce the number of variables a priori either by something like factor analysis or by substantive knowledge. The types of variables you mention often have high collinearity and you may be able to combine them without much loss of information."},{"context_id":"677134","html":"<p>I think this depends entirely on what you mean by &quot;identify&quot; and &quot;associated&quot;.</p>\n<p>Barring any unrealistic asks (e.g. hoping that LASSO can magically identify truly associated variables, causal or otherwise, in a manner which could generalize to new samples and new populations across time and space), there seems to be some evidence LASSO can identify predictors under some understandable assumptions.</p>\n<p>Simulations from <a href=\"https://pmc.ncbi.nlm.nih.gov/articles/PMC2732298/\" rel=\"nofollow noreferrer\">Genome-wide association analysis by lasso penalized logistic regression</a> seem to suggest that LASSO <em>can</em> correctly identify main effects (and interactions) in large scale scenarios.  The approach seems to do particularly well when:</p>\n<ul>\n<li>The sample size was sufficiently large, and</li>\n<li>Predictors were not strongly correlated.</li>\n</ul>\n<p>Your <span class=\"math-container\">$p/n = 1/2$</span>, whereas they examine <span class=\"math-container\">$p/n$</span> as large as 50 (although their <span class=\"math-container\">$n$</span> is much larger than yours). Now, the approach described is not a 1:1 with your problem.  In particular, this study requires the analyst to choose in advance the number of predictors to retain meaning you can't magically &quot;identify which of these screening items and test scores are more strongly associated with the biomarker concentration&quot;.  Additionally, the approach described in the paper seems to be deficient when predictors are highly correlated.  This is to be expected.</p>\n<p>If you were to use this approach for your stated <span class=\"math-container\">$n$</span> and <span class=\"math-container\">$p$</span>, I would suggest performing similar simulations as described in the linked paper to better understand the operating characteristics of the procedure.  If this sounds like too high a bar to meet, I would suggest avoiding the approach completely (lest you erroneously lend too much credit to the method).</p>\n","text":"I think this depends entirely on what you mean by \"identify\" and \"associated\".\n\n\n\n\nBarring any unrealistic asks (e.g. hoping that LASSO can magically identify truly associated variables, causal or otherwise, in a manner which could generalize to new samples and new populations across time and space), there seems to be some evidence LASSO can identify predictors under some understandable assumptions.\n\n\n\n\nSimulations from Genome-wide association analysis by lasso penalized logistic regression (https://pmc.ncbi.nlm.nih.gov/articles/PMC2732298/) seem to suggest that LASSO can correctly identify main effects (and interactions) in large scale scenarios.  The approach seems to do particularly well when:\n\n\n\n\n\nThe sample size was sufficiently large, and\n\n\n\n\nPredictors were not strongly correlated.\n\n\n\n\n\nYour $p/n = 1/2$, whereas they examine $p/n$ as large as 50 (although their $n$ is much larger than yours). Now, the approach described is not a 1:1 with your problem.  In particular, this study requires the analyst to choose in advance the number of predictors to retain meaning you can't magically \"identify which of these screening items and test scores are more strongly associated with the biomarker concentration\".  Additionally, the approach described in the paper seems to be deficient when predictors are highly correlated.  This is to be expected.\n\n\n\n\nIf you were to use this approach for your stated $n$ and $p$, I would suggest performing similar simulations as described in the linked paper to better understand the operating characteristics of the procedure.  If this sounds like too high a bar to meet, I would suggest avoiding the approach completely (lest you erroneously lend too much credit to the method)."}],"domain":"statistics","external_citations":["https://hbiostat.org/hdata","https://hbiostat.org/ordinal","https://pmc.ncbi.nlm.nih.gov/articles/PMC2732298/"],"ground_truth_type":"metadata_grounded","group_id":"1ca773ac77418f5537eb4cb3f4b5cc3ffa61e1176ab3e0966b510cd8fa46abd0","hard_case_family":["multiple_sources","multiple_answer_candidates"],"id":"RHM-e716d0859b01a89e92869c96","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":"always.learning","profile_url":"https://stats.stackexchange.com/users/425636/always-learning","user_type":"registered"},"created_at":"2026-09-10T19:13:22+00:00","raw_file":"raw/codex_api_v1/3f959895a29b33d83894e5370d82e1c0cf87f20ac57fa423ebc923738357c657_1790825253957066500_0.json","raw_sha256":"ddd8808039e410ca99f97e2a7f12c307f046c4e5c3e184683bc12f816e6f49fc","revision_guid":"64EEF096-F835-4A53-A6C1-1E6FEE21AC05","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/64EEF096-F835-4A53-A6C1-1E6FEE21AC05/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-09-11T03:18:37+00:00","raw_file":"raw/codex_api_v1/3f959895a29b33d83894e5370d82e1c0cf87f20ac57fa423ebc923738357c657_1790825253957066500_0.json","raw_sha256":"ddd8808039e410ca99f97e2a7f12c307f046c4e5c3e184683bc12f816e6f49fc","revision_guid":"CC408FD4-8B76-43EC-AC41-7C9D3104DB64","revision_number":null,"revision_type":"vote_based","revision_url":"https://stats.stackexchange.com/revisions/CC408FD4-8B76-43EC-AC41-7C9D3104DB64/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:677131","source_record_sha256":"cc1560da7369f756e5016f7a1c68b2a77298aab60a4baada91fedefea64d0b5e","source_url":"https://stats.stackexchange.com/questions/677131/lasso-to-identify-which-of-50-screening-variables-relate-to-a-biomarker-with-n","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"LASSO to identify which of ~50 screening variables relate to a biomarker, with n = 100?\nI have baseline data on 100 participants from an ongoing longitudinal study. At the screening visit each participant answered sociodemographic, clinical and lifestyle questions and completed a cognitive screening battery — more than 50 candidate variables in total. A blood sample drawn at the same visit gives the serum concentration of a protein of interest, which is my (continuous) outcome.\n\n\n\n\nFor a secondary, exploratory analysis I want to identify which of these screening items and test scores are more strongly associated with the biomarker concentration. However, this is not a prediction problem: I am not building a model to apply to new individuals, but trying to establish which of the screening variables are associated with the biomarker.\n\n\n\n\nSince the number of candidate variables is large relative to the sample size (n/p ≈ 2), an unpenalised model with all variables is not viable and stepwise selection is widely discouraged, so my first thought was LASSO with λ chosen by cross-validation. I am unsure this is defensible: selection at this ratio seems likely to be unstable, and inference on LASSO-selected variables is not valid.\n\n\n\n\n\nIs LASSO appropriate when the goal is identifying associated variables rather than predicting new observations?\n\n\n\n\nWith n = 100 and ~50 candidate predictors, is the selected set stable enough to support any substantive association?\n\n\n\n\nIf it is not, what would you recommend instead?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":677132,"score":7},{"answer_id":677133,"score":2},{"answer_id":677134,"score":4}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":677268,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I would not go through mean and variance here. Your model for data generation is based on <span class=\"math-container\">$\\alpha$</span> and <span class=\"math-container\">$\\beta$</span> right? So why not work with them? Your population variable <span class=\"math-container\">$\\theta$</span>, as per your model is beta-distirbuted, so why not work with beta-likelihood? The problem is that sample variance and sample mean of a beta-distributed variable set, such as <span class=\"math-container\">$\\{\\theta_i\\}$</span>, are not independent variables, so you should not estimate them independently of each other.</p>\n<p>If I had a sample <span class=\"math-container\">$\\{y_{ij}\\}$</span> I would estimate it like this:</p>\n<ol>\n<li>Have variables <span class=\"math-container\">$u$</span>, <span class=\"math-container\">$v$</span>, and take <span class=\"math-container\">$\\frac{\\alpha}{\\alpha+\\beta}=expit\\left(u\\right)=\\frac{1}{1+\\exp\\left(-u\\right)}$</span>, <span class=\"math-container\">$\\alpha=softplus(v)=\\log\\left(1+\\exp(v)\\right)$</span></li>\n<li><span class=\"math-container\">$\\sum_{j}y_{ij}=y_i\\sim BetaBinomial\\left(k, \\alpha,\\beta\\right)$</span></li>\n</ol>\n<p>Optimise jointly <span class=\"math-container\">$u,v$</span> (maximum likelihood).</p>\n<p>So your sample size calculation would be a wrap-around for this procedure, i.e. select, <span class=\"math-container\">$n, k$</span> etc. It may be slower, but not too slow with your numbers. But it will be giving correct estimates even when <span class=\"math-container\">$\\theta$</span> is close to the edges for the given variance (and thus cannot be treated as normal).</p>\n<hr />\n<p>If you want to stick to variance and mean, you should be honest with yourself and state <span class=\"math-container\">$\\theta_i \\sim Normal\\left(\\mu,\\sigma^2\\right)$</span>. If you get reasonable numbers, good, if not then you know your approximation is not suitable</p>\n","answer_id":677267,"answer_text":"I would not go through mean and variance here. Your model for data generation is based on $\\alpha$ and $\\beta$ right? So why not work with them? Your population variable $\\theta$, as per your model is beta-distirbuted, so why not work with beta-likelihood? The problem is that sample variance and sample mean of a beta-distributed variable set, such as $\\{\\theta_i\\}$, are not independent variables, so you should not estimate them independently of each other.\n\n\n\n\nIf I had a sample $\\{y_{ij}\\}$ I would estimate it like this:\n\n\n\n\n\nHave variables $u$, $v$, and take $\\frac{\\alpha}{\\alpha+\\beta}=expit\\left(u\\right)=\\frac{1}{1+\\exp\\left(-u\\right)}$, $\\alpha=softplus(v)=\\log\\left(1+\\exp(v)\\right)$\n\n\n\n\n$\\sum_{j}y_{ij}=y_i\\sim BetaBinomial\\left(k, \\alpha,\\beta\\right)$\n\n\n\n\n\nOptimise jointly $u,v$ (maximum likelihood).\n\n\n\n\nSo your sample size calculation would be a wrap-around for this procedure, i.e. select, $n, k$ etc. It may be slower, but not too slow with your numbers. But it will be giving correct estimates even when $\\theta$ is close to the edges for the given variance (and thus cannot be treated as normal).\n\n\n\n\n\n\n\nIf you want to stick to variance and mean, you should be honest with yourself and state $\\theta_i \\sim Normal\\left(\\mu,\\sigma^2\\right)$. If you get reasonable numbers, good, if not then you know your approximation is not suitable","answer_url":"https://stats.stackexchange.com/a/677267","author":"Cryo","author_url":"https://stats.stackexchange.com/users/275239/cryo","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-09-26T12:24:08+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":677266,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Cryo","profile_url":"https://stats.stackexchange.com/users/275239/cryo","user_type":"registered"},"created_at":"2026-09-26T12:24:08+00:00","raw_file":"raw/codex_api_v1/ab5f4cd7f0a10bde5970354a9b213efcc81e232042487437e8579705d4ca6a20_1790825258916612700_0.json","raw_sha256":"4cf167c399d03b9ae013b65260fcb4e38139c42cfc70aba4807f070550c1768e","revision_guid":"D52BEFB1-287A-4A8F-B3B4-FF67FD14E1AD","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/D52BEFB1-287A-4A8F-B3B4-FF67FD14E1AD/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Cryo","profile_url":"https://stats.stackexchange.com/users/275239/cryo","user_type":"registered"},"created_at":"2026-09-26T12:33:54+00:00","raw_file":"raw/codex_api_v1/ab5f4cd7f0a10bde5970354a9b213efcc81e232042487437e8579705d4ca6a20_1790825258916612700_0.json","raw_sha256":"4cf167c399d03b9ae013b65260fcb4e38139c42cfc70aba4807f070550c1768e","revision_guid":"24348886-EE3F-4779-9F2E-6DF7895E9D85","revision_number":2,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/24348886-EE3F-4779-9F2E-6DF7895E9D85/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"User1865345","profile_url":"https://stats.stackexchange.com/users/362671/user1865345","user_type":"registered"},"created_at":"2026-09-26T13:34:16+00:00","raw_file":"raw/codex_api_v1/ab5f4cd7f0a10bde5970354a9b213efcc81e232042487437e8579705d4ca6a20_1790825258916612700_0.json","raw_sha256":"4cf167c399d03b9ae013b65260fcb4e38139c42cfc70aba4807f070550c1768e","revision_guid":"57B9D992-5586-4BC1-9973-DD3482A5AA98","revision_number":3,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/57B9D992-5586-4BC1-9973-DD3482A5AA98/view-source"}],"score":5,"updated_at":"2026-09-26T13:34:16+00:00"},{"answer_html":"<p>I think you can find the mean and variance of <span class=\"math-container\">$\\bar y$</span> analytically.  Clearly <span class=\"math-container\">$\\mathbb E[\\bar y]=\\frac{\\alpha}{\\alpha+\\beta}$</span> and, using the law of total variance <span class=\"math-container\">$$\\operatorname{Var}(\\bar y) = \\frac{\\alpha \\beta}{nk(\\alpha+\\beta)^2} \\frac{\\alpha+\\beta+n}{\\alpha+\\beta+1} = \\frac{1}{nk}E[\\bar y]\\left(1-E[\\bar y]\\right) \\frac{\\alpha+\\beta+k}{\\alpha+\\beta+1}.$$</span></p>\n<p>Since <span class=\"math-container\">$\\alpha\\ge 0, \\beta\\ge 0, 0 \\le E[\\bar y]\\le 1$</span>, you can then say <span class=\"math-container\">$$\\operatorname{Var}(\\bar y) \\le \\frac{1}{n}E[\\bar y]\\left(1-E[\\bar y]\\right) \\le \\frac1{4n}.$$</span></p>\n<p>For given <span class=\"math-container\">$nk$</span>, you will minimise <span class=\"math-container\">$\\operatorname{Var}(\\bar y)$</span> when <span class=\"math-container\">$k$</span> is as small as possible, i.e. when <span class=\"math-container\">$k=1$</span> and <span class=\"math-container\">$n=nk$</span>, at which point <span class=\"math-container\">$\\operatorname{Var}(\\bar y) = \\frac{\\alpha \\beta}{n(\\alpha+\\beta)^2}= \\frac{1}{n}E[\\bar y]\\left(1-E[\\bar y]\\right)$</span>, again bounded above by <span class=\"math-container\">$\\frac1{4n}$</span>. As discussed on <a href=\"https://stats.stackexchange.com/q/677226/2958\">your previous question</a>, having <span class=\"math-container\">$k=1$</span> would make it impossible to estimate <span class=\"math-container\">$\\alpha$</span> and <span class=\"math-container\">$\\beta$</span> separately.</p>\n<p>So using <span class=\"math-container\">$k=1$</span> together with <span class=\"math-container\">$n$</span> large enough to make <span class=\"math-container\">$\\frac1{4n}$</span> small enough to meet your needs as an upper bound for <span class=\"math-container\">$\\operatorname{Var}(\\bar y)$</span> should work well.</p>\n<hr />\n<p>Here is an illustrative simulation in R confirming these (with minor simulation noise) for <span class=\"math-container\">$\\alpha=2$</span>, <span class=\"math-container\">$\\beta=3$</span> and <span class=\"math-container\">$nk=12$</span></p>\n<pre><code>yhatsim &lt;- function(alpha, beta, n, k){\n  thetai &lt;- rbeta(n, alpha, beta)\n  sum(rbinom(n, k, thetai)) / (n * k) \n  }\nyhat &lt;- function(alpha, beta, n, k, cases=10^6){\n  simyhat &lt;- replicate(cases, yhatsim(alpha, beta, n, k))\n  c(simulatedmean=mean(simyhat), \n    expectedmean=alpha/(alpha+beta), \n    simulatedvar=var(simyhat),\n    expectedvar=alpha*beta/(alpha+beta)^2*(alpha+beta+k)/(alpha+beta+1)/(n*k))\n  }\n\n\nset.seed(2026)\n\nyhat(alpha=2, beta=3, n=12, k=1)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#     0.4000867     0.4000000     0.0199709     0.0200000 \n\nyhat(alpha=2, beta=3, n=6, k=2)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.39994625    0.40000000    0.02330732    0.02333333 \n\nyhat(alpha=2, beta=3, n=4, k=3)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#   0.40013683    0.40000000    0.02668078    0.02666667 \n\nyhat(alpha=2, beta=3, n=3, k=4)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.39973175    0.40000000    0.03001747    0.03000000 \n\nyhat(alpha=2, beta=3, n=2, k=6)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.40039333    0.40000000    0.03666519    0.03666667 \n\nyhat(alpha=2, beta=3, n=1, k=12)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.39992283    0.40000000    0.05659828    0.05666667 \n</code></pre>\n","answer_id":677268,"answer_text":"I think you can find the mean and variance of $\\bar y$ analytically.  Clearly $\\mathbb E[\\bar y]=\\frac{\\alpha}{\\alpha+\\beta}$ and, using the law of total variance $$\\operatorname{Var}(\\bar y) = \\frac{\\alpha \\beta}{nk(\\alpha+\\beta)^2} \\frac{\\alpha+\\beta+n}{\\alpha+\\beta+1} = \\frac{1}{nk}E[\\bar y]\\left(1-E[\\bar y]\\right) \\frac{\\alpha+\\beta+k}{\\alpha+\\beta+1}.$$\n\n\n\n\nSince $\\alpha\\ge 0, \\beta\\ge 0, 0 \\le E[\\bar y]\\le 1$, you can then say $$\\operatorname{Var}(\\bar y) \\le \\frac{1}{n}E[\\bar y]\\left(1-E[\\bar y]\\right) \\le \\frac1{4n}.$$\n\n\n\n\nFor given $nk$, you will minimise $\\operatorname{Var}(\\bar y)$ when $k$ is as small as possible, i.e. when $k=1$ and $n=nk$, at which point $\\operatorname{Var}(\\bar y) = \\frac{\\alpha \\beta}{n(\\alpha+\\beta)^2}= \\frac{1}{n}E[\\bar y]\\left(1-E[\\bar y]\\right)$, again bounded above by $\\frac1{4n}$. As discussed on your previous question (https://stats.stackexchange.com/q/677226/2958), having $k=1$ would make it impossible to estimate $\\alpha$ and $\\beta$ separately.\n\n\n\n\nSo using $k=1$ together with $n$ large enough to make $\\frac1{4n}$ small enough to meet your needs as an upper bound for $\\operatorname{Var}(\\bar y)$ should work well.\n\n\n\n\n\n\n\nHere is an illustrative simulation in R confirming these (with minor simulation noise) for $\\alpha=2$, $\\beta=3$ and $nk=12$\n\n\n\n\nyhatsim <- function(alpha, beta, n, k){\n  thetai <- rbeta(n, alpha, beta)\n  sum(rbinom(n, k, thetai)) / (n * k) \n  }\nyhat <- function(alpha, beta, n, k, cases=10^6){\n  simyhat <- replicate(cases, yhatsim(alpha, beta, n, k))\n  c(simulatedmean=mean(simyhat), \n    expectedmean=alpha/(alpha+beta), \n    simulatedvar=var(simyhat),\n    expectedvar=alpha*beta/(alpha+beta)^2*(alpha+beta+k)/(alpha+beta+1)/(n*k))\n  }\n\n\nset.seed(2026)\n\nyhat(alpha=2, beta=3, n=12, k=1)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#     0.4000867     0.4000000     0.0199709     0.0200000 \n\nyhat(alpha=2, beta=3, n=6, k=2)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.39994625    0.40000000    0.02330732    0.02333333 \n\nyhat(alpha=2, beta=3, n=4, k=3)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#   0.40013683    0.40000000    0.02668078    0.02666667 \n\nyhat(alpha=2, beta=3, n=3, k=4)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.39973175    0.40000000    0.03001747    0.03000000 \n\nyhat(alpha=2, beta=3, n=2, k=6)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.40039333    0.40000000    0.03666519    0.03666667 \n\nyhat(alpha=2, beta=3, n=1, k=12)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.39992283    0.40000000    0.05659828    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4.0","contributor":{"display_name":"User1865345","profile_url":"https://stats.stackexchange.com/users/362671/user1865345","user_type":"registered"},"created_at":"2026-09-26T13:34:16+00:00","raw_file":"raw/codex_api_v1/ab5f4cd7f0a10bde5970354a9b213efcc81e232042487437e8579705d4ca6a20_1790825258916612700_0.json","raw_sha256":"4cf167c399d03b9ae013b65260fcb4e38139c42cfc70aba4807f070550c1768e","revision_guid":"57B9D992-5586-4BC1-9973-DD3482A5AA98","revision_number":3,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/57B9D992-5586-4BC1-9973-DD3482A5AA98/view-source"}],"url":"https://stats.stackexchange.com/a/677267"},{"author":"Henry","author_url":"https://stats.stackexchange.com/users/2958/henry","content_license":"CC BY-SA 4.0","context_id":"677268","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Henry","profile_url":"https://stats.stackexchange.com/users/2958/henry","user_type":"registered"},"created_at":"2026-09-26T14:10:23+00:00","raw_file":"raw/codex_api_v1/ab5f4cd7f0a10bde5970354a9b213efcc81e232042487437e8579705d4ca6a20_1790825258916612700_0.json","raw_sha256":"4cf167c399d03b9ae013b65260fcb4e38139c42cfc70aba4807f070550c1768e","revision_guid":"C96EACA9-97B0-4929-B972-DA5D20ED4759","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/C96EACA9-97B0-4929-B972-DA5D20ED4759/view-source"}],"url":"https://stats.stackexchange.com/a/677268"}],"contexts":[{"context_id":"question","html":"<p>Here is a hierarchical data generating process (DGP):</p>\n<blockquote>\n<p>(Population) Layer 1: <span class=\"math-container\">$$\\theta_i \\overset{\\text{iid}}{\\sim} \\text{Beta}(\\alpha,\\ \\beta), \\qquad i = 1, \\dots, n$$</span></p>\n<p>(Individual) Layer 2: <span class=\"math-container\">$$y_{ij} \\mid \\theta_i \\overset{\\text{iid}}{\\sim}  \\text{Bernoulli}(\\theta_i), \\qquad j = 1, \\dots, k$$</span></p>\n</blockquote>\n<p><span class=\"math-container\">$$\\mu = E[\\theta_i], \\qquad \\tau^2 = \\operatorname{Var}(\\theta_i)$$</span></p>\n<p>Using a sample, my purpose is only to estimate the mean and the variance of the mean estimator. I want to know what values of <span class=\"math-container\">$n$</span> and <span class=\"math-container\">$k$</span> I should select to get good results (I know this hugely subjective) such that <span class=\"math-container\">$nk$</span> is minimized (assume that increasing <span class=\"math-container\">$n$</span> by 1 costs the same as increase <span class=\"math-container\">$k$</span> by 1).</p>\n<p>After doing some research, it seems the best way to handle this question is by a simulation study. Assuming <span class=\"math-container\">$\\alpha,\\ \\beta$</span> are known, I could sample from the DGP for different combinations of <span class=\"math-container\">$n$</span> and <span class=\"math-container\">$k$</span> and record the average length of the confidence intervals and average coverage rate at each combination. Since the mean estimator is unbiased regardless of the choice in <span class=\"math-container\">$n$</span> or <span class=\"math-container\">$k$</span>, I could use average CI length and average coverage rate to make sure I am not getting a misleadingly good coverage rate at the expense of a large CI.</p>\n<p>Here is how I plan to do this in R (I wrote the code to focus on readability instead of speed - I use a moment based estimator and consider different true combinations of parameters):</p>\n<pre><code>set.seed(2026)\n\nmu_vals &lt;- c(0.01, 0.05, 0.15, 0.25, 0.35, 0.45, 0.55, 0.65, 0.75, 0.85, 0.95, 0.99)\nn_var   &lt;- 10\nn_vals  &lt;- c(5, 15, 30, 50, 100, 200)\nk_vals  &lt;- c(1, 2, 3, 4, 5, 6)\nR       &lt;- 2000\nconf    &lt;- 0.95\n\nscenarios &lt;- data.frame()\n\nfor (mu in mu_vals) {\n  max_var &lt;- mu * (1 - mu)\n  for (v in 1:n_var) {\n    tau2 &lt;- (v / (n_var + 1)) * max_var\n    scenarios &lt;- rbind(scenarios, data.frame(mu = mu, tau2 = tau2))\n  }\n}\n\n\ncalc_mean &lt;- function(ybar_i) {\n  mean(ybar_i)\n}\n\ncalc_var_of_mean &lt;- function(ybar_i) {\n  n &lt;- length(ybar_i)\n  var(ybar_i) / n\n}\n\ncalc_coverage &lt;- function(lower, upper, mu) {\n  mean(lower &lt;= mu &amp; mu &lt;= upper)\n}\n\ncalc_avg_ci_length &lt;- function(lower, upper) {\n  mean(upper - lower)\n}\n\nresults &lt;- data.frame()\n\nfor (s in 1:nrow(scenarios)) {\n\n  mu   &lt;- scenarios<span class=\"math-container\">$mu[s]\n  tau2 &lt;- scenarios$</span>tau2[s]\n\n  alpha_plus_beta &lt;- mu * (1 - mu) / tau2 - 1\n  alpha &lt;- mu * alpha_plus_beta\n  beta  &lt;- (1 - mu) * alpha_plus_beta\n\n  cat(sprintf(&quot;Scenario %d of %d: mu = %.2f, tau2 = %.4f\\n&quot;,\n              s, nrow(scenarios), mu, tau2))\n\n  for (n in n_vals) {\n    for (k in k_vals) {\n\n      estimates     &lt;- numeric(R)\n      var_estimates &lt;- numeric(R)\n      lower         &lt;- numeric(R)\n      upper         &lt;- numeric(R)\n\n      t_crit &lt;- qt(1 - (1 - conf) / 2, df = n - 1)\n\n      for (r in 1:R) {\n\n        theta &lt;- rbeta(n, alpha, beta)\n\n        ybar_i &lt;- numeric(n)\n        for (i in 1:n) {\n          y &lt;- rbinom(k, size = 1, prob = theta[i])\n          ybar_i[i] &lt;- mean(y)\n        }\n\n        est   &lt;- calc_mean(ybar_i)\n        v_est &lt;- calc_var_of_mean(ybar_i)\n\n        estimates[r]     &lt;- est\n        var_estimates[r] &lt;- v_est\n        lower[r]         &lt;- est - t_crit * sqrt(v_est)\n        upper[r]         &lt;- est + t_crit * sqrt(v_est)\n      }\n\n      true_var_of_mean &lt;- (tau2 + (mu * (1 - mu) - tau2) / k) / n\n\n      results &lt;- rbind(results, data.frame(\n        mu                  = mu,\n        tau2                = tau2,\n        n                   = n,\n        k                   = k,\n        avg_estimate        = mean(estimates),\n        true_var_of_mean    = true_var_of_mean,\n        sim_var_of_mean     = var(estimates),\n        avg_est_var_of_mean = mean(var_estimates),\n        coverage            = calc_coverage(lower, upper, mu),\n        avg_ci_length       = calc_avg_ci_length(lower, upper)\n      ))\n    }\n  }\n}\n</code></pre>\n<p>When visualized, the results look like this (direct upload was not working - however it seems to show that when <span class=\"math-container\">$n$</span> and <span class=\"math-container\">$k$</span> are both large, for many cases, we get high coverage and smaller CI lengths on average): <a href=\"https://imgur.com/a/tgHbtLz\" rel=\"nofollow noreferrer\">https://imgur.com/a/tgHbtLz</a></p>\n<p>The tricky part now is to try and guess what the true value of <span class=\"math-container\">$\\alpha,\\ \\beta$</span> might be. If I can get some knowledge of this beforehand (e.g. possible range), I could try to determine what <span class=\"math-container\">$n,k$</span> to use if I want average CI length and average coverage rate to be within certain ranges.</p>\n<p>I am looking for feedback on my methodology. Should I have done this a different way?</p>\n","text":"Here is a hierarchical data generating process (DGP):\n\n\n\n\n\n\n\n(Population) Layer 1: $$\\theta_i \\overset{\\text{iid}}{\\sim} \\text{Beta}(\\alpha,\\ \\beta), \\qquad i = 1, \\dots, n$$\n\n\n\n\n(Individual) Layer 2: $$y_{ij} \\mid \\theta_i \\overset{\\text{iid}}{\\sim}  \\text{Bernoulli}(\\theta_i), \\qquad j = 1, \\dots, k$$\n\n\n\n\n\n\n\n$$\\mu = E[\\theta_i], \\qquad \\tau^2 = \\operatorname{Var}(\\theta_i)$$\n\n\n\n\nUsing a sample, my purpose is only to estimate the mean and the variance of the mean estimator. I want to know what values of $n$ and $k$ I should select to get good results (I know this hugely subjective) such that $nk$ is minimized (assume that increasing $n$ by 1 costs the same as increase $k$ by 1).\n\n\n\n\nAfter doing some research, it seems the best way to handle this question is by a simulation study. Assuming $\\alpha,\\ \\beta$ are known, I could sample from the DGP for different combinations of $n$ and $k$ and record the average length of the confidence intervals and average coverage rate at each combination. Since the mean estimator is unbiased regardless of the choice in $n$ or $k$, I could use average CI length and average coverage rate to make sure I am not getting a misleadingly good coverage rate at the expense of a large CI.\n\n\n\n\nHere is how I plan to do this in R (I wrote the code to focus on readability instead of speed - I use a moment based estimator and consider different true combinations of parameters):\n\n\n\n\nset.seed(2026)\n\nmu_vals <- c(0.01, 0.05, 0.15, 0.25, 0.35, 0.45, 0.55, 0.65, 0.75, 0.85, 0.95, 0.99)\nn_var   <- 10\nn_vals  <- c(5, 15, 30, 50, 100, 200)\nk_vals  <- c(1, 2, 3, 4, 5, 6)\nR       <- 2000\nconf    <- 0.95\n\nscenarios <- data.frame()\n\nfor (mu in mu_vals) {\n  max_var <- mu * (1 - mu)\n  for (v in 1:n_var) {\n    tau2 <- (v / (n_var + 1)) * max_var\n    scenarios <- rbind(scenarios, data.frame(mu = mu, tau2 = tau2))\n  }\n}\n\n\ncalc_mean <- function(ybar_i) {\n  mean(ybar_i)\n}\n\ncalc_var_of_mean <- function(ybar_i) {\n  n <- length(ybar_i)\n  var(ybar_i) / n\n}\n\ncalc_coverage <- function(lower, upper, mu) {\n  mean(lower <= mu & mu <= upper)\n}\n\ncalc_avg_ci_length <- function(lower, upper) {\n  mean(upper - lower)\n}\n\nresults <- data.frame()\n\nfor (s in 1:nrow(scenarios)) {\n\n  mu   <- scenarios$mu[s]\n  tau2 <- scenarios$tau2[s]\n\n  alpha_plus_beta <- mu * (1 - mu) / tau2 - 1\n  alpha <- mu * alpha_plus_beta\n  beta  <- (1 - mu) * alpha_plus_beta\n\n  cat(sprintf(\"Scenario %d of %d: mu = %.2f, tau2 = %.4f\\n\",\n              s, nrow(scenarios), mu, tau2))\n\n  for (n in n_vals) {\n    for (k in k_vals) {\n\n      estimates     <- numeric(R)\n      var_estimates <- numeric(R)\n      lower         <- numeric(R)\n      upper         <- numeric(R)\n\n      t_crit <- qt(1 - (1 - conf) / 2, df = n - 1)\n\n      for (r in 1:R) {\n\n        theta <- rbeta(n, alpha, beta)\n\n        ybar_i <- numeric(n)\n        for (i in 1:n) {\n          y <- rbinom(k, size = 1, prob = theta[i])\n          ybar_i[i] <- mean(y)\n        }\n\n        est   <- calc_mean(ybar_i)\n        v_est <- calc_var_of_mean(ybar_i)\n\n        estimates[r]     <- est\n        var_estimates[r] <- v_est\n        lower[r]         <- est - t_crit * sqrt(v_est)\n        upper[r]         <- est + t_crit * sqrt(v_est)\n      }\n\n      true_var_of_mean <- (tau2 + (mu * (1 - mu) - tau2) / k) / n\n\n      results <- rbind(results, data.frame(\n        mu                  = mu,\n        tau2                = tau2,\n        n                   = n,\n        k                   = k,\n        avg_estimate        = mean(estimates),\n        true_var_of_mean    = true_var_of_mean,\n        sim_var_of_mean     = var(estimates),\n        avg_est_var_of_mean = mean(var_estimates),\n        coverage            = calc_coverage(lower, upper, mu),\n        avg_ci_length       = calc_avg_ci_length(lower, upper)\n      ))\n    }\n  }\n}\n\n\n\n\n\nWhen visualized, the results look like this (direct upload was not working - however it seems to show that when $n$ and $k$ are both large, for many cases, we get high coverage and smaller CI lengths on average): https://imgur.com/a/tgHbtLz (https://imgur.com/a/tgHbtLz)\n\n\n\n\nThe tricky part now is to try and guess what the true value of $\\alpha,\\ \\beta$ might be. If I can get some knowledge of this beforehand (e.g. possible range), I could try to determine what $n,k$ to use if I want average CI length and average coverage rate to be within certain ranges.\n\n\n\n\nI am looking for feedback on my methodology. Should I have done this a different way?"},{"context_id":"677267","html":"<p>I would not go through mean and variance here. Your model for data generation is based on <span class=\"math-container\">$\\alpha$</span> and <span class=\"math-container\">$\\beta$</span> right? So why not work with them? Your population variable <span class=\"math-container\">$\\theta$</span>, as per your model is beta-distirbuted, so why not work with beta-likelihood? The problem is that sample variance and sample mean of a beta-distributed variable set, such as <span class=\"math-container\">$\\{\\theta_i\\}$</span>, are not independent variables, so you should not estimate them independently of each other.</p>\n<p>If I had a sample <span class=\"math-container\">$\\{y_{ij}\\}$</span> I would estimate it like this:</p>\n<ol>\n<li>Have variables <span class=\"math-container\">$u$</span>, <span class=\"math-container\">$v$</span>, and take <span class=\"math-container\">$\\frac{\\alpha}{\\alpha+\\beta}=expit\\left(u\\right)=\\frac{1}{1+\\exp\\left(-u\\right)}$</span>, <span class=\"math-container\">$\\alpha=softplus(v)=\\log\\left(1+\\exp(v)\\right)$</span></li>\n<li><span class=\"math-container\">$\\sum_{j}y_{ij}=y_i\\sim BetaBinomial\\left(k, \\alpha,\\beta\\right)$</span></li>\n</ol>\n<p>Optimise jointly <span class=\"math-container\">$u,v$</span> (maximum likelihood).</p>\n<p>So your sample size calculation would be a wrap-around for this procedure, i.e. select, <span class=\"math-container\">$n, k$</span> etc. It may be slower, but not too slow with your numbers. But it will be giving correct estimates even when <span class=\"math-container\">$\\theta$</span> is close to the edges for the given variance (and thus cannot be treated as normal).</p>\n<hr />\n<p>If you want to stick to variance and mean, you should be honest with yourself and state <span class=\"math-container\">$\\theta_i \\sim Normal\\left(\\mu,\\sigma^2\\right)$</span>. If you get reasonable numbers, good, if not then you know your approximation is not suitable</p>\n","text":"I would not go through mean and variance here. Your model for data generation is based on $\\alpha$ and $\\beta$ right? So why not work with them? Your population variable $\\theta$, as per your model is beta-distirbuted, so why not work with beta-likelihood? The problem is that sample variance and sample mean of a beta-distributed variable set, such as $\\{\\theta_i\\}$, are not independent variables, so you should not estimate them independently of each other.\n\n\n\n\nIf I had a sample $\\{y_{ij}\\}$ I would estimate it like this:\n\n\n\n\n\nHave variables $u$, $v$, and take $\\frac{\\alpha}{\\alpha+\\beta}=expit\\left(u\\right)=\\frac{1}{1+\\exp\\left(-u\\right)}$, $\\alpha=softplus(v)=\\log\\left(1+\\exp(v)\\right)$\n\n\n\n\n$\\sum_{j}y_{ij}=y_i\\sim BetaBinomial\\left(k, \\alpha,\\beta\\right)$\n\n\n\n\n\nOptimise jointly $u,v$ (maximum likelihood).\n\n\n\n\nSo your sample size calculation would be a wrap-around for this procedure, i.e. select, $n, k$ etc. It may be slower, but not too slow with your numbers. But it will be giving correct estimates even when $\\theta$ is close to the edges for the given variance (and thus cannot be treated as normal).\n\n\n\n\n\n\n\nIf you want to stick to variance and mean, you should be honest with yourself and state $\\theta_i \\sim Normal\\left(\\mu,\\sigma^2\\right)$. If you get reasonable numbers, good, if not then you know your approximation is not suitable"},{"context_id":"677268","html":"<p>I think you can find the mean and variance of <span class=\"math-container\">$\\bar y$</span> analytically.  Clearly <span class=\"math-container\">$\\mathbb E[\\bar y]=\\frac{\\alpha}{\\alpha+\\beta}$</span> and, using the law of total variance <span class=\"math-container\">$$\\operatorname{Var}(\\bar y) = \\frac{\\alpha \\beta}{nk(\\alpha+\\beta)^2} \\frac{\\alpha+\\beta+n}{\\alpha+\\beta+1} = \\frac{1}{nk}E[\\bar y]\\left(1-E[\\bar y]\\right) \\frac{\\alpha+\\beta+k}{\\alpha+\\beta+1}.$$</span></p>\n<p>Since <span class=\"math-container\">$\\alpha\\ge 0, \\beta\\ge 0, 0 \\le E[\\bar y]\\le 1$</span>, you can then say <span class=\"math-container\">$$\\operatorname{Var}(\\bar y) \\le \\frac{1}{n}E[\\bar y]\\left(1-E[\\bar y]\\right) \\le \\frac1{4n}.$$</span></p>\n<p>For given <span class=\"math-container\">$nk$</span>, you will minimise <span class=\"math-container\">$\\operatorname{Var}(\\bar y)$</span> when <span class=\"math-container\">$k$</span> is as small as possible, i.e. when <span class=\"math-container\">$k=1$</span> and <span class=\"math-container\">$n=nk$</span>, at which point <span class=\"math-container\">$\\operatorname{Var}(\\bar y) = \\frac{\\alpha \\beta}{n(\\alpha+\\beta)^2}= \\frac{1}{n}E[\\bar y]\\left(1-E[\\bar y]\\right)$</span>, again bounded above by <span class=\"math-container\">$\\frac1{4n}$</span>. As discussed on <a href=\"https://stats.stackexchange.com/q/677226/2958\">your previous question</a>, having <span class=\"math-container\">$k=1$</span> would make it impossible to estimate <span class=\"math-container\">$\\alpha$</span> and <span class=\"math-container\">$\\beta$</span> separately.</p>\n<p>So using <span class=\"math-container\">$k=1$</span> together with <span class=\"math-container\">$n$</span> large enough to make <span class=\"math-container\">$\\frac1{4n}$</span> small enough to meet your needs as an upper bound for <span class=\"math-container\">$\\operatorname{Var}(\\bar y)$</span> should work well.</p>\n<hr />\n<p>Here is an illustrative simulation in R confirming these (with minor simulation noise) for <span class=\"math-container\">$\\alpha=2$</span>, <span class=\"math-container\">$\\beta=3$</span> and <span class=\"math-container\">$nk=12$</span></p>\n<pre><code>yhatsim &lt;- function(alpha, beta, n, k){\n  thetai &lt;- rbeta(n, alpha, beta)\n  sum(rbinom(n, k, thetai)) / (n * k) \n  }\nyhat &lt;- function(alpha, beta, n, k, cases=10^6){\n  simyhat &lt;- replicate(cases, yhatsim(alpha, beta, n, k))\n  c(simulatedmean=mean(simyhat), \n    expectedmean=alpha/(alpha+beta), \n    simulatedvar=var(simyhat),\n    expectedvar=alpha*beta/(alpha+beta)^2*(alpha+beta+k)/(alpha+beta+1)/(n*k))\n  }\n\n\nset.seed(2026)\n\nyhat(alpha=2, beta=3, n=12, k=1)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#     0.4000867     0.4000000     0.0199709     0.0200000 \n\nyhat(alpha=2, beta=3, n=6, k=2)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.39994625    0.40000000    0.02330732    0.02333333 \n\nyhat(alpha=2, beta=3, n=4, k=3)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#   0.40013683    0.40000000    0.02668078    0.02666667 \n\nyhat(alpha=2, beta=3, n=3, k=4)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.39973175    0.40000000    0.03001747    0.03000000 \n\nyhat(alpha=2, beta=3, n=2, k=6)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.40039333    0.40000000    0.03666519    0.03666667 \n\nyhat(alpha=2, beta=3, n=1, k=12)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.39992283    0.40000000    0.05659828    0.05666667 \n</code></pre>\n","text":"I think you can find the mean and variance of $\\bar y$ analytically.  Clearly $\\mathbb E[\\bar y]=\\frac{\\alpha}{\\alpha+\\beta}$ and, using the law of total variance $$\\operatorname{Var}(\\bar y) = \\frac{\\alpha \\beta}{nk(\\alpha+\\beta)^2} \\frac{\\alpha+\\beta+n}{\\alpha+\\beta+1} = \\frac{1}{nk}E[\\bar y]\\left(1-E[\\bar y]\\right) \\frac{\\alpha+\\beta+k}{\\alpha+\\beta+1}.$$\n\n\n\n\nSince $\\alpha\\ge 0, \\beta\\ge 0, 0 \\le E[\\bar y]\\le 1$, you can then say $$\\operatorname{Var}(\\bar y) \\le \\frac{1}{n}E[\\bar y]\\left(1-E[\\bar y]\\right) \\le \\frac1{4n}.$$\n\n\n\n\nFor given $nk$, you will minimise $\\operatorname{Var}(\\bar y)$ when $k$ is as small as possible, i.e. when $k=1$ and $n=nk$, at which point $\\operatorname{Var}(\\bar y) = \\frac{\\alpha \\beta}{n(\\alpha+\\beta)^2}= \\frac{1}{n}E[\\bar y]\\left(1-E[\\bar y]\\right)$, again bounded above by $\\frac1{4n}$. As discussed on your previous question (https://stats.stackexchange.com/q/677226/2958), having $k=1$ would make it impossible to estimate $\\alpha$ and $\\beta$ separately.\n\n\n\n\nSo using $k=1$ together with $n$ large enough to make $\\frac1{4n}$ small enough to meet your needs as an upper bound for $\\operatorname{Var}(\\bar y)$ should work well.\n\n\n\n\n\n\n\nHere is an illustrative simulation in R confirming these (with minor simulation noise) for $\\alpha=2$, $\\beta=3$ and $nk=12$\n\n\n\n\nyhatsim <- function(alpha, beta, n, k){\n  thetai <- rbeta(n, alpha, beta)\n  sum(rbinom(n, k, thetai)) / (n * k) \n  }\nyhat <- function(alpha, beta, n, k, cases=10^6){\n  simyhat <- replicate(cases, yhatsim(alpha, beta, n, k))\n  c(simulatedmean=mean(simyhat), \n    expectedmean=alpha/(alpha+beta), \n    simulatedvar=var(simyhat),\n    expectedvar=alpha*beta/(alpha+beta)^2*(alpha+beta+k)/(alpha+beta+1)/(n*k))\n  }\n\n\nset.seed(2026)\n\nyhat(alpha=2, beta=3, n=12, k=1)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#     0.4000867     0.4000000     0.0199709     0.0200000 \n\nyhat(alpha=2, beta=3, n=6, k=2)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.39994625    0.40000000    0.02330732    0.02333333 \n\nyhat(alpha=2, beta=3, n=4, k=3)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#   0.40013683    0.40000000    0.02668078    0.02666667 \n\nyhat(alpha=2, beta=3, n=3, k=4)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.39973175    0.40000000    0.03001747    0.03000000 \n\nyhat(alpha=2, beta=3, n=2, k=6)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.40039333    0.40000000    0.03666519    0.03666667 \n\nyhat(alpha=2, beta=3, n=1, k=12)\n# simulatedmean  expectedmean  simulatedvar   expectedvar \n#    0.39992283    0.40000000    0.05659828    0.05666667"}],"domain":"statistics","external_citations":["https://imgur.com/a/tgHbtLz","https://stats.stackexchange.com/q/677226/2958"],"ground_truth_type":"metadata_grounded","group_id":"c5411ae39ba554450b6b3b2edef9e51b56c99ce766a9a447c37d80a7be04830f","hard_case_family":["accepted_vs_highest_score_disagreement","multiple_sources","multiple_answer_candidates"],"id":"RHM-42d960c211f0e28649b827c9","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":"adamkostanov","profile_url":"https://stats.stackexchange.com/users/512554/adamkostanov","user_type":"registered"},"created_at":"2026-09-25T19:59:10+00:00","raw_file":"raw/codex_api_v1/ab5f4cd7f0a10bde5970354a9b213efcc81e232042487437e8579705d4ca6a20_1790825258916612700_0.json","raw_sha256":"4cf167c399d03b9ae013b65260fcb4e38139c42cfc70aba4807f070550c1768e","revision_guid":"BDACA524-F3A6-491A-880E-A6871C920AE2","revision_number":1,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/BDACA524-F3A6-491A-880E-A6871C920AE2/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"adamkostanov","profile_url":"https://stats.stackexchange.com/users/512554/adamkostanov","user_type":"registered"},"created_at":"2026-09-25T20:06:02+00:00","raw_file":"raw/codex_api_v1/ab5f4cd7f0a10bde5970354a9b213efcc81e232042487437e8579705d4ca6a20_1790825258916612700_0.json","raw_sha256":"4cf167c399d03b9ae013b65260fcb4e38139c42cfc70aba4807f070550c1768e","revision_guid":"AD0D55CA-D20D-43CE-AF14-F3B414CC07CC","revision_number":2,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/AD0D55CA-D20D-43CE-AF14-F3B414CC07CC/view-source"},{"content_license":null,"contributor":{"display_name":"[deleted/unavailable user]","profile_url":null,"user_type":"does_not_exist"},"created_at":"2026-09-26T14:16:51+00:00","raw_file":"raw/codex_api_v1/ab5f4cd7f0a10bde5970354a9b213efcc81e232042487437e8579705d4ca6a20_1790825258916612700_0.json","raw_sha256":"4cf167c399d03b9ae013b65260fcb4e38139c42cfc70aba4807f070550c1768e","revision_guid":"33D7D8BE-907F-442F-B2B0-F7C572555835","revision_number":null,"revision_type":"vote_based","revision_url":"https://stats.stackexchange.com/revisions/33D7D8BE-907F-442F-B2B0-F7C572555835/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"adamkostanov","profile_url":"https://stats.stackexchange.com/users/512554/adamkostanov","user_type":"registered"},"created_at":"2026-09-26T17:38:27+00:00","raw_file":"raw/codex_api_v1/ab5f4cd7f0a10bde5970354a9b213efcc81e232042487437e8579705d4ca6a20_1790825258916612700_0.json","raw_sha256":"4cf167c399d03b9ae013b65260fcb4e38139c42cfc70aba4807f070550c1768e","revision_guid":"CAC7EE3C-CE9C-4299-BF6B-07246FC0E1C1","revision_number":3,"revision_type":"single_user","revision_url":"https://stats.stackexchange.com/revisions/CAC7EE3C-CE9C-4299-BF6B-07246FC0E1C1/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:677266","source_record_sha256":"b82084e5d8e57f26e03b51c47a0e7301bc1d4f18e88c15d6d34084eca669e20d","source_url":"https://stats.stackexchange.com/questions/677266/how-to-set-up-a-simulation-study","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"How to set up a simulation study?\nHere is a hierarchical data generating process (DGP):\n\n\n\n\n\n\n\n(Population) Layer 1: $$\\theta_i \\overset{\\text{iid}}{\\sim} \\text{Beta}(\\alpha,\\ \\beta), \\qquad i = 1, \\dots, n$$\n\n\n\n\n(Individual) Layer 2: $$y_{ij} \\mid \\theta_i \\overset{\\text{iid}}{\\sim}  \\text{Bernoulli}(\\theta_i), \\qquad j = 1, \\dots, k$$\n\n\n\n\n\n\n\n$$\\mu = E[\\theta_i], \\qquad \\tau^2 = \\operatorname{Var}(\\theta_i)$$\n\n\n\n\nUsing a sample, my purpose is only to estimate the mean and the variance of the mean estimator. I want to know what values of $n$ and $k$ I should select to get good results (I know this hugely subjective) such that $nk$ is minimized (assume that increasing $n$ by 1 costs the same as increase $k$ by 1).\n\n\n\n\nAfter doing some research, it seems the best way to handle this question is by a simulation study. Assuming $\\alpha,\\ \\beta$ are known, I could sample from the DGP for different combinations of $n$ and $k$ and record the average length of the confidence intervals and average coverage rate at each combination. Since the mean estimator is unbiased regardless of the choice in $n$ or $k$, I could use average CI length and average coverage rate to make sure I am not getting a misleadingly good coverage rate at the expense of a large CI.\n\n\n\n\nHere is how I plan to do this in R (I wrote the code to focus on readability instead of speed - I use a moment based estimator and consider different true combinations of parameters):\n\n\n\n\nset.seed(2026)\n\nmu_vals <- c(0.01, 0.05, 0.15, 0.25, 0.35, 0.45, 0.55, 0.65, 0.75, 0.85, 0.95, 0.99)\nn_var   <- 10\nn_vals  <- c(5, 15, 30, 50, 100, 200)\nk_vals  <- c(1, 2, 3, 4, 5, 6)\nR       <- 2000\nconf    <- 0.95\n\nscenarios <- data.frame()\n\nfor (mu in mu_vals) {\n  max_var <- mu * (1 - mu)\n  for (v in 1:n_var) {\n    tau2 <- (v / (n_var + 1)) * max_var\n    scenarios <- rbind(scenarios, data.frame(mu = mu, tau2 = tau2))\n  }\n}\n\n\ncalc_mean <- function(ybar_i) {\n  mean(ybar_i)\n}\n\ncalc_var_of_mean <- function(ybar_i) {\n  n <- length(ybar_i)\n  var(ybar_i) / n\n}\n\ncalc_coverage <- function(lower, upper, mu) {\n  mean(lower <= mu & mu <= upper)\n}\n\ncalc_avg_ci_length <- function(lower, upper) {\n  mean(upper - lower)\n}\n\nresults <- data.frame()\n\nfor (s in 1:nrow(scenarios)) {\n\n  mu   <- scenarios$mu[s]\n  tau2 <- scenarios$tau2[s]\n\n  alpha_plus_beta <- mu * (1 - mu) / tau2 - 1\n  alpha <- mu * alpha_plus_beta\n  beta  <- (1 - mu) * alpha_plus_beta\n\n  cat(sprintf(\"Scenario %d of %d: mu = %.2f, tau2 = %.4f\\n\",\n              s, nrow(scenarios), mu, tau2))\n\n  for (n in n_vals) {\n    for (k in k_vals) {\n\n      estimates     <- numeric(R)\n      var_estimates <- numeric(R)\n      lower         <- numeric(R)\n      upper         <- numeric(R)\n\n      t_crit <- qt(1 - (1 - conf) / 2, df = n - 1)\n\n      for (r in 1:R) {\n\n        theta <- rbeta(n, alpha, beta)\n\n        ybar_i <- numeric(n)\n        for (i in 1:n) {\n          y <- rbinom(k, size = 1, prob = theta[i])\n          ybar_i[i] <- mean(y)\n        }\n\n        est   <- calc_mean(ybar_i)\n        v_est <- calc_var_of_mean(ybar_i)\n\n        estimates[r]     <- est\n        var_estimates[r] <- v_est\n        lower[r]         <- est - t_crit * sqrt(v_est)\n        upper[r]         <- est + t_crit * sqrt(v_est)\n      }\n\n      true_var_of_mean <- (tau2 + (mu * (1 - mu) - tau2) / k) / n\n\n      results <- rbind(results, data.frame(\n        mu                  = mu,\n        tau2                = tau2,\n        n                   = n,\n        k                   = k,\n        avg_estimate        = mean(estimates),\n        true_var_of_mean    = true_var_of_mean,\n        sim_var_of_mean     = var(estimates),\n        avg_est_var_of_mean = mean(var_estimates),\n        coverage            = calc_coverage(lower, upper, mu),\n        avg_ci_length       = calc_avg_ci_length(lower, upper)\n      ))\n    }\n  }\n}\n\n\n\n\n\nWhen visualized, the results look like this (direct upload was not working - however it seems to show that when $n$ and $k$ are both large, for many cases, we get high coverage and smaller CI lengths on average): https://imgur.com/a/tgHbtLz (https://imgur.com/a/tgHbtLz)\n\n\n\n\nThe tricky part now is to try and guess what the true value of $\\alpha,\\ \\beta$ might be. If I can get some knowledge of this beforehand (e.g. possible range), I could try to determine what $n,k$ to use if I want average CI length and average coverage rate to be within certain ranges.\n\n\n\n\nI am looking for feedback on my methodology. Should I have done this a different way?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":677267,"score":5},{"answer_id":677268,"score":4}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>The issue is not with your solver but with how you set up the matrix and right hand side. Whether you use Gauss-Seidel or CG+Incomplete Cholesky, you're still solving the linear system\n<span class=\"math-container\">$$\n  A x = b.\n$$</span>\nBoth, if correctly implemented, will simply find <span class=\"math-container\">$x=A^{-1}b$</span>, just a bit faster or slower. If you have the same problem with boundary nodes in both methods, then in all likelihood you have a problem in assembling the matrix <span class=\"math-container\">$A$</span> or right hand side <span class=\"math-container\">$b$</span>. To test this hypothesis, solve the linear system with a slow and reliable method: Gauss elimination or any other direct solver such as what you have in Matlab or Python. You should assume that these solvers give you the correct answer, and if the correct answer has problems at the boundaries, then you know that the issue isn't with the solver, but with how you came up with the linear system to begin with.</p>\n","answer_id":45140,"answer_text":"The issue is not with your solver but with how you set up the matrix and right hand side. Whether you use Gauss-Seidel or CG+Incomplete Cholesky, you're still solving the linear system\n$$\n  A x = b.\n$$\nBoth, if correctly implemented, will simply find $x=A^{-1}b$, just a bit faster or slower. If you have the same problem with boundary nodes in both methods, then in all likelihood you have a problem in assembling the matrix $A$ or right hand side $b$. To test this hypothesis, solve the linear system with a slow and reliable method: Gauss elimination or any other direct solver such as what you have in Matlab or Python. You should assume that these solvers give you the correct answer, and if the correct answer has problems at the boundaries, then you know that the issue isn't with the solver, but with how you came up with the linear system to begin with.","answer_url":"https://scicomp.stackexchange.com/a/45140","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":"2025-06-25T15:03:19+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":45139,"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":"2025-06-25T15:03:19+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"8E9F9949-9229-4484-95BC-54BABEF67999","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/8E9F9949-9229-4484-95BC-54BABEF67999/view-source"}],"score":3,"updated_at":"2025-06-25T15:03:19+00:00"}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Krrish Dhiman","author_url":"https://scicomp.stackexchange.com/users/54184/krrish-dhiman","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Krrish Dhiman","profile_url":"https://scicomp.stackexchange.com/users/54184/krrish-dhiman","user_type":"registered"},"created_at":"2025-06-25T11:46:10+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"A6C925D4-1EC5-4A3D-A417-26657A938F23","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/A6C925D4-1EC5-4A3D-A417-26657A938F23/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Krrish Dhiman","profile_url":"https://scicomp.stackexchange.com/users/54184/krrish-dhiman","user_type":"registered"},"created_at":"2025-06-25T11:55:04+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"CDB8A629-F6B0-4176-9FCA-567707C9373C","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/CDB8A629-F6B0-4176-9FCA-567707C9373C/view-source"}],"url":"https://scicomp.stackexchange.com/questions/45139/miccg0-for-a-fluid-sim-fails-at-neumann-boundaries"},{"author":"Wolfgang Bangerth","author_url":"https://scicomp.stackexchange.com/users/393/wolfgang-bangerth","content_license":"CC BY-SA 4.0","context_id":"45140","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":"2025-06-25T15:03:19+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"8E9F9949-9229-4484-95BC-54BABEF67999","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/8E9F9949-9229-4484-95BC-54BABEF67999/view-source"}],"url":"https://scicomp.stackexchange.com/a/45140"}],"contexts":[{"context_id":"question","html":"<p>I am trying to follow Robert Bridson's Fluid Simulation Notes (<a href=\"https://www.cs.ubc.ca/%7Erbridson/fluidsimulation/fluids_notes.pdf\" rel=\"nofollow noreferrer\">https://www.cs.ubc.ca/~rbridson/fluidsimulation/fluids_notes.pdf</a>) to implement my own eulerian fluid simulator for the first time.</p>\n<p>I was previously using a <strong>Gauss-Seidel</strong> pressure solver for my fluid. But it turns out it had many limitations, eg: it was slow to converge, and boundaries were not well managed at higher resolution grids.</p>\n<p>So according to the notes, I tried to implement <strong>MICCG0 = Modified Incomplete Cholesky Conjugate Gradient, Level Zero</strong> for solving the pressure as it was promised to solve it way faster and more accurately.</p>\n<p>I am running into some fatal issues following the pseudocode given in his book.</p>\n<p>The liquid just when reaches/tries to touch a solid boundary the solver breaks down, all pressure values become -Nan(ind) and the error shows up in the advection step, where the <code>x_prev = x - v * dt</code> step (<strong>Semi langragian advection</strong>) is impossible to carry out! (because the velocities also become Nan after the projection step)</p>\n<p>If anyone has implemented this in the past, I would be grateful if you could share me some code of your solver, it might greatly benefit me in solving my problem. Anyone else wanting to take a look is welcome too.</p>\n<p>My repo: <a href=\"https://github.com/KrrishDhiman/Buoyancy-Simulator/blob/main/main.cpp\" rel=\"nofollow noreferrer\">https://github.com/KrrishDhiman/Buoyancy-Simulator/blob/main/main.cpp</a> (all the code in this file)</p>\n<p>My main question: How should Neumann Boundary Conditions be integrated into MIC(0) preconditioning for the Poisson equation in fluid simulation to prevent pressure blowing up?</p>\n<p>I followed my pressure solver code from the pseudocode given on pg 34, fig 4.1 and the preconditioner code from a few pages later, fig 4.2 and how to apply the preconditioner from fig 4.3.</p>\n","text":"I am trying to follow Robert Bridson's Fluid Simulation Notes (https://www.cs.ubc.ca/~rbridson/fluidsimulation/fluids_notes.pdf (https://www.cs.ubc.ca/%7Erbridson/fluidsimulation/fluids_notes.pdf)) to implement my own eulerian fluid simulator for the first time.\n\n\n\n\nI was previously using a Gauss-Seidel pressure solver for my fluid. But it turns out it had many limitations, eg: it was slow to converge, and boundaries were not well managed at higher resolution grids.\n\n\n\n\nSo according to the notes, I tried to implement MICCG0 = Modified Incomplete Cholesky Conjugate Gradient, Level Zero for solving the pressure as it was promised to solve it way faster and more accurately.\n\n\n\n\nI am running into some fatal issues following the pseudocode given in his book.\n\n\n\n\nThe liquid just when reaches/tries to touch a solid boundary the solver breaks down, all pressure values become -Nan(ind) and the error shows up in the advection step, where the x_prev = x - v * dt step (Semi langragian advection) is impossible to carry out! (because the velocities also become Nan after the projection step)\n\n\n\n\nIf anyone has implemented this in the past, I would be grateful if you could share me some code of your solver, it might greatly benefit me in solving my problem. Anyone else wanting to take a look is welcome too.\n\n\n\n\nMy repo: https://github.com/KrrishDhiman/Buoyancy-Simulator/blob/main/main.cpp (https://github.com/KrrishDhiman/Buoyancy-Simulator/blob/main/main.cpp) (all the code in this file)\n\n\n\n\nMy main question: How should Neumann Boundary Conditions be integrated into MIC(0) preconditioning for the Poisson equation in fluid simulation to prevent pressure blowing up?\n\n\n\n\nI followed my pressure solver code from the pseudocode given on pg 34, fig 4.1 and the preconditioner code from a few pages later, fig 4.2 and how to apply the preconditioner from fig 4.3."},{"context_id":"45140","html":"<p>The issue is not with your solver but with how you set up the matrix and right hand side. Whether you use Gauss-Seidel or CG+Incomplete Cholesky, you're still solving the linear system\n<span class=\"math-container\">$$\n  A x = b.\n$$</span>\nBoth, if correctly implemented, will simply find <span class=\"math-container\">$x=A^{-1}b$</span>, just a bit faster or slower. If you have the same problem with boundary nodes in both methods, then in all likelihood you have a problem in assembling the matrix <span class=\"math-container\">$A$</span> or right hand side <span class=\"math-container\">$b$</span>. To test this hypothesis, solve the linear system with a slow and reliable method: Gauss elimination or any other direct solver such as what you have in Matlab or Python. You should assume that these solvers give you the correct answer, and if the correct answer has problems at the boundaries, then you know that the issue isn't with the solver, but with how you came up with the linear system to begin with.</p>\n","text":"The issue is not with your solver but with how you set up the matrix and right hand side. Whether you use Gauss-Seidel or CG+Incomplete Cholesky, you're still solving the linear system\n$$\n  A x = b.\n$$\nBoth, if correctly implemented, will simply find $x=A^{-1}b$, just a bit faster or slower. If you have the same problem with boundary nodes in both methods, then in all likelihood you have a problem in assembling the matrix $A$ or right hand side $b$. To test this hypothesis, solve the linear system with a slow and reliable method: Gauss elimination or any other direct solver such as what you have in Matlab or Python. You should assume that these solvers give you the correct answer, and if the correct answer has problems at the boundaries, then you know that the issue isn't with the solver, but with how you came up with the linear system to begin with."}],"domain":"computational_science","external_citations":["https://github.com/KrrishDhiman/Buoyancy-Simulator/blob/main/main.cpp","https://www.cs.ubc.ca/%7Erbridson/fluidsimulation/fluids_notes.pdf"],"ground_truth_type":"metadata_grounded","group_id":"b967ef14fd09c220aa1cc1bcc784ab6913a948341ece1f0a7883e82e95bfc96f","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-d8236a978375d2b23cf08e20","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":"Krrish Dhiman","profile_url":"https://scicomp.stackexchange.com/users/54184/krrish-dhiman","user_type":"registered"},"created_at":"2025-06-25T11:46:10+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"A6C925D4-1EC5-4A3D-A417-26657A938F23","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/A6C925D4-1EC5-4A3D-A417-26657A938F23/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Krrish Dhiman","profile_url":"https://scicomp.stackexchange.com/users/54184/krrish-dhiman","user_type":"registered"},"created_at":"2025-06-25T11:55:04+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"CDB8A629-F6B0-4176-9FCA-567707C9373C","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/CDB8A629-F6B0-4176-9FCA-567707C9373C/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":"45139","source_record_sha256":"25caec55652bf9b1d8fe9a8b3b8576ce3114c3960a6510493f5bf733116f24a9","source_url":"https://scicomp.stackexchange.com/questions/45139/miccg0-for-a-fluid-sim-fails-at-neumann-boundaries","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"MICCG(0) for a fluid sim fails at Neumann Boundaries\nI am trying to follow Robert Bridson's Fluid Simulation Notes (https://www.cs.ubc.ca/~rbridson/fluidsimulation/fluids_notes.pdf (https://www.cs.ubc.ca/%7Erbridson/fluidsimulation/fluids_notes.pdf)) to implement my own eulerian fluid simulator for the first time.\n\n\n\n\nI was previously using a Gauss-Seidel pressure solver for my fluid. But it turns out it had many limitations, eg: it was slow to converge, and boundaries were not well managed at higher resolution grids.\n\n\n\n\nSo according to the notes, I tried to implement MICCG0 = Modified Incomplete Cholesky Conjugate Gradient, Level Zero for solving the pressure as it was promised to solve it way faster and more accurately.\n\n\n\n\nI am running into some fatal issues following the pseudocode given in his book.\n\n\n\n\nThe liquid just when reaches/tries to touch a solid boundary the solver breaks down, all pressure values become -Nan(ind) and the error shows up in the advection step, where the x_prev = x - v * dt step (Semi langragian advection) is impossible to carry out! (because the velocities also become Nan after the projection step)\n\n\n\n\nIf anyone has implemented this in the past, I would be grateful if you could share me some code of your solver, it might greatly benefit me in solving my problem. Anyone else wanting to take a look is welcome too.\n\n\n\n\nMy repo: https://github.com/KrrishDhiman/Buoyancy-Simulator/blob/main/main.cpp (https://github.com/KrrishDhiman/Buoyancy-Simulator/blob/main/main.cpp) (all the code in this file)\n\n\n\n\nMy main question: How should Neumann Boundary Conditions be integrated into MIC(0) preconditioning for the Poisson equation in fluid simulation to prevent pressure blowing up?\n\n\n\n\nI followed my pressure solver code from the pseudocode given on pg 34, fig 4.1 and the preconditioner code from a few pages later, fig 4.2 and how to apply the preconditioner from fig 4.3.","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45140,"score":3}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":45187,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I assume that you want to calculate the determinant exactly and that the matrix <span class=\"math-container\">$A$</span> has no special structure. The determinant of an <span class=\"math-container\">$n \\times n$</span> matrix with <span class=\"math-container\">$\\|A\\|_{\\max} \\le 2^m-1$</span> is bounded in absolute value by <span class=\"math-container\">$B = (2^m-1)^n n^{n/2}$</span>; this bound is tight in the worst case (and pretty accurate for random matrices without special structure). Let us consider <span class=\"math-container\">$m$</span> a constant for simplicity (the difficulty will scale approximately linearly with <span class=\"math-container\">$m$</span>). Since the determinant has <span class=\"math-container\">$\\tilde O(n)$</span> bits, the standard Chinese remainder theorem (CRT) method requires about <span class=\"math-container\">$\\tilde O(n^4)$</span> bit operations.</p>\n<p>Here is a ballpark estimate of what the CRT method would cost.  Let us consider the fixed value <span class=\"math-container\">$m = 7$</span>, in which case each matrix entry fits in a byte. The matrix requires 1 TB of storage, while <span class=\"math-container\">$B \\approx 5.3 \\cdot 10^{5103803}$</span>. The determinant itself only requires about 2 MB of storage. The product of the 773015 prime numbers <span class=\"math-container\">$2 \\le p \\le 11755171$</span> is <span class=\"math-container\">$\\approx 2.3 \\cdot 10^{5103806}$</span>, so the determinant can be recovered unambiguously (including sign) from the determinants modulo these primes using CRT. You can do one prime at a time or several in parallel, but you might not want to do too many in parallel since storing <span class=\"math-container\">$A$</span> mod <span class=\"math-container\">$p$</span> requires 4 TB if you use 32-bit integers. Computing a single determinant mod <span class=\"math-container\">$p$</span> using LU factorization over <span class=\"math-container\">$\\mathbb{F}_p$</span> costs roughly <span class=\"math-container\">$2 n^3 / 3$</span> finite field operations. The total cost for all determinants is thus about <span class=\"math-container\">$773015 \\cdot (2/3) \\cdot (10^6)^3 \\approx 5 \\cdot 10^{23}$</span> finite field operations.</p>\n<p>Large dense LU factorizations parallelize very well by recursing into matrix multiplication of appropriately sized sub-blocks. Since <span class=\"math-container\">$65 \\cdot 11755171^2 &lt; 2^{53}$</span>, you can accumulate a dot product of length around 65 in a 64-bit float before requiring a modular reduction, so you might want to use something like a 64x64 FP64 kernel for bigger matrix multiplications over <span class=\"math-container\">$\\mathbb{F}_p$</span>. This should allow performing all computations using essentially <span class=\"math-container\">$\\approx 5 \\cdot 10^{23}$</span> FP64 operations. A current top-of-the-line GPU, the AMD Instinct MI250X, is reported to achieve 48 Tflop/s FP64. Assuming that you have a cluster of 3 million of these, you should theoretically be able to finish the computation in <span class=\"math-container\">$5 \\cdot 10^{23} / (48 \\cdot 10^{12}) / (30 \\cdot 10^6) \\approx 3500$</span> seconds.</p>\n<p>Strassen matrix multiplication would help; the constant factors are hard to estimate, but since <span class=\"math-container\">$(10^6)^3 / (10^6)^{2.8} \\approx 16$</span>, a guesstimate is that it would save less than a factor 10. You can also improve the CRT method as follows: compute the exact rational solution vector of <span class=\"math-container\">$Ax = b$</span> for some randomly chosen vector <span class=\"math-container\">$b$</span>, say with entries in <span class=\"math-container\">$(-1,0,1)$</span>. The LCM of the denominators of <span class=\"math-container\">$x$</span> gives you a divisor of <span class=\"math-container\">$d$</span> of <span class=\"math-container\">$\\det(A)$</span>, which with very high probability will be almost as large as <span class=\"math-container\">$\\det(A)$</span> itself. You can thus compute <span class=\"math-container\">$\\det(A) / d$</span> rather than <span class=\"math-container\">$\\det(A)$</span> itself using CRT, requiring (probabilistically) vastly fewer primes. To solve <span class=\"math-container\">$Ax = b$</span>, you can use <span class=\"math-container\">$p$</span>-adic lifting. This only requires a single matrix inversion modulo <span class=\"math-container\">$p$</span>, followed by several matrix-vector products. To illustrate, here are timings to compute determinant of a random 7-bit integer matrix on an 8-core CPU with FLINT 3.3. &quot;Modular&quot; is the straightforward CRT determinant algorithm, &quot;Accelerated&quot; is the version solving for a random divisor.</p>\n<pre><code>n       Modular       Accelerated     speedup\n64      0.0014 s      0.00094 s       1.5x\n128     0.0126 s      0.00531 s       2.4x\n256     0.127 s       0.0345 s        3.7x\n512     1.34 s        0.244 s         5.5x\n1024    15.2 s        2.149 s         7.1x\n2048    185.6 s       20.3 s          9.1x\n</code></pre>\n<p>Extrapolating, we might expect something like a 20x speedup over the simple CRT method for <span class=\"math-container\">$n = 10^6$</span>, but it is hard to predict whether this trend scales to a distributed setting and the less cache-friendly matrix-vector products for larger <span class=\"math-container\">$n$</span>.</p>\n<p>Can we do better? Fortunately, yes. The state of the art methods for integer determinants require only <span class=\"math-container\">$\\tilde O(n^3)$</span> bit operations (probabilistically). I believe the best currently available algorithm is the one by Colton Pauderis and Arne Storjohann described in <a href=\"https://cs.uwaterloo.ca/%7Eastorjoh/issac13.pdf\" rel=\"nofollow noreferrer\">https://cs.uwaterloo.ca/~astorjoh/issac13.pdf</a>. It is reported in <a href=\"https://arxiv.org/abs/2404.08358\" rel=\"nofollow noreferrer\">https://arxiv.org/abs/2404.08358</a> that a version of this algorithm is implemented in OSCAR (<a href=\"https://www.oscar-system.org/\" rel=\"nofollow noreferrer\">https://www.oscar-system.org/</a>) and performs much better than the CRT method described above at least for moderately sized matrices. Assuming that the <span class=\"math-container\">$\\tilde O(n^3)$</span> of Pauderis-Storjohann is <span class=\"math-container\">$\\approx 10^6$</span> times smaller than the <span class=\"math-container\">$\\tilde O(n^4)$</span> of the standard CRT method for <span class=\"math-container\">$n = 10^6$</span>, it looks in theory like your determinant challenge should be doable on a small GPU cluster. But I don't know what the constraints are for running the Pauderis-Storjohann algorithm at scale and whether the constant factors are comparable; someone else would have to comment on the practicality of this.</p>\n","answer_id":45187,"answer_text":"I assume that you want to calculate the determinant exactly and that the matrix $A$ has no special structure. The determinant of an $n \\times n$ matrix with $\\|A\\|_{\\max} \\le 2^m-1$ is bounded in absolute value by $B = (2^m-1)^n n^{n/2}$; this bound is tight in the worst case (and pretty accurate for random matrices without special structure). Let us consider $m$ a constant for simplicity (the difficulty will scale approximately linearly with $m$). Since the determinant has $\\tilde O(n)$ bits, the standard Chinese remainder theorem (CRT) method requires about $\\tilde O(n^4)$ bit operations.\n\n\n\n\nHere is a ballpark estimate of what the CRT method would cost.  Let us consider the fixed value $m = 7$, in which case each matrix entry fits in a byte. The matrix requires 1 TB of storage, while $B \\approx 5.3 \\cdot 10^{5103803}$. The determinant itself only requires about 2 MB of storage. The product of the 773015 prime numbers $2 \\le p \\le 11755171$ is $\\approx 2.3 \\cdot 10^{5103806}$, so the determinant can be recovered unambiguously (including sign) from the determinants modulo these primes using CRT. You can do one prime at a time or several in parallel, but you might not want to do too many in parallel since storing $A$ mod $p$ requires 4 TB if you use 32-bit integers. Computing a single determinant mod $p$ using LU factorization over $\\mathbb{F}_p$ costs roughly $2 n^3 / 3$ finite field operations. The total cost for all determinants is thus about $773015 \\cdot (2/3) \\cdot (10^6)^3 \\approx 5 \\cdot 10^{23}$ finite field operations.\n\n\n\n\nLarge dense LU factorizations parallelize very well by recursing into matrix multiplication of appropriately sized sub-blocks. Since $65 \\cdot 11755171^2 < 2^{53}$, you can accumulate a dot product of length around 65 in a 64-bit float before requiring a modular reduction, so you might want to use something like a 64x64 FP64 kernel for bigger matrix multiplications over $\\mathbb{F}_p$. This should allow performing all computations using essentially $\\approx 5 \\cdot 10^{23}$ FP64 operations. A current top-of-the-line GPU, the AMD Instinct MI250X, is reported to achieve 48 Tflop/s FP64. Assuming that you have a cluster of 3 million of these, you should theoretically be able to finish the computation in $5 \\cdot 10^{23} / (48 \\cdot 10^{12}) / (30 \\cdot 10^6) \\approx 3500$ seconds.\n\n\n\n\nStrassen matrix multiplication would help; the constant factors are hard to estimate, but since $(10^6)^3 / (10^6)^{2.8} \\approx 16$, a guesstimate is that it would save less than a factor 10. You can also improve the CRT method as follows: compute the exact rational solution vector of $Ax = b$ for some randomly chosen vector $b$, say with entries in $(-1,0,1)$. The LCM of the denominators of $x$ gives you a divisor of $d$ of $\\det(A)$, which with very high probability will be almost as large as $\\det(A)$ itself. You can thus compute $\\det(A) / d$ rather than $\\det(A)$ itself using CRT, requiring (probabilistically) vastly fewer primes. To solve $Ax = b$, you can use $p$-adic lifting. This only requires a single matrix inversion modulo $p$, followed by several matrix-vector products. To illustrate, here are timings to compute determinant of a random 7-bit integer matrix on an 8-core CPU with FLINT 3.3. \"Modular\" is the straightforward CRT determinant algorithm, \"Accelerated\" is the version solving for a random divisor.\n\n\n\n\nn       Modular       Accelerated     speedup\n64      0.0014 s      0.00094 s       1.5x\n128     0.0126 s      0.00531 s       2.4x\n256     0.127 s       0.0345 s        3.7x\n512     1.34 s        0.244 s         5.5x\n1024    15.2 s        2.149 s         7.1x\n2048    185.6 s       20.3 s          9.1x\n\n\n\n\n\nExtrapolating, we might expect something like a 20x speedup over the simple CRT method for $n = 10^6$, but it is hard to predict whether this trend scales to a distributed setting and the less cache-friendly matrix-vector products for larger $n$.\n\n\n\n\nCan we do better? Fortunately, yes. The state of the art methods for integer determinants require only $\\tilde O(n^3)$ bit operations (probabilistically). I believe the best currently available algorithm is the one by Colton Pauderis and Arne Storjohann described in https://cs.uwaterloo.ca/~astorjoh/issac13.pdf (https://cs.uwaterloo.ca/%7Eastorjoh/issac13.pdf). It is reported in https://arxiv.org/abs/2404.08358 (https://arxiv.org/abs/2404.08358) that a version of this algorithm is implemented in OSCAR (https://www.oscar-system.org/ (https://www.oscar-system.org/)) and performs much better than the CRT method described above at least for moderately sized matrices. Assuming that the $\\tilde O(n^3)$ of Pauderis-Storjohann is $\\approx 10^6$ times smaller than the $\\tilde O(n^4)$ of the standard CRT method for $n = 10^6$, it looks in theory like your determinant challenge should be doable on a small GPU cluster. But I don't know what the constraints are for running the Pauderis-Storjohann algorithm at scale and whether the constant factors are comparable; someone else would have to comment on the practicality of this.","answer_url":"https://scicomp.stackexchange.com/a/45187","author":"Fredrik Johansson","author_url":"https://scicomp.stackexchange.com/users/3420/fredrik-johansson","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2025-07-29T15:26:42+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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M","profile_url":"https://scicomp.stackexchange.com/users/16934/abhilash-reddy-m","user_type":"registered"},"created_at":"2025-07-29T22:13:07+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"43D0DAED-22A8-4867-A497-582FC1B9AEFF","revision_number":4,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/43D0DAED-22A8-4867-A497-582FC1B9AEFF/view-source"}],"url":"https://scicomp.stackexchange.com/a/45187"}],"contexts":[{"context_id":"question","html":"<p>I have a dense <span class=\"math-container\">$10^6\\times10^6$</span> matrix having entries in <span class=\"math-container\">$[-2^m+1,2^m-1]\\cap\\mathbb Z$</span>.</p>\n<p>What resources do I require in <span class=\"math-container\">$2025$</span> state of the art for computing the determinant in a reasonable time of say <span class=\"math-container\">$1$</span> hour? Is it parallelizable?</p>\n","text":"I have a dense $10^6\\times10^6$ matrix having entries in $[-2^m+1,2^m-1]\\cap\\mathbb Z$.\n\n\n\n\nWhat resources do I require in $2025$ state of the art for computing the determinant in a reasonable time of say $1$ hour? Is it parallelizable?"},{"context_id":"45187","html":"<p>I assume that you want to calculate the determinant exactly and that the matrix <span class=\"math-container\">$A$</span> has no special structure. The determinant of an <span class=\"math-container\">$n \\times n$</span> matrix with <span class=\"math-container\">$\\|A\\|_{\\max} \\le 2^m-1$</span> is bounded in absolute value by <span class=\"math-container\">$B = (2^m-1)^n n^{n/2}$</span>; this bound is tight in the worst case (and pretty accurate for random matrices without special structure). Let us consider <span class=\"math-container\">$m$</span> a constant for simplicity (the difficulty will scale approximately linearly with <span class=\"math-container\">$m$</span>). Since the determinant has <span class=\"math-container\">$\\tilde O(n)$</span> bits, the standard Chinese remainder theorem (CRT) method requires about <span class=\"math-container\">$\\tilde O(n^4)$</span> bit operations.</p>\n<p>Here is a ballpark estimate of what the CRT method would cost.  Let us consider the fixed value <span class=\"math-container\">$m = 7$</span>, in which case each matrix entry fits in a byte. The matrix requires 1 TB of storage, while <span class=\"math-container\">$B \\approx 5.3 \\cdot 10^{5103803}$</span>. The determinant itself only requires about 2 MB of storage. The product of the 773015 prime numbers <span class=\"math-container\">$2 \\le p \\le 11755171$</span> is <span class=\"math-container\">$\\approx 2.3 \\cdot 10^{5103806}$</span>, so the determinant can be recovered unambiguously (including sign) from the determinants modulo these primes using CRT. You can do one prime at a time or several in parallel, but you might not want to do too many in parallel since storing <span class=\"math-container\">$A$</span> mod <span class=\"math-container\">$p$</span> requires 4 TB if you use 32-bit integers. Computing a single determinant mod <span class=\"math-container\">$p$</span> using LU factorization over <span class=\"math-container\">$\\mathbb{F}_p$</span> costs roughly <span class=\"math-container\">$2 n^3 / 3$</span> finite field operations. The total cost for all determinants is thus about <span class=\"math-container\">$773015 \\cdot (2/3) \\cdot (10^6)^3 \\approx 5 \\cdot 10^{23}$</span> finite field operations.</p>\n<p>Large dense LU factorizations parallelize very well by recursing into matrix multiplication of appropriately sized sub-blocks. Since <span class=\"math-container\">$65 \\cdot 11755171^2 &lt; 2^{53}$</span>, you can accumulate a dot product of length around 65 in a 64-bit float before requiring a modular reduction, so you might want to use something like a 64x64 FP64 kernel for bigger matrix multiplications over <span class=\"math-container\">$\\mathbb{F}_p$</span>. This should allow performing all computations using essentially <span class=\"math-container\">$\\approx 5 \\cdot 10^{23}$</span> FP64 operations. A current top-of-the-line GPU, the AMD Instinct MI250X, is reported to achieve 48 Tflop/s FP64. Assuming that you have a cluster of 3 million of these, you should theoretically be able to finish the computation in <span class=\"math-container\">$5 \\cdot 10^{23} / (48 \\cdot 10^{12}) / (30 \\cdot 10^6) \\approx 3500$</span> seconds.</p>\n<p>Strassen matrix multiplication would help; the constant factors are hard to estimate, but since <span class=\"math-container\">$(10^6)^3 / (10^6)^{2.8} \\approx 16$</span>, a guesstimate is that it would save less than a factor 10. You can also improve the CRT method as follows: compute the exact rational solution vector of <span class=\"math-container\">$Ax = b$</span> for some randomly chosen vector <span class=\"math-container\">$b$</span>, say with entries in <span class=\"math-container\">$(-1,0,1)$</span>. The LCM of the denominators of <span class=\"math-container\">$x$</span> gives you a divisor of <span class=\"math-container\">$d$</span> of <span class=\"math-container\">$\\det(A)$</span>, which with very high probability will be almost as large as <span class=\"math-container\">$\\det(A)$</span> itself. You can thus compute <span class=\"math-container\">$\\det(A) / d$</span> rather than <span class=\"math-container\">$\\det(A)$</span> itself using CRT, requiring (probabilistically) vastly fewer primes. To solve <span class=\"math-container\">$Ax = b$</span>, you can use <span class=\"math-container\">$p$</span>-adic lifting. This only requires a single matrix inversion modulo <span class=\"math-container\">$p$</span>, followed by several matrix-vector products. To illustrate, here are timings to compute determinant of a random 7-bit integer matrix on an 8-core CPU with FLINT 3.3. &quot;Modular&quot; is the straightforward CRT determinant algorithm, &quot;Accelerated&quot; is the version solving for a random divisor.</p>\n<pre><code>n       Modular       Accelerated     speedup\n64      0.0014 s      0.00094 s       1.5x\n128     0.0126 s      0.00531 s       2.4x\n256     0.127 s       0.0345 s        3.7x\n512     1.34 s        0.244 s         5.5x\n1024    15.2 s        2.149 s         7.1x\n2048    185.6 s       20.3 s          9.1x\n</code></pre>\n<p>Extrapolating, we might expect something like a 20x speedup over the simple CRT method for <span class=\"math-container\">$n = 10^6$</span>, but it is hard to predict whether this trend scales to a distributed setting and the less cache-friendly matrix-vector products for larger <span class=\"math-container\">$n$</span>.</p>\n<p>Can we do better? Fortunately, yes. The state of the art methods for integer determinants require only <span class=\"math-container\">$\\tilde O(n^3)$</span> bit operations (probabilistically). I believe the best currently available algorithm is the one by Colton Pauderis and Arne Storjohann described in <a href=\"https://cs.uwaterloo.ca/%7Eastorjoh/issac13.pdf\" rel=\"nofollow noreferrer\">https://cs.uwaterloo.ca/~astorjoh/issac13.pdf</a>. It is reported in <a href=\"https://arxiv.org/abs/2404.08358\" rel=\"nofollow noreferrer\">https://arxiv.org/abs/2404.08358</a> that a version of this algorithm is implemented in OSCAR (<a href=\"https://www.oscar-system.org/\" rel=\"nofollow noreferrer\">https://www.oscar-system.org/</a>) and performs much better than the CRT method described above at least for moderately sized matrices. Assuming that the <span class=\"math-container\">$\\tilde O(n^3)$</span> of Pauderis-Storjohann is <span class=\"math-container\">$\\approx 10^6$</span> times smaller than the <span class=\"math-container\">$\\tilde O(n^4)$</span> of the standard CRT method for <span class=\"math-container\">$n = 10^6$</span>, it looks in theory like your determinant challenge should be doable on a small GPU cluster. But I don't know what the constraints are for running the Pauderis-Storjohann algorithm at scale and whether the constant factors are comparable; someone else would have to comment on the practicality of this.</p>\n","text":"I assume that you want to calculate the determinant exactly and that the matrix $A$ has no special structure. The determinant of an $n \\times n$ matrix with $\\|A\\|_{\\max} \\le 2^m-1$ is bounded in absolute value by $B = (2^m-1)^n n^{n/2}$; this bound is tight in the worst case (and pretty accurate for random matrices without special structure). Let us consider $m$ a constant for simplicity (the difficulty will scale approximately linearly with $m$). Since the determinant has $\\tilde O(n)$ bits, the standard Chinese remainder theorem (CRT) method requires about $\\tilde O(n^4)$ bit operations.\n\n\n\n\nHere is a ballpark estimate of what the CRT method would cost.  Let us consider the fixed value $m = 7$, in which case each matrix entry fits in a byte. The matrix requires 1 TB of storage, while $B \\approx 5.3 \\cdot 10^{5103803}$. The determinant itself only requires about 2 MB of storage. The product of the 773015 prime numbers $2 \\le p \\le 11755171$ is $\\approx 2.3 \\cdot 10^{5103806}$, so the determinant can be recovered unambiguously (including sign) from the determinants modulo these primes using CRT. You can do one prime at a time or several in parallel, but you might not want to do too many in parallel since storing $A$ mod $p$ requires 4 TB if you use 32-bit integers. Computing a single determinant mod $p$ using LU factorization over $\\mathbb{F}_p$ costs roughly $2 n^3 / 3$ finite field operations. The total cost for all determinants is thus about $773015 \\cdot (2/3) \\cdot (10^6)^3 \\approx 5 \\cdot 10^{23}$ finite field operations.\n\n\n\n\nLarge dense LU factorizations parallelize very well by recursing into matrix multiplication of appropriately sized sub-blocks. Since $65 \\cdot 11755171^2 < 2^{53}$, you can accumulate a dot product of length around 65 in a 64-bit float before requiring a modular reduction, so you might want to use something like a 64x64 FP64 kernel for bigger matrix multiplications over $\\mathbb{F}_p$. This should allow performing all computations using essentially $\\approx 5 \\cdot 10^{23}$ FP64 operations. A current top-of-the-line GPU, the AMD Instinct MI250X, is reported to achieve 48 Tflop/s FP64. Assuming that you have a cluster of 3 million of these, you should theoretically be able to finish the computation in $5 \\cdot 10^{23} / (48 \\cdot 10^{12}) / (30 \\cdot 10^6) \\approx 3500$ seconds.\n\n\n\n\nStrassen matrix multiplication would help; the constant factors are hard to estimate, but since $(10^6)^3 / (10^6)^{2.8} \\approx 16$, a guesstimate is that it would save less than a factor 10. You can also improve the CRT method as follows: compute the exact rational solution vector of $Ax = b$ for some randomly chosen vector $b$, say with entries in $(-1,0,1)$. The LCM of the denominators of $x$ gives you a divisor of $d$ of $\\det(A)$, which with very high probability will be almost as large as $\\det(A)$ itself. You can thus compute $\\det(A) / d$ rather than $\\det(A)$ itself using CRT, requiring (probabilistically) vastly fewer primes. To solve $Ax = b$, you can use $p$-adic lifting. This only requires a single matrix inversion modulo $p$, followed by several matrix-vector products. To illustrate, here are timings to compute determinant of a random 7-bit integer matrix on an 8-core CPU with FLINT 3.3. \"Modular\" is the straightforward CRT determinant algorithm, \"Accelerated\" is the version solving for a random divisor.\n\n\n\n\nn       Modular       Accelerated     speedup\n64      0.0014 s      0.00094 s       1.5x\n128     0.0126 s      0.00531 s       2.4x\n256     0.127 s       0.0345 s        3.7x\n512     1.34 s        0.244 s         5.5x\n1024    15.2 s        2.149 s         7.1x\n2048    185.6 s       20.3 s          9.1x\n\n\n\n\n\nExtrapolating, we might expect something like a 20x speedup over the simple CRT method for $n = 10^6$, but it is hard to predict whether this trend scales to a distributed setting and the less cache-friendly matrix-vector products for larger $n$.\n\n\n\n\nCan we do better? Fortunately, yes. The state of the art methods for integer determinants require only $\\tilde O(n^3)$ bit operations (probabilistically). I believe the best currently available algorithm is the one by Colton Pauderis and Arne Storjohann described in https://cs.uwaterloo.ca/~astorjoh/issac13.pdf (https://cs.uwaterloo.ca/%7Eastorjoh/issac13.pdf). It is reported in https://arxiv.org/abs/2404.08358 (https://arxiv.org/abs/2404.08358) that a version of this algorithm is implemented in OSCAR (https://www.oscar-system.org/ (https://www.oscar-system.org/)) and performs much better than the CRT method described above at least for moderately sized matrices. Assuming that the $\\tilde O(n^3)$ of Pauderis-Storjohann is $\\approx 10^6$ times smaller than the $\\tilde O(n^4)$ of the standard CRT method for $n = 10^6$, it looks in theory like your determinant challenge should be doable on a small GPU cluster. But I don't know what the constraints are for running the Pauderis-Storjohann algorithm at scale and whether the constant factors are comparable; someone else would have to comment on the practicality of this."}],"domain":"computational_science","external_citations":["https://arxiv.org/abs/2404.08358","https://cs.uwaterloo.ca/%7Eastorjoh/issac13.pdf","https://www.oscar-system.org/"],"ground_truth_type":"metadata_grounded","group_id":"15b70f0fde25aa2fe97b1624f6230f853929910585af4e9da4c76fba308dc1bb","hard_case_family":["multiple_sources"],"id":"RHM-74ac78105de798434bd47ba8","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":"Turbo","profile_url":"https://scicomp.stackexchange.com/users/7676/turbo","user_type":"registered"},"created_at":"2025-07-24T21:35:32+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"20E9474F-B13D-4547-9316-63E1DFC259FE","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/20E9474F-B13D-4547-9316-63E1DFC259FE/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Turbo","profile_url":"https://scicomp.stackexchange.com/users/7676/turbo","user_type":"registered"},"created_at":"2025-07-25T13:29:39+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"9A500271-79BF-4487-87F8-6DB126123CFB","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/9A500271-79BF-4487-87F8-6DB126123CFB/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"nicoguaro","profile_url":"https://scicomp.stackexchange.com/users/9667/nicoguaro","user_type":"moderator"},"created_at":"2025-07-25T14:22:10+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"61F09D1B-1C02-4E6D-96AD-CF04B1D22268","revision_number":3,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/61F09D1B-1C02-4E6D-96AD-CF04B1D22268/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Turbo","profile_url":"https://scicomp.stackexchange.com/users/7676/turbo","user_type":"registered"},"created_at":"2025-07-26T02:38:07+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"D747B912-C7F3-4D57-B971-085C47CC2AE4","revision_number":4,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/D747B912-C7F3-4D57-B971-085C47CC2AE4/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":"45183","source_record_sha256":"8364379fff6b1b42f5350c3ccc483e53136f0c4bcfb2b6599c6a3dadcac3b12e","source_url":"https://scicomp.stackexchange.com/questions/45183/feasibility-of-computing-large-determinants","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Feasibility of computing large determinants\nI have a dense $10^6\\times10^6$ matrix having entries in $[-2^m+1,2^m-1]\\cap\\mathbb Z$.\n\n\n\n\nWhat resources do I require in $2025$ state of the art for computing the determinant in a reasonable time of say $1$ hour? Is it parallelizable?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45187,"score":7}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>By definition, the principal inertia moments are the eigenvalues of the inertia tensor. Its eigenvectors are the principal directions, in the sense that a change of coordinates to a coordinate system described by those (normalized) vectors would make the inertia tensor diagonal. For a solid body, this tensor should be symmetric and positive definite, and the eigenvectors should be orthogonal.</p>\n<p>It is customary to order the eigenvalues in ascending order by their value. I would call them <span class=\"math-container\">$I_1$</span>, <span class=\"math-container\">$I_2$</span>, and <span class=\"math-container\">$I_3$</span>. Where the associated axes are labeled accordingly. I can understand that someone might want to use <span class=\"math-container\">$I_x$</span> instead of <span class=\"math-container\">$I_1$</span>, but here we should differentiate <span class=\"math-container\">$I_x$</span>, which is a principal (eigen) value, and <span class=\"math-container\">$I_{xx},$</span> which is the component of the tensor in the original framework. That might be confusing.</p>\n","answer_id":45239,"answer_text":"By definition, the principal inertia moments are the eigenvalues of the inertia tensor. Its eigenvectors are the principal directions, in the sense that a change of coordinates to a coordinate system described by those (normalized) vectors would make the inertia tensor diagonal. For a solid body, this tensor should be symmetric and positive definite, and the eigenvectors should be orthogonal.\n\n\n\n\nIt is customary to order the eigenvalues in ascending order by their value. I would call them $I_1$, $I_2$, and $I_3$. Where the associated axes are labeled accordingly. I can understand that someone might want to use $I_x$ instead of $I_1$, but here we should differentiate $I_x$, which is a principal (eigen) value, and $I_{xx},$ which is the component of the tensor in the original framework. That might be confusing.","answer_url":"https://scicomp.stackexchange.com/a/45239","author":"nicoguaro","author_url":"https://scicomp.stackexchange.com/users/9667/nicoguaro","author_user_type":"moderator","content_license":"CC BY-SA 4.0","created_at":"2025-09-17T14:39:01+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":45238,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"nicoguaro","profile_url":"https://scicomp.stackexchange.com/users/9667/nicoguaro","user_type":"moderator"},"created_at":"2025-09-17T14:39:01+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"115D17AD-BA25-47DC-B4E2-A030482D2868","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/115D17AD-BA25-47DC-B4E2-A030482D2868/view-source"}],"score":3,"updated_at":"2025-09-17T14:39:01+00:00"}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Matt","author_url":"https://scicomp.stackexchange.com/users/27532/matt","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Matt","profile_url":"https://scicomp.stackexchange.com/users/27532/matt","user_type":"registered"},"created_at":"2025-09-17T03:52:18+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"1AD38280-6243-47AE-B3FF-856B713D3D3A","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/1AD38280-6243-47AE-B3FF-856B713D3D3A/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"nicoguaro","profile_url":"https://scicomp.stackexchange.com/users/9667/nicoguaro","user_type":"moderator"},"created_at":"2025-09-17T14:32:46+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"6DDDDC36-8C85-4144-ACBD-C9B0EF8F8F84","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/6DDDDC36-8C85-4144-ACBD-C9B0EF8F8F84/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Matt","profile_url":"https://scicomp.stackexchange.com/users/27532/matt","user_type":"registered"},"created_at":"2025-09-17T16:04:00+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"896E0F76-CD24-494A-9832-6F58BCB07886","revision_number":3,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/896E0F76-CD24-494A-9832-6F58BCB07886/view-source"}],"url":"https://scicomp.stackexchange.com/questions/45238/relationship-between-eigenvalues-of-the-inertia-tensor-and-the-principal-moments"},{"author":"nicoguaro","author_url":"https://scicomp.stackexchange.com/users/9667/nicoguaro","content_license":"CC BY-SA 4.0","context_id":"45239","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"nicoguaro","profile_url":"https://scicomp.stackexchange.com/users/9667/nicoguaro","user_type":"moderator"},"created_at":"2025-09-17T14:39:01+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"115D17AD-BA25-47DC-B4E2-A030482D2868","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/115D17AD-BA25-47DC-B4E2-A030482D2868/view-source"}],"url":"https://scicomp.stackexchange.com/a/45239"}],"contexts":[{"context_id":"question","html":"<p>Given an inertia tensor, <span class=\"math-container\">$I$</span>:</p>\n<p><span class=\"math-container\">$$\n\\mathbf{I} = \\begin{bmatrix}\nI_{xx} &amp; I_{xy} &amp; I_{xz} \\\\\nI_{yx} &amp; I_{yy} &amp; I_{yz} \\\\\nI_{zx} &amp; I_{zy} &amp; I_{zz}\n\\end{bmatrix}\n$$</span></p>\n<p>The principal moments of inertia can be found by performing an eigensolution on I.\n<span class=\"math-container\">$$\n\\mathbf{I}_{\\text{p}} = Q^\\top \\mathbf{I} Q\n$$</span></p>\n<p>Using a package like <a href=\"https://eigen.tuxfamily.org/index.php?title=Main_Page\" rel=\"nofollow noreferrer\">Eigen</a> or <a href=\"https://www.mathworks.com/products/matlab.html\" rel=\"nofollow noreferrer\">Matlab</a>, the eigenvalues come out in ascending order (<span class=\"math-container\">$I_1$</span>,<span class=\"math-container\">$I_2$</span>,<span class=\"math-container\">$I_3$</span>). Nastran (MSC and NX) selects <span class=\"math-container\">$I_x$</span>, <span class=\"math-container\">$I_y$</span>, and <span class=\"math-container\">$I_z$</span> that are not always in ascending or descending order.  I didn't find any documentation on how to make that decision.  My textbook always equates <span class=\"math-container\">$I_1$</span> with <span class=\"math-container\">$I_x$</span> as the smallest, but this also seems arbitrary.  It assigns the easiest rotation as the principal x axis.  I didn't find a source to say that this is a standard or not.</p>\n<p>What determines which eigenvalue is <span class=\"math-container\">$I_x$</span>, <span class=\"math-container\">$I_y$</span>, and <span class=\"math-container\">$I_z$</span>?</p>\n","text":"Given an inertia tensor, $I$:\n\n\n\n\n$$\n\\mathbf{I} = \\begin{bmatrix}\nI_{xx} & I_{xy} & I_{xz} \\\\\nI_{yx} & I_{yy} & I_{yz} \\\\\nI_{zx} & I_{zy} & I_{zz}\n\\end{bmatrix}\n$$\n\n\n\n\nThe principal moments of inertia can be found by performing an eigensolution on I.\n$$\n\\mathbf{I}_{\\text{p}} = Q^\\top \\mathbf{I} Q\n$$\n\n\n\n\nUsing a package like Eigen (https://eigen.tuxfamily.org/index.php?title=Main_Page) or Matlab (https://www.mathworks.com/products/matlab.html), the eigenvalues come out in ascending order ($I_1$,$I_2$,$I_3$). Nastran (MSC and NX) selects $I_x$, $I_y$, and $I_z$ that are not always in ascending or descending order.  I didn't find any documentation on how to make that decision.  My textbook always equates $I_1$ with $I_x$ as the smallest, but this also seems arbitrary.  It assigns the easiest rotation as the principal x axis.  I didn't find a source to say that this is a standard or not.\n\n\n\n\nWhat determines which eigenvalue is $I_x$, $I_y$, and $I_z$?"},{"context_id":"45239","html":"<p>By definition, the principal inertia moments are the eigenvalues of the inertia tensor. Its eigenvectors are the principal directions, in the sense that a change of coordinates to a coordinate system described by those (normalized) vectors would make the inertia tensor diagonal. For a solid body, this tensor should be symmetric and positive definite, and the eigenvectors should be orthogonal.</p>\n<p>It is customary to order the eigenvalues in ascending order by their value. I would call them <span class=\"math-container\">$I_1$</span>, <span class=\"math-container\">$I_2$</span>, and <span class=\"math-container\">$I_3$</span>. Where the associated axes are labeled accordingly. I can understand that someone might want to use <span class=\"math-container\">$I_x$</span> instead of <span class=\"math-container\">$I_1$</span>, but here we should differentiate <span class=\"math-container\">$I_x$</span>, which is a principal (eigen) value, and <span class=\"math-container\">$I_{xx},$</span> which is the component of the tensor in the original framework. That might be confusing.</p>\n","text":"By definition, the principal inertia moments are the eigenvalues of the inertia tensor. Its eigenvectors are the principal directions, in the sense that a change of coordinates to a coordinate system described by those (normalized) vectors would make the inertia tensor diagonal. For a solid body, this tensor should be symmetric and positive definite, and the eigenvectors should be orthogonal.\n\n\n\n\nIt is customary to order the eigenvalues in ascending order by their value. I would call them $I_1$, $I_2$, and $I_3$. Where the associated axes are labeled accordingly. I can understand that someone might want to use $I_x$ instead of $I_1$, but here we should differentiate $I_x$, which is a principal (eigen) value, and $I_{xx},$ which is the component of the tensor in the original framework. That might be confusing."}],"domain":"computational_science","external_citations":["https://eigen.tuxfamily.org/index.php?title=Main_Page","https://www.mathworks.com/products/matlab.html"],"ground_truth_type":"metadata_grounded","group_id":"fc1aebfb4140810bcd27ab49aa8fa9a6b226d0c6bb229df3a135135f1d4aedb8","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-96665175a849739d3ec3ffe1","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":"Matt","profile_url":"https://scicomp.stackexchange.com/users/27532/matt","user_type":"registered"},"created_at":"2025-09-17T03:52:18+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"1AD38280-6243-47AE-B3FF-856B713D3D3A","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/1AD38280-6243-47AE-B3FF-856B713D3D3A/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"nicoguaro","profile_url":"https://scicomp.stackexchange.com/users/9667/nicoguaro","user_type":"moderator"},"created_at":"2025-09-17T14:32:46+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"6DDDDC36-8C85-4144-ACBD-C9B0EF8F8F84","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/6DDDDC36-8C85-4144-ACBD-C9B0EF8F8F84/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Matt","profile_url":"https://scicomp.stackexchange.com/users/27532/matt","user_type":"registered"},"created_at":"2025-09-17T16:04:00+00:00","raw_file":"raw/codex_api_v1/8b02bbba3a1a1a633af4866e7fea0bd6789190b52c4b8380b0538b5c670e7131_1790825346551636200_0.json","raw_sha256":"33050439b68e1f78cef06bf4c2ce07c0ec45a5fdf656fa1a9efd04691108f5e0","revision_guid":"896E0F76-CD24-494A-9832-6F58BCB07886","revision_number":3,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/896E0F76-CD24-494A-9832-6F58BCB07886/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":"45238","source_record_sha256":"07eb74b1dd5968f2f3606bb21bae3cf4149ee7a6825a05ea3aed28ee7dbe5512","source_url":"https://scicomp.stackexchange.com/questions/45238/relationship-between-eigenvalues-of-the-inertia-tensor-and-the-principal-moments","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Relationship between eigenvalues of the inertia tensor and the principal moments\nGiven an inertia tensor, $I$:\n\n\n\n\n$$\n\\mathbf{I} = \\begin{bmatrix}\nI_{xx} & I_{xy} & I_{xz} \\\\\nI_{yx} & I_{yy} & I_{yz} \\\\\nI_{zx} & I_{zy} & I_{zz}\n\\end{bmatrix}\n$$\n\n\n\n\nThe principal moments of inertia can be found by performing an eigensolution on I.\n$$\n\\mathbf{I}_{\\text{p}} = Q^\\top \\mathbf{I} Q\n$$\n\n\n\n\nUsing a package like Eigen (https://eigen.tuxfamily.org/index.php?title=Main_Page) or Matlab (https://www.mathworks.com/products/matlab.html), the eigenvalues come out in ascending order ($I_1$,$I_2$,$I_3$). Nastran (MSC and NX) selects $I_x$, $I_y$, and $I_z$ that are not always in ascending or descending order.  I didn't find any documentation on how to make that decision.  My textbook always equates $I_1$ with $I_x$ as the smallest, but this also seems arbitrary.  It assigns the easiest rotation as the principal x axis.  I didn't find a source to say that this is a standard or not.\n\n\n\n\nWhat determines which eigenvalue is $I_x$, $I_y$, and $I_z$?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45239,"score":3}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>it seems you are trying to simulate a Rayleigh-Benard convection in a cavity. It is typically coupled with flow field, which you are trying to simulate through omega-psi formulation. No, I believe the convection currents and temperature fields will look different than what you have shown in the picture. For clarity, can you check the following steps 1) Simulate a moving cavity lid at different Re numbers and compare against standard literature (like Ghia et.al (1982)). This freezes multiple things like verification of upwind schemes etc. 2) Recheck the enthalpy/heat equation whether the convection terms are taken care properly. For reference, typically over time, it should develop into convection cells. Please find my simulations for omega-psi attached in below picture<a href=\"https://i.sstatic.net/9Qqv2fdK.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/9Qqv2fdK.jpg\" alt=\"enter image description here\" /></a></p>\n","answer_id":45441,"answer_text":"it seems you are trying to simulate a Rayleigh-Benard convection in a cavity. It is typically coupled with flow field, which you are trying to simulate through omega-psi formulation. No, I believe the convection currents and temperature fields will look different than what you have shown in the picture. For clarity, can you check the following steps 1) Simulate a moving cavity lid at different Re numbers and compare against standard literature (like Ghia et.al (1982)). This freezes multiple things like verification of upwind schemes etc. 2) Recheck the enthalpy/heat equation whether the convection terms are taken care properly. For reference, typically over time, it should develop into convection cells. Please find my simulations for omega-psi attached in below picture[image: enter image description here; source: https://i.sstatic.net/9Qqv2fdK.jpg] (https://i.sstatic.net/9Qqv2fdK.jpg)","answer_url":"https://scicomp.stackexchange.com/a/45441","author":"Basham Govindan","author_url":"https://scicomp.stackexchange.com/users/41959/basham-govindan","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-05-05T09:13:01+00:00","is_accepted":false,"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 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=2&pagesize=100&site=scicomp&sort=creation","transformation":"API HTML retained; mechanical HTML-to-text; no LLM rewriting"},"question_id":45377,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Basham Govindan","profile_url":"https://scicomp.stackexchange.com/users/41959/basham-govindan","user_type":"registered"},"created_at":"2026-05-05T09:13:01+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"E5E280BD-52E3-4097-8B86-76EFC763D8A7","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/E5E280BD-52E3-4097-8B86-76EFC763D8A7/view-source"}],"score":1,"updated_at":"2026-05-05T09:13:01+00:00"}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Maroon Racoon","author_url":"https://scicomp.stackexchange.com/users/51966/maroon-racoon","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maroon Racoon","profile_url":"https://scicomp.stackexchange.com/users/51966/maroon-racoon","user_type":"registered"},"created_at":"2026-02-18T13:01:18+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"09701D0D-57FD-4430-8F2E-2E781ED01247","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/09701D0D-57FD-4430-8F2E-2E781ED01247/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maroon Racoon","profile_url":"https://scicomp.stackexchange.com/users/51966/maroon-racoon","user_type":"registered"},"created_at":"2026-02-18T15:47:31+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"9CE08707-17D2-4B7A-9212-4CA82E4ABE1B","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/9CE08707-17D2-4B7A-9212-4CA82E4ABE1B/view-source"}],"url":"https://scicomp.stackexchange.com/questions/45377/my-code-gives-inverted-temperatures-for-natural-convection-problem-c"},{"author":"Basham Govindan","author_url":"https://scicomp.stackexchange.com/users/41959/basham-govindan","content_license":"CC BY-SA 4.0","context_id":"45441","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Basham Govindan","profile_url":"https://scicomp.stackexchange.com/users/41959/basham-govindan","user_type":"registered"},"created_at":"2026-05-05T09:13:01+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"E5E280BD-52E3-4097-8B86-76EFC763D8A7","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/E5E280BD-52E3-4097-8B86-76EFC763D8A7/view-source"}],"url":"https://scicomp.stackexchange.com/a/45441"}],"contexts":[{"context_id":"question","html":"<p>Trying to solve natural convection probalem in a square region. Dimensionless. Here are the conditions:</p>\n<blockquote>\n<p><span class=\"math-container\">$0 \\leq x \\leq 1.5 0 \\leq y \\leq 1.0$</span> Pr = 7, Re = 7 Ra= 1e3, 1e4 <span class=\"math-container\">$\\ldots$</span>1e7.\nLeft and right walls are insulated. At the bottom wall <span class=\"math-container\">$q_1= 1000$</span> and at\nthe upper wall <span class=\"math-container\">$q_2=0.5*q_1$</span></p>\n</blockquote>\n<p>The temperature field generated by my cpp code was used on <em>SurferProgram</em> to visualize the isothermic lines. Physically it does not make sense, at the bottom where the heat flux is positive, temperature is the lowest, at the upper-- the hottest.</p>\n<p>The isotherms are straight horizontal lines. It looks like the heat conduction of a block of copper when one of the wall has higher constant temperature</p>\n<p>May be a problem when defining the heat flux in <code>solveTemperature</code> function. <strong>Shouldnt the isotherms be waivier?</strong> The walls are nonpermeable (no liquid passes trouht them).</p>\n<p>I tried using higher Ra, there were substancial changes, but still dont know if is physically accurate.\nThis image is for Ra = 1e3\n<a href=\"https://i.sstatic.net/Z4fMSBrm.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/Z4fMSBrm.png\" alt=\"for Ra = 1e3\" /></a></p>\n<p>This image is for Ra = 1e7\n<a href=\"https://i.sstatic.net/4a2ls0zL.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/4a2ls0zL.png\" alt=\"for Ra = 1e7\" /></a></p>\n<p>Here is the piece of code for calculating the temperatures</p>\n<pre><code>    // TEMPERATURE\nvoid solveTemperature(\n    double theta[Nx + 1][Ny + 1],\n    double u[Nx + 1][Ny + 1],\n    double v[Nx + 1][Ny + 1],\n    double alpha[], double beta[],\n    double hx, double hy, double dt, double Pr, double Ra)\n{\n    double A, B, C, F;\n\n    // in x direction\n    for (int j = 1; j &lt; Ny; j++)\n    {\n        alpha[0] = 1.0;\n        beta[0] = 0.0; // because boundary condition on left wall: theta=1\n\n        for (int i = 1; i &lt; Nx; i++)\n        {\n            double k = 1.0 /\n                (sqrt(Pr * Ra) * (1.0 + fabs(u[i][j]) * hx * 0.5 * sqrt(Pr * Ra)));\n\n            A = k / (hx * hx) - u[i][j] / (2 * hx) + fabs(u[i][j]) / (2 * hx);\n            C = k / (hx * hx) + u[i][j] / (2 * hx) + fabs(u[i][j]) / (2 * hx);\n            B = A + C + 1.0 / dt;\n\n            F = -theta[i][j] / dt;\n\n            alpha[i] = A / (B - C * alpha[i - 1]);\n            beta[i] = (C * beta[i - 1] - F) / (B - C * alpha[i - 1]);\n        }\n\n        // Right wall (i = Nx) - insulated\n        // For Neumann condition on the right wall, we need a special formula\n        // Using first order: Theta[Nx] = Theta[Nx-1]\n        theta[Nx][j] = beta[Nx - 1] / (1.0 - alpha[Nx - 1]);        // back substitution\n        for (int i = Nx - 1; i &gt;= 0; i--)\n        {\n            theta[i][j] = alpha[i] * theta[i + 1][j] + beta[i];\n        }\n    }\n\n    // sweep in y direction (vertical)\n    for (int i = 1; i &lt; Nx; i++)\n    {\n        // BOTTOM wall (j = 0) - heat flux IN: dTheta/dY = -1\n        // Using implicit scheme for Neumann condition with flux\n        double flux_bottom = -1.0;  // heat enters\n\n        alpha[0] = 2.0 * dt / (hy * hy * sqrt(Pr * Ra) + 2.0 * dt);\n        beta[0] = (hy * hy * sqrt(Pr * Ra) / (hy * hy * sqrt(Pr * Ra) + 2.0 * dt)) *\n            (theta[i][0] + (dt * flux_bottom) / (hy * sqrt(Pr * Ra)));\n\n        // Forward sweep for interior nodes\n        for (int j = 1; j &lt; Ny; j++)\n        {\n            double k = 1.0 / (sqrt(Pr * Ra) * (1.0 + fabs(v[i][j]) * hy * 0.5 * sqrt(Pr * Ra)));\n\n            double A = k / (hy * hy) - v[i][j] / (2 * hy) + fabs(v[i][j]) / (2 * hy);\n            double C = k / (hy * hy) + v[i][j] / (2 * hy) + fabs(v[i][j]) / (2 * hy);\n            double B = A + C + 1.0 / dt;\n\n            double F = -theta[i][j] / dt;\n\n            alpha[j] = A / (B - C * alpha[j - 1]);\n            beta[j] = (C * beta[j - 1] - F) / (B - C * alpha[j - 1]);\n        }\n\n        // TOP wall (j = Ny) - heat flux OUT: dTheta/dY = +0.5\n        double flux_top = 0.5;  // heat exits\n\n        // For top wall with flux, we use the relationship from the forward sweep\n        // combined with the flux condition\n        theta[i][Ny] = (beta[Ny - 1] + hy * flux_top) / (1.0 - alpha[Ny - 1]);\n\n        // Back substitution\n        for (int j = Ny - 1; j &gt;= 0; j--)\n        {\n            theta[i][j] = alpha[j] * theta[i][j + 1] + beta[j];\n        }\n    }\n}\n</code></pre>\n<p>Vortex solver</p>\n<pre><code>// Omega in x direction\nvoid solveOmegaX(\n    double psi[Nx + 1][Ny + 1],\n    double theta[Nx + 1][Ny + 1],\n    double u[Nx + 1][Ny + 1],\n    double omega[Nx + 1][Ny + 1],\n    double alpha[], double beta[],\n    double hx, double dt, double Pr, double Ra)\n{\n    double A, B, C, F;\n\n    for (int j = 1; j &lt; Ny; j++)\n    {\n        alpha[0] = 0.0; // from boundary conditions\n        beta[0] = -2.0 * psi[1][j] / (hx * hx);\n\n        for (int i = 1; i &lt; Nx; i++)\n        {\n            double k = sqrt(Pr / Ra) /\n                (1.0 + fabs(u[i][j]) * hx * 0.5 * sqrt(Ra / Pr));\n\n            A = k / (hx * hx) - u[i][j] / (2 * hx) + fabs(u[i][j]) / (2 * hx);\n            C = k / (hx * hx) + u[i][j] / (2 * hx) + fabs(u[i][j]) / (2 * hx);\n            B = A + C + 1.0 / dt;\n\n            F = -omega[i][j] / dt - (theta[i + 1][j] - theta[i - 1][j]) / (2 * hx);\n\n            alpha[i] = A / (B - C * alpha[i - 1]);\n            beta[i] = (C * beta[i - 1] - F) / (B - C * alpha[i - 1]); // All formulas from lecture in notebook\n        }\n\n        omega[Nx][j] = -2.0 * (psi[Nx - 1][j] - psi[Nx][j]) / (hx * hx); // right wall\n\n        // back substitution\n        for (int i = Nx - 1; i &gt;= 0; i--)\n            omega[i][j] = alpha[i] * omega[i + 1][j] + beta[i];\n    }\n}\n\n// Omega in y direction\nvoid solveOmegaY(\n    double psi[Nx + 1][Ny + 1],\n    double v[Nx + 1][Ny + 1],\n    double omega[Nx + 1][Ny + 1],\n    double alpha[], double beta[],\n    double hy, double dt, double Pr, double Ra)\n{\n    double A, B, C, F;\n\n    for (int i = 1; i &lt; Nx; i++)\n    {\n        alpha[0] = 0.0; // bottom wall\n        beta[0] = -2.0 * psi[i][1] / (hy * hy);\n\n        for (int j = 1; j &lt; Ny; j++)\n        {\n            double k = 1.0 /\n                (sqrt(Pr * Ra) * (1.0 + fabs(v[i][j]) * hy * 0.5 * sqrt(Pr * Ra)));\n\n            A = k / (hy * hy) - v[i][j] / (2 * hy) + fabs(v[i][j]) / (2 * hy);\n            C = k / (hy * hy) + v[i][j] / (2 * hy) + fabs(v[i][j]) / (2 * hy);\n            B = A + C + 1.0 / dt;\n\n            F = -omega[i][j] / dt;\n\n            alpha[j] = A / (B - C * alpha[j - 1]);\n            beta[j] = (C * beta[j - 1] - F) / (B - C * alpha[j - 1]);\n        }\n\n        omega[i][Ny] = -2.0 * (psi[i][Ny - 1] - psi[i][Ny]) / (hy * hy); // top wall\n\n        // back substitution\n        for (int j = Ny - 1; j &gt;= 0; j--)\n            omega[i][j] = alpha[j] * omega[i][j + 1] + beta[j];\n    }\n}\n</code></pre>\n<p>Stream function solver</p>\n<pre><code>// PSI equation\nvoid solvePsi(\n    double psi[Nx + 1][Ny + 1],\n    double psik[Nx + 1][Ny + 1],\n    double omega[Nx + 1][Ny + 1],\n    double hx, double hy,\n    double relax, double eps)\n{\n    double max_diff = 1.0, psi_new;\n    // This cycle from the lecture line ***\n    while (max_diff &gt; eps)\n    {\n        max_diff = 0.0;\n\n        for (int i = 1; i &lt; Nx; i++)\n            for (int j = 1; j &lt; Ny; j++)\n            {\n                psik[i][j] = psi[i][j]; // psi_k - from previous iteration\n\n                psi_new =\n                    (hy * hy * (psi[i - 1][j] + psi[i + 1][j]) +\n                        hx * hx * (psi[i][j - 1] + psi[i][j + 1]) +\n                        hx * hx * hy * hy * omega[i][j]) /\n                    (2.0 * (hx * hx + hy * hy)); // psi_new is psi with hat from lecture\n\n                psi[i][j] = psik[i][j] + relax * (psi_new - psik[i][j]);\n\n                double diff = fabs(psi[i][j] - psik[i][j]);\n                if (diff &gt; max_diff)\n                    max_diff = diff;\n            }\n    }\n}\n</code></pre>\n<p>Velocity calculator</p>\n<pre><code>// Velocities\n//  using formula \nvoid computeVelocity(\n    double psi[Nx + 1][Ny + 1],\n    double u[Nx + 1][Ny + 1],\n    double v[Nx + 1][Ny + 1],\n    double hx, double hy)\n{\n    for (int i = 1; i &lt; Nx; i++)\n        for (int j = 1; j &lt; Ny; j++)\n        {\n            u[i][j] = (psi[i][j + 1] - psi[i][j - 1]) / (2.0 * hy); // central difference approximation\n            v[i][j] = -(psi[i + 1][j] - psi[i - 1][j]) / (2.0 * hx);\n        }\n}\n</code></pre>\n<p>Setting boundary conditions</p>\n<pre><code>    // Boundary conditions for PSI\nvoid applyPsiBC(double psi[Nx + 1][Ny + 1])\n{\n    // Boundary conditions for psi (psi=0 on all walls)\n    for (int i = 0; i &lt;= Nx; i++)\n    {\n        psi[i][0] = 0.0;  // bottom wall\n        psi[i][Ny] = 0.0; // top wall\n    }\n    for (int j = 0; j &lt;= Ny; j++)\n    {\n        psi[0][j] = 0.0;  // left wall\n        psi[Nx][j] = 0.0; // right wall\n    }\n}\n</code></pre>\n<p>This is the main code</p>\n<pre><code>#include &lt;iostream&gt;\n#include &lt;fstream&gt;\n#include &lt;cmath&gt;\n\nusing namespace std;\nconstexpr int Nx = 180;\nconstexpr int Ny = 60;\n\n        int main()\n    {\n        const double Lx = 1.5, Ly = 1.0;\n        const double hx = Lx / Nx, hy = Ly / Ny;\n        const double Pr = 0.7, Ra = 1e8, dt = 0.001;\n        const double eps = 1e-6, relax = 1.0;\n    \n        double t = 0.0, t_k = 10.0;\n    \n        static double psi[Nx + 1][Ny + 1]{}, psik[Nx + 1][Ny + 1]{}, omega[Nx + 1][Ny + 1]{};\n        static double theta[Nx + 1][Ny + 1]{}, u[Nx + 1][Ny + 1]{}, v[Nx + 1][Ny + 1]{};\n        static double alpha[(Nx &gt; Ny ? Nx : Ny) + 1]{}, beta[(Nx &gt; Ny ? Nx : Ny) + 1]{}; // if Nx &gt; Ny then take Nx\n        // otherwise take Ny\n    \n        while (t &lt; t_k)\n        {\n            applyPsiBC(psi);\n            solvePsi(psi, psik, omega, hx, hy, relax, eps);\n            computeVelocity(psi, u, v, hx, hy);\n            solveOmegaX(psi, theta, u, omega, alpha, beta, hx, dt, Pr, Ra);\n            solveOmegaY(psi, v, omega, alpha, beta, hy, dt, Pr, Ra);\n            solveTemperature(theta, u, v, alpha, beta, hx, hy, dt, Pr, Ra);\n    \n            t += dt;\n            cout &lt;&lt; t &lt;&lt; endl;\n        }\n    \n        // OUTPUT to files\n        ofstream fpsi(&quot;psitest.txt&quot;), fomega(&quot;omegatest.txt&quot;), ftheta(&quot;thetatest.txt&quot;);\n    \n        for (int i = 0; i &lt;= Nx; i++)\n        {\n            for (int j = 0; j &lt;= Ny; j++)\n            {\n                double x = i * hx;\n                double y = j * hy;\n                fomega &lt;&lt; x &lt;&lt; &quot; &quot; &lt;&lt; y &lt;&lt; &quot; &quot; &lt;&lt; omega[i][j] &lt;&lt; &quot;\\n&quot;;\n                ftheta &lt;&lt; x &lt;&lt; &quot; &quot; &lt;&lt; y &lt;&lt; &quot; &quot; &lt;&lt; theta[i][j] &lt;&lt; &quot;\\n&quot;;\n                fpsi &lt;&lt; x &lt;&lt; &quot; &quot; &lt;&lt; y &lt;&lt; &quot; &quot; &lt;&lt; psi[i][j] &lt;&lt; &quot;\\n&quot;;\n            }\n        }\n    \n        cout &lt;&lt; &quot;Calculation completed. Files: psitest.txt, omegatest.txt, thetatest.txt\\n&quot;;\n        return 0;\n    }\n</code></pre>\n","text":"Trying to solve natural convection probalem in a square region. Dimensionless. Here are the conditions:\n\n\n\n\n\n\n\n$0 \\leq x \\leq 1.5 0 \\leq y \\leq 1.0$ Pr = 7, Re = 7 Ra= 1e3, 1e4 $\\ldots$1e7.\nLeft and right walls are insulated. At the bottom wall $q_1= 1000$ and at\nthe upper wall $q_2=0.5*q_1$\n\n\n\n\n\n\n\nThe temperature field generated by my cpp code was used on SurferProgram to visualize the isothermic lines. Physically it does not make sense, at the bottom where the heat flux is positive, temperature is the lowest, at the upper-- the hottest.\n\n\n\n\nThe isotherms are straight horizontal lines. It looks like the heat conduction of a block of copper when one of the wall has higher constant temperature\n\n\n\n\nMay be a problem when defining the heat flux in solveTemperature function. Shouldnt the isotherms be waivier? The walls are nonpermeable (no liquid passes trouht them).\n\n\n\n\nI tried using higher Ra, there were substancial changes, but still dont know if is physically accurate.\nThis image is for Ra = 1e3\n[image: for Ra = 1e3; source: https://i.sstatic.net/Z4fMSBrm.png] (https://i.sstatic.net/Z4fMSBrm.png)\n\n\n\n\nThis image is for Ra = 1e7\n[image: for Ra = 1e7; source: https://i.sstatic.net/4a2ls0zL.png] (https://i.sstatic.net/4a2ls0zL.png)\n\n\n\n\nHere is the piece of code for calculating the temperatures\n\n\n\n\n    // TEMPERATURE\nvoid solveTemperature(\n    double theta[Nx + 1][Ny + 1],\n    double u[Nx + 1][Ny + 1],\n    double v[Nx + 1][Ny + 1],\n    double alpha[], double beta[],\n    double hx, double hy, double dt, double Pr, double Ra)\n{\n    double A, B, C, F;\n\n    // in x direction\n    for (int j = 1; j < Ny; j++)\n    {\n        alpha[0] = 1.0;\n        beta[0] = 0.0; // because boundary condition on left wall: theta=1\n\n        for (int i = 1; i < Nx; i++)\n        {\n            double k = 1.0 /\n                (sqrt(Pr * Ra) * (1.0 + fabs(u[i][j]) * hx * 0.5 * sqrt(Pr * Ra)));\n\n            A = k / (hx * hx) - u[i][j] / (2 * hx) + fabs(u[i][j]) / (2 * hx);\n            C = k / (hx * hx) + u[i][j] / (2 * hx) + fabs(u[i][j]) / (2 * hx);\n            B = A + C + 1.0 / dt;\n\n            F = -theta[i][j] / dt;\n\n            alpha[i] = A / (B - C * alpha[i - 1]);\n            beta[i] = (C * beta[i - 1] - F) / (B - C * alpha[i - 1]);\n        }\n\n        // Right wall (i = Nx) - insulated\n        // For Neumann condition on the right wall, we need a special formula\n        // Using first order: Theta[Nx] = Theta[Nx-1]\n        theta[Nx][j] = beta[Nx - 1] / (1.0 - alpha[Nx - 1]);        // back substitution\n        for (int i = Nx - 1; i >= 0; i--)\n        {\n            theta[i][j] = alpha[i] * theta[i + 1][j] + beta[i];\n        }\n    }\n\n    // sweep in y direction (vertical)\n    for (int i = 1; i < Nx; i++)\n    {\n        // BOTTOM wall (j = 0) - heat flux IN: dTheta/dY = -1\n        // Using implicit scheme for Neumann condition with flux\n        double flux_bottom = -1.0;  // heat enters\n\n        alpha[0] = 2.0 * dt / (hy * hy * sqrt(Pr * Ra) + 2.0 * dt);\n        beta[0] = (hy * hy * sqrt(Pr * Ra) / (hy * hy * sqrt(Pr * Ra) + 2.0 * dt)) *\n            (theta[i][0] + (dt * flux_bottom) / (hy * sqrt(Pr * Ra)));\n\n        // Forward sweep for interior nodes\n        for (int j = 1; j < Ny; j++)\n        {\n            double k = 1.0 / (sqrt(Pr * Ra) * (1.0 + fabs(v[i][j]) * hy * 0.5 * sqrt(Pr * Ra)));\n\n            double A = k / (hy * hy) - v[i][j] / (2 * hy) + fabs(v[i][j]) / (2 * hy);\n            double C = k / (hy * hy) + v[i][j] / (2 * hy) + fabs(v[i][j]) / (2 * hy);\n            double B = A + C + 1.0 / dt;\n\n            double F = -theta[i][j] / dt;\n\n            alpha[j] = A / (B - C * alpha[j - 1]);\n            beta[j] = (C * beta[j - 1] - F) / (B - C * alpha[j - 1]);\n        }\n\n        // TOP wall (j = Ny) - heat flux OUT: dTheta/dY = +0.5\n        double flux_top = 0.5;  // heat exits\n\n        // For top wall with flux, we use the relationship from the forward sweep\n        // combined with the flux condition\n        theta[i][Ny] = (beta[Ny - 1] + hy * flux_top) / (1.0 - alpha[Ny - 1]);\n\n        // Back substitution\n        for (int j = Ny - 1; j >= 0; j--)\n        {\n            theta[i][j] = alpha[j] * theta[i][j + 1] + beta[j];\n        }\n    }\n}\n\n\n\n\n\nVortex solver\n\n\n\n\n// Omega in x direction\nvoid solveOmegaX(\n    double psi[Nx + 1][Ny + 1],\n    double theta[Nx + 1][Ny + 1],\n    double u[Nx + 1][Ny + 1],\n    double omega[Nx + 1][Ny + 1],\n    double alpha[], double beta[],\n    double hx, double dt, double Pr, double Ra)\n{\n    double A, B, C, F;\n\n    for (int j = 1; j < Ny; j++)\n    {\n        alpha[0] = 0.0; // from boundary conditions\n        beta[0] = -2.0 * psi[1][j] / (hx * hx);\n\n        for (int i = 1; i < Nx; i++)\n        {\n            double k = sqrt(Pr / Ra) /\n                (1.0 + fabs(u[i][j]) * hx * 0.5 * sqrt(Ra / Pr));\n\n            A = k / (hx * hx) - u[i][j] / (2 * hx) + fabs(u[i][j]) / (2 * hx);\n            C = k / (hx * hx) + u[i][j] / (2 * hx) + fabs(u[i][j]) / (2 * hx);\n            B = A + C + 1.0 / dt;\n\n            F = -omega[i][j] / dt - (theta[i + 1][j] - theta[i - 1][j]) / (2 * hx);\n\n            alpha[i] = A / (B - C * alpha[i - 1]);\n            beta[i] = (C * beta[i - 1] - F) / (B - C * alpha[i - 1]); // All formulas from lecture in notebook\n        }\n\n        omega[Nx][j] = -2.0 * (psi[Nx - 1][j] - psi[Nx][j]) / (hx * hx); // right wall\n\n        // back substitution\n        for (int i = Nx - 1; i >= 0; i--)\n            omega[i][j] = alpha[i] * omega[i + 1][j] + beta[i];\n    }\n}\n\n// Omega in y direction\nvoid solveOmegaY(\n    double psi[Nx + 1][Ny + 1],\n    double v[Nx + 1][Ny + 1],\n    double omega[Nx + 1][Ny + 1],\n    double alpha[], double beta[],\n    double hy, double dt, double Pr, double Ra)\n{\n    double A, B, C, F;\n\n    for (int i = 1; i < Nx; i++)\n    {\n        alpha[0] = 0.0; // bottom wall\n        beta[0] = -2.0 * psi[i][1] / (hy * hy);\n\n        for (int j = 1; j < Ny; j++)\n        {\n            double k = 1.0 /\n                (sqrt(Pr * Ra) * (1.0 + fabs(v[i][j]) * hy * 0.5 * sqrt(Pr * Ra)));\n\n            A = k / (hy * hy) - v[i][j] / (2 * hy) + fabs(v[i][j]) / (2 * hy);\n            C = k / (hy * hy) + v[i][j] / (2 * hy) + fabs(v[i][j]) / (2 * hy);\n            B = A + C + 1.0 / dt;\n\n            F = -omega[i][j] / dt;\n\n            alpha[j] = A / (B - C * alpha[j - 1]);\n            beta[j] = (C * beta[j - 1] - F) / (B - C * alpha[j - 1]);\n        }\n\n        omega[i][Ny] = -2.0 * (psi[i][Ny - 1] - psi[i][Ny]) / (hy * hy); // top wall\n\n        // back substitution\n        for (int j = Ny - 1; j >= 0; j--)\n            omega[i][j] = alpha[j] * omega[i][j + 1] + beta[j];\n    }\n}\n\n\n\n\n\nStream function solver\n\n\n\n\n// PSI equation\nvoid solvePsi(\n    double psi[Nx + 1][Ny + 1],\n    double psik[Nx + 1][Ny + 1],\n    double omega[Nx + 1][Ny + 1],\n    double hx, double hy,\n    double relax, double eps)\n{\n    double max_diff = 1.0, psi_new;\n    // This cycle from the lecture line ***\n    while (max_diff > eps)\n    {\n        max_diff = 0.0;\n\n        for (int i = 1; i < Nx; i++)\n            for (int j = 1; j < Ny; j++)\n            {\n                psik[i][j] = psi[i][j]; // psi_k - from previous iteration\n\n                psi_new =\n                    (hy * hy * (psi[i - 1][j] + psi[i + 1][j]) +\n                        hx * hx * (psi[i][j - 1] + psi[i][j + 1]) +\n                        hx * hx * hy * hy * omega[i][j]) /\n                    (2.0 * (hx * hx + hy * hy)); // psi_new is psi with hat from lecture\n\n                psi[i][j] = psik[i][j] + relax * (psi_new - psik[i][j]);\n\n                double diff = fabs(psi[i][j] - psik[i][j]);\n                if (diff > max_diff)\n                    max_diff = diff;\n            }\n    }\n}\n\n\n\n\n\nVelocity calculator\n\n\n\n\n// Velocities\n//  using formula \nvoid computeVelocity(\n    double psi[Nx + 1][Ny + 1],\n    double u[Nx + 1][Ny + 1],\n    double v[Nx + 1][Ny + 1],\n    double hx, double hy)\n{\n    for (int i = 1; i < Nx; i++)\n        for (int j = 1; j < Ny; j++)\n        {\n            u[i][j] = (psi[i][j + 1] - psi[i][j - 1]) / (2.0 * hy); // central difference approximation\n            v[i][j] = -(psi[i + 1][j] - psi[i - 1][j]) / (2.0 * hx);\n        }\n}\n\n\n\n\n\nSetting boundary conditions\n\n\n\n\n    // Boundary conditions for PSI\nvoid applyPsiBC(double psi[Nx + 1][Ny + 1])\n{\n    // Boundary conditions for psi (psi=0 on all walls)\n    for (int i = 0; i <= Nx; i++)\n    {\n        psi[i][0] = 0.0;  // bottom wall\n        psi[i][Ny] = 0.0; // top wall\n    }\n    for (int j = 0; j <= Ny; j++)\n    {\n        psi[0][j] = 0.0;  // left wall\n        psi[Nx][j] = 0.0; // right wall\n    }\n}\n\n\n\n\n\nThis is the main code\n\n\n\n\n#include <iostream>\n#include <fstream>\n#include <cmath>\n\nusing namespace std;\nconstexpr int Nx = 180;\nconstexpr int Ny = 60;\n\n        int main()\n    {\n        const double Lx = 1.5, Ly = 1.0;\n        const double hx = Lx / Nx, hy = Ly / Ny;\n        const double Pr = 0.7, Ra = 1e8, dt = 0.001;\n        const double eps = 1e-6, relax = 1.0;\n    \n        double t = 0.0, t_k = 10.0;\n    \n        static double psi[Nx + 1][Ny + 1]{}, psik[Nx + 1][Ny + 1]{}, omega[Nx + 1][Ny + 1]{};\n        static double theta[Nx + 1][Ny + 1]{}, u[Nx + 1][Ny + 1]{}, v[Nx + 1][Ny + 1]{};\n        static double alpha[(Nx > Ny ? Nx : Ny) + 1]{}, beta[(Nx > Ny ? Nx : Ny) + 1]{}; // if Nx > Ny then take Nx\n        // otherwise take Ny\n    \n        while (t < t_k)\n        {\n            applyPsiBC(psi);\n            solvePsi(psi, psik, omega, hx, hy, relax, eps);\n            computeVelocity(psi, u, v, hx, hy);\n            solveOmegaX(psi, theta, u, omega, alpha, beta, hx, dt, Pr, Ra);\n            solveOmegaY(psi, v, omega, alpha, beta, hy, dt, Pr, Ra);\n            solveTemperature(theta, u, v, alpha, beta, hx, hy, dt, Pr, Ra);\n    \n            t += dt;\n            cout << t << endl;\n        }\n    \n        // OUTPUT to files\n        ofstream fpsi(\"psitest.txt\"), fomega(\"omegatest.txt\"), ftheta(\"thetatest.txt\");\n    \n        for (int i = 0; i <= Nx; i++)\n        {\n            for (int j = 0; j <= Ny; j++)\n            {\n                double x = i * hx;\n                double y = j * hy;\n                fomega << x << \" \" << y << \" \" << omega[i][j] << \"\\n\";\n                ftheta << x << \" \" << y << \" \" << theta[i][j] << \"\\n\";\n                fpsi << x << \" \" << y << \" \" << psi[i][j] << \"\\n\";\n            }\n        }\n    \n        cout << \"Calculation completed. Files: psitest.txt, omegatest.txt, thetatest.txt\\n\";\n        return 0;\n    }"},{"context_id":"45441","html":"<p>it seems you are trying to simulate a Rayleigh-Benard convection in a cavity. It is typically coupled with flow field, which you are trying to simulate through omega-psi formulation. No, I believe the convection currents and temperature fields will look different than what you have shown in the picture. For clarity, can you check the following steps 1) Simulate a moving cavity lid at different Re numbers and compare against standard literature (like Ghia et.al (1982)). This freezes multiple things like verification of upwind schemes etc. 2) Recheck the enthalpy/heat equation whether the convection terms are taken care properly. For reference, typically over time, it should develop into convection cells. Please find my simulations for omega-psi attached in below picture<a href=\"https://i.sstatic.net/9Qqv2fdK.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.sstatic.net/9Qqv2fdK.jpg\" alt=\"enter image description here\" /></a></p>\n","text":"it seems you are trying to simulate a Rayleigh-Benard convection in a cavity. It is typically coupled with flow field, which you are trying to simulate through omega-psi formulation. No, I believe the convection currents and temperature fields will look different than what you have shown in the picture. For clarity, can you check the following steps 1) Simulate a moving cavity lid at different Re numbers and compare against standard literature (like Ghia et.al (1982)). This freezes multiple things like verification of upwind schemes etc. 2) Recheck the enthalpy/heat equation whether the convection terms are taken care properly. For reference, typically over time, it should develop into convection cells. Please find my simulations for omega-psi attached in below picture[image: enter image description here; source: https://i.sstatic.net/9Qqv2fdK.jpg] (https://i.sstatic.net/9Qqv2fdK.jpg)"}],"domain":"computational_science","external_citations":["https://i.sstatic.net/4a2ls0zL.png","https://i.sstatic.net/9Qqv2fdK.jpg","https://i.sstatic.net/Z4fMSBrm.png"],"ground_truth_type":"metadata_grounded","group_id":"cc357211dee6b26e8f557f524542a04070eb4a56f8fd52554d6c7cd501771dd2","hard_case_family":["no_accepted_answer","multiple_sources"],"id":"RHM-47d4305d502f009a7408d81e","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":"Maroon Racoon","profile_url":"https://scicomp.stackexchange.com/users/51966/maroon-racoon","user_type":"registered"},"created_at":"2026-02-18T13:01:18+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"09701D0D-57FD-4430-8F2E-2E781ED01247","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/09701D0D-57FD-4430-8F2E-2E781ED01247/view-source"},{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Maroon Racoon","profile_url":"https://scicomp.stackexchange.com/users/51966/maroon-racoon","user_type":"registered"},"created_at":"2026-02-18T15:47:31+00:00","raw_file":"raw/codex_api_v1/d49b4ef7856602e9d6b1a79d56b143976504b0637af4b266f03f2b60112c6c15_1790825353984908500_0.json","raw_sha256":"4ebc32b188652be208cbfb32007d2c8fcbe5419e5ab336ca46a3e9eb5ef04d0e","revision_guid":"9CE08707-17D2-4B7A-9212-4CA82E4ABE1B","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/9CE08707-17D2-4B7A-9212-4CA82E4ABE1B/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":"45377","source_record_sha256":"0e6e4be9e4d56155b1cbf127375f00b0ff15aa418f14b301fbdcbe0674f0ca6b","source_url":"https://scicomp.stackexchange.com/questions/45377/my-code-gives-inverted-temperatures-for-natural-convection-problem-c","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"My code gives inverted temperatures for natural convection problem [C++]\nTrying to solve natural convection probalem in a square region. Dimensionless. Here are the conditions:\n\n\n\n\n\n\n\n$0 \\leq x \\leq 1.5 0 \\leq y \\leq 1.0$ Pr = 7, Re = 7 Ra= 1e3, 1e4 $\\ldots$1e7.\nLeft and right walls are insulated. At the bottom wall $q_1= 1000$ and at\nthe upper wall $q_2=0.5*q_1$\n\n\n\n\n\n\n\nThe temperature field generated by my cpp code was used on SurferProgram to visualize the isothermic lines. Physically it does not make sense, at the bottom where the heat flux is positive, temperature is the lowest, at the upper-- the hottest.\n\n\n\n\nThe isotherms are straight horizontal lines. It looks like the heat conduction of a block of copper when one of the wall has higher constant temperature\n\n\n\n\nMay be a problem when defining the heat flux in solveTemperature function. Shouldnt the isotherms be waivier? The walls are nonpermeable (no liquid passes trouht them).\n\n\n\n\nI tried using higher Ra, there were substancial changes, but still dont know if is physically accurate.\nThis image is for Ra = 1e3\n[image: for Ra = 1e3; source: https://i.sstatic.net/Z4fMSBrm.png] (https://i.sstatic.net/Z4fMSBrm.png)\n\n\n\n\nThis image is for Ra = 1e7\n[image: for Ra = 1e7; source: https://i.sstatic.net/4a2ls0zL.png] (https://i.sstatic.net/4a2ls0zL.png)\n\n\n\n\nHere is the piece of code for calculating the temperatures\n\n\n\n\n    // TEMPERATURE\nvoid solveTemperature(\n    double theta[Nx + 1][Ny + 1],\n    double u[Nx + 1][Ny + 1],\n    double v[Nx + 1][Ny + 1],\n    double alpha[], double beta[],\n    double hx, double hy, double dt, double Pr, double Ra)\n{\n    double A, B, C, F;\n\n    // in x direction\n    for (int j = 1; j < Ny; j++)\n    {\n        alpha[0] = 1.0;\n        beta[0] = 0.0; // because boundary condition on left wall: theta=1\n\n        for (int i = 1; i < Nx; i++)\n        {\n            double k = 1.0 /\n                (sqrt(Pr * Ra) * (1.0 + fabs(u[i][j]) * hx * 0.5 * sqrt(Pr * Ra)));\n\n            A = k / (hx * hx) - u[i][j] / (2 * hx) + fabs(u[i][j]) / (2 * hx);\n            C = k / (hx * hx) + u[i][j] / (2 * hx) + fabs(u[i][j]) / (2 * hx);\n            B = A + C + 1.0 / dt;\n\n            F = -theta[i][j] / dt;\n\n            alpha[i] = A / (B - C * alpha[i - 1]);\n            beta[i] = (C * beta[i - 1] - F) / (B - C * alpha[i - 1]);\n        }\n\n        // Right wall (i = Nx) - insulated\n        // For Neumann condition on the right wall, we need a special formula\n        // Using first order: Theta[Nx] = Theta[Nx-1]\n        theta[Nx][j] = beta[Nx - 1] / (1.0 - alpha[Nx - 1]);        // back substitution\n        for (int i = Nx - 1; i >= 0; i--)\n        {\n            theta[i][j] = alpha[i] * theta[i + 1][j] + beta[i];\n        }\n    }\n\n    // sweep in y direction (vertical)\n    for (int i = 1; i < Nx; i++)\n    {\n        // BOTTOM wall (j = 0) - heat flux IN: dTheta/dY = -1\n        // Using implicit scheme for Neumann condition with flux\n        double flux_bottom = -1.0;  // heat enters\n\n        alpha[0] = 2.0 * dt / (hy * hy * sqrt(Pr * Ra) + 2.0 * dt);\n        beta[0] = (hy * hy * sqrt(Pr * Ra) / (hy * hy * sqrt(Pr * Ra) + 2.0 * dt)) *\n            (theta[i][0] + (dt * flux_bottom) / (hy * sqrt(Pr * Ra)));\n\n        // Forward sweep for interior nodes\n        for (int j = 1; j < Ny; j++)\n        {\n            double k = 1.0 / (sqrt(Pr * Ra) * (1.0 + fabs(v[i][j]) * hy * 0.5 * sqrt(Pr * Ra)));\n\n            double A = k / (hy * hy) - v[i][j] / (2 * hy) + fabs(v[i][j]) / (2 * hy);\n            double C = k / (hy * hy) + v[i][j] / (2 * hy) + fabs(v[i][j]) / (2 * hy);\n            double B = A + C + 1.0 / dt;\n\n            double F = -theta[i][j] / dt;\n\n            alpha[j] = A / (B - C * alpha[j - 1]);\n            beta[j] = (C * beta[j - 1] - F) / (B - C * alpha[j - 1]);\n        }\n\n        // TOP wall (j = Ny) - heat flux OUT: dTheta/dY = +0.5\n        double flux_top = 0.5;  // heat exits\n\n        // For top wall with flux, we use the relationship from the forward sweep\n        // combined with the flux condition\n        theta[i][Ny] = (beta[Ny - 1] + hy * flux_top) / (1.0 - alpha[Ny - 1]);\n\n        // Back substitution\n        for (int j = Ny - 1; j >= 0; j--)\n        {\n            theta[i][j] = alpha[j] * theta[i][j + 1] + beta[j];\n        }\n    }\n}\n\n\n\n\n\nVortex solver\n\n\n\n\n// Omega in x direction\nvoid solveOmegaX(\n    double psi[Nx + 1][Ny + 1],\n    double theta[Nx + 1][Ny + 1],\n    double u[Nx + 1][Ny + 1],\n    double omega[Nx + 1][Ny + 1],\n    double alpha[], double beta[],\n    double hx, double dt, double Pr, double Ra)\n{\n    double A, B, C, F;\n\n    for (int j = 1; j < Ny; j++)\n    {\n        alpha[0] = 0.0; // from boundary conditions\n        beta[0] = -2.0 * psi[1][j] / (hx * hx);\n\n        for (int i = 1; i < Nx; i++)\n        {\n            double k = sqrt(Pr / Ra) /\n                (1.0 + fabs(u[i][j]) * hx * 0.5 * sqrt(Ra / Pr));\n\n            A = k / (hx * hx) - u[i][j] / (2 * hx) + fabs(u[i][j]) / (2 * hx);\n            C = k / (hx * hx) + u[i][j] / (2 * hx) + fabs(u[i][j]) / (2 * hx);\n            B = A + C + 1.0 / dt;\n\n            F = -omega[i][j] / dt - (theta[i + 1][j] - theta[i - 1][j]) / (2 * hx);\n\n            alpha[i] = A / (B - C * alpha[i - 1]);\n            beta[i] = (C * beta[i - 1] - F) / (B - C * alpha[i - 1]); // All formulas from lecture in notebook\n        }\n\n        omega[Nx][j] = -2.0 * (psi[Nx - 1][j] - psi[Nx][j]) / (hx * hx); // right wall\n\n        // back substitution\n        for (int i = Nx - 1; i >= 0; i--)\n            omega[i][j] = alpha[i] * omega[i + 1][j] + beta[i];\n    }\n}\n\n// Omega in y direction\nvoid solveOmegaY(\n    double psi[Nx + 1][Ny + 1],\n    double v[Nx + 1][Ny + 1],\n    double omega[Nx + 1][Ny + 1],\n    double alpha[], double beta[],\n    double hy, double dt, double Pr, double Ra)\n{\n    double A, B, C, F;\n\n    for (int i = 1; i < Nx; i++)\n    {\n        alpha[0] = 0.0; // bottom wall\n        beta[0] = -2.0 * psi[i][1] / (hy * hy);\n\n        for (int j = 1; j < Ny; j++)\n        {\n            double k = 1.0 /\n                (sqrt(Pr * Ra) * (1.0 + fabs(v[i][j]) * hy * 0.5 * sqrt(Pr * Ra)));\n\n            A = k / (hy * hy) - v[i][j] / (2 * hy) + fabs(v[i][j]) / (2 * hy);\n            C = k / (hy * hy) + v[i][j] / (2 * hy) + fabs(v[i][j]) / (2 * hy);\n            B = A + C + 1.0 / dt;\n\n            F = -omega[i][j] / dt;\n\n            alpha[j] = A / (B - C * alpha[j - 1]);\n            beta[j] = (C * beta[j - 1] - F) / (B - C * alpha[j - 1]);\n        }\n\n        omega[i][Ny] = -2.0 * (psi[i][Ny - 1] - psi[i][Ny]) / (hy * hy); // top wall\n\n        // back substitution\n        for (int j = Ny - 1; j >= 0; j--)\n            omega[i][j] = alpha[j] * omega[i][j + 1] + beta[j];\n    }\n}\n\n\n\n\n\nStream function solver\n\n\n\n\n// PSI equation\nvoid solvePsi(\n    double psi[Nx + 1][Ny + 1],\n    double psik[Nx + 1][Ny + 1],\n    double omega[Nx + 1][Ny + 1],\n    double hx, double hy,\n    double relax, double eps)\n{\n    double max_diff = 1.0, psi_new;\n    // This cycle from the lecture line ***\n    while (max_diff > eps)\n    {\n        max_diff = 0.0;\n\n        for (int i = 1; i < Nx; i++)\n            for (int j = 1; j < Ny; j++)\n            {\n                psik[i][j] = psi[i][j]; // psi_k - from previous iteration\n\n                psi_new =\n                    (hy * hy * (psi[i - 1][j] + psi[i + 1][j]) +\n                        hx * hx * (psi[i][j - 1] + psi[i][j + 1]) +\n                        hx * hx * hy * hy * omega[i][j]) /\n                    (2.0 * (hx * hx + hy * hy)); // psi_new is psi with hat from lecture\n\n                psi[i][j] = psik[i][j] + relax * (psi_new - psik[i][j]);\n\n                double diff = fabs(psi[i][j] - psik[i][j]);\n                if (diff > max_diff)\n                    max_diff = diff;\n            }\n    }\n}\n\n\n\n\n\nVelocity calculator\n\n\n\n\n// Velocities\n//  using formula \nvoid computeVelocity(\n    double psi[Nx + 1][Ny + 1],\n    double u[Nx + 1][Ny + 1],\n    double v[Nx + 1][Ny + 1],\n    double hx, double hy)\n{\n    for (int i = 1; i < Nx; i++)\n        for (int j = 1; j < Ny; j++)\n        {\n            u[i][j] = (psi[i][j + 1] - psi[i][j - 1]) / (2.0 * hy); // central difference approximation\n            v[i][j] = -(psi[i + 1][j] - psi[i - 1][j]) / (2.0 * hx);\n        }\n}\n\n\n\n\n\nSetting boundary conditions\n\n\n\n\n    // Boundary conditions for PSI\nvoid applyPsiBC(double psi[Nx + 1][Ny + 1])\n{\n    // Boundary conditions for psi (psi=0 on all walls)\n    for (int i = 0; i <= Nx; i++)\n    {\n        psi[i][0] = 0.0;  // bottom wall\n        psi[i][Ny] = 0.0; // top wall\n    }\n    for (int j = 0; j <= Ny; j++)\n    {\n        psi[0][j] = 0.0;  // left wall\n        psi[Nx][j] = 0.0; // right wall\n    }\n}\n\n\n\n\n\nThis is the main code\n\n\n\n\n#include <iostream>\n#include <fstream>\n#include <cmath>\n\nusing namespace std;\nconstexpr int Nx = 180;\nconstexpr int Ny = 60;\n\n        int main()\n    {\n        const double Lx = 1.5, Ly = 1.0;\n        const double hx = Lx / Nx, hy = Ly / Ny;\n        const double Pr = 0.7, Ra = 1e8, dt = 0.001;\n        const double eps = 1e-6, relax = 1.0;\n    \n        double t = 0.0, t_k = 10.0;\n    \n        static double psi[Nx + 1][Ny + 1]{}, psik[Nx + 1][Ny + 1]{}, omega[Nx + 1][Ny + 1]{};\n        static double theta[Nx + 1][Ny + 1]{}, u[Nx + 1][Ny + 1]{}, v[Nx + 1][Ny + 1]{};\n        static double alpha[(Nx > Ny ? Nx : Ny) + 1]{}, beta[(Nx > Ny ? Nx : Ny) + 1]{}; // if Nx > Ny then take Nx\n        // otherwise take Ny\n    \n        while (t < t_k)\n        {\n            applyPsiBC(psi);\n            solvePsi(psi, psik, omega, hx, hy, relax, eps);\n            computeVelocity(psi, u, v, hx, hy);\n            solveOmegaX(psi, theta, u, omega, alpha, beta, hx, dt, Pr, Ra);\n            solveOmegaY(psi, v, omega, alpha, beta, hy, dt, Pr, Ra);\n            solveTemperature(theta, u, v, alpha, beta, hx, hy, dt, Pr, Ra);\n    \n            t += dt;\n            cout << t << endl;\n        }\n    \n        // OUTPUT to files\n        ofstream fpsi(\"psitest.txt\"), fomega(\"omegatest.txt\"), ftheta(\"thetatest.txt\");\n    \n        for (int i = 0; i <= Nx; i++)\n        {\n            for (int j = 0; j <= Ny; j++)\n            {\n                double x = i * hx;\n                double y = j * hy;\n                fomega << x << \" \" << y << \" \" << omega[i][j] << \"\\n\";\n                ftheta << x << \" \" << y << \" \" << theta[i][j] << \"\\n\";\n                fpsi << x << \" \" << y << \" \" << psi[i][j] << \"\\n\";\n            }\n        }\n    \n        cout << \"Calculation completed. Files: psitest.txt, omegatest.txt, thetatest.txt\\n\";\n        return 0;\n    }","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45441,"score":1}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>I know that this answer is off topic, but I hope that this answer can help you in your implementation and that afterwards you can check your quadrature scheme.</p>\n<h1>Re-writing the integral with Euler formula</h1>\n<p>By exploiting Euler formula, we can write the cos and sin into an exponential form:\n<span class=\"math-container\">\\begin{align}\n   \\cos{(nx)} &amp;= \\frac{1}{2}(e^{inx}+e^{-inx})\\\\ \n   \\sin{(nx)} &amp;= \\frac{1}{2i}(e^{inx}-e^{-inx})\\\\ \n\\end{align}</span></p>\n<p>Inserting the formulas into the integral gives:\n<span class=\"math-container\">\\begin{align}\nI_{mn} &amp;= \\int_a^b \\frac{1}{2}(e^{inx}+e^{-inx})\\frac{1}{2i}(e^{imx}-e^{-imx})P_l(x)dx\n\\end{align}</span></p>\n<p>Four terms of the form:\n<span class=\"math-container\">$$\n\\hat{I}_{mn} = \\int_a^b e^{i(m+n)x}P_l(x)dx\n$$</span> will then appear. I'll focus on one of them and leave the evaluation of <span class=\"math-container\">$I_{mn}$</span> as an the first exercise. Without loss of generality, I set <span class=\"math-container\">$P_l(x)=x^l$</span>. The generalization to any polynomial is straighforward by linear combination.</p>\n<h1>Focus on <span class=\"math-container\">$\\hat{I}_{mn}^l =\\int_a^b e^{i(m+n)x}x^ldx$</span></h1>\n<p>By applying the integral by parts trick:\n<span class=\"math-container\">\\begin{align}\n\\hat{I}_{mn}^l &amp;=\\int_a^b e^{i(m+n)x}x^ldx\\\\\n&amp;= [\\frac{1}{i(m+n)}e^{i(m+n)x}x^l]_a^b-\\int_a^b \\frac{1}{i(m+n)}e^{i(m+n)x}lx^{l-1}dx\\\\\n\\end{align}</span></p>\n<h1>Last step</h1>\n<p>You may have notices that the last intregral of the RHS almost looks like the orignal integral and that you can write this last equation as some recurrence formulae giving you the value of <span class=\"math-container\">$\\hat{I}^l_{mn}$</span> depending on <span class=\"math-container\">$\\hat{I}^{l-1}_{mn}$</span> (last exercise).</p>\n<p>Good luck! If this post needs more details do not hesitate.</p>\n","answer_id":45393,"answer_text":"I know that this answer is off topic, but I hope that this answer can help you in your implementation and that afterwards you can check your quadrature scheme.\n\n\n\n\nRe-writing the integral with Euler formula\n\n\n\n\nBy exploiting Euler formula, we can write the cos and sin into an exponential form:\n\\begin{align}\n   \\cos{(nx)} &= \\frac{1}{2}(e^{inx}+e^{-inx})\\\\ \n   \\sin{(nx)} &= \\frac{1}{2i}(e^{inx}-e^{-inx})\\\\ \n\\end{align}\n\n\n\n\nInserting the formulas into the integral gives:\n\\begin{align}\nI_{mn} &= \\int_a^b \\frac{1}{2}(e^{inx}+e^{-inx})\\frac{1}{2i}(e^{imx}-e^{-imx})P_l(x)dx\n\\end{align}\n\n\n\n\nFour terms of the form:\n$$\n\\hat{I}_{mn} = \\int_a^b e^{i(m+n)x}P_l(x)dx\n$$ will then appear. I'll focus on one of them and leave the evaluation of $I_{mn}$ as an the first exercise. Without loss of generality, I set $P_l(x)=x^l$. The generalization to any polynomial is straighforward by linear combination.\n\n\n\n\nFocus on $\\hat{I}_{mn}^l =\\int_a^b e^{i(m+n)x}x^ldx$\n\n\n\n\nBy applying the integral by parts trick:\n\\begin{align}\n\\hat{I}_{mn}^l &=\\int_a^b e^{i(m+n)x}x^ldx\\\\\n&= [\\frac{1}{i(m+n)}e^{i(m+n)x}x^l]_a^b-\\int_a^b \\frac{1}{i(m+n)}e^{i(m+n)x}lx^{l-1}dx\\\\\n\\end{align}\n\n\n\n\nLast step\n\n\n\n\nYou may have notices that the last intregral of the RHS almost looks like the orignal integral and that you can write this last equation as some recurrence formulae giving you the value of $\\hat{I}^l_{mn}$ depending on $\\hat{I}^{l-1}_{mn}$ (last exercise).\n\n\n\n\nGood luck! If this post needs more details do not hesitate.","answer_url":"https://scicomp.stackexchange.com/a/45393","author":"L Maxime","author_url":"https://scicomp.stackexchange.com/users/46525/l-maxime","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-03-04T09:40:44+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":45391,"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":"2026-03-04T09:40:44+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"90799FC5-F11A-4DBD-99A1-FFF984E63A91","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/90799FC5-F11A-4DBD-99A1-FFF984E63A91/view-source"}],"score":3,"updated_at":"2026-03-04T09:40:44+00:00"}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"vibe","author_url":"https://scicomp.stackexchange.com/users/28440/vibe","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"vibe","profile_url":"https://scicomp.stackexchange.com/users/28440/vibe","user_type":"registered"},"created_at":"2026-03-02T01:36:30+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"C62997C2-2915-4370-87EE-E96826E51772","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/C62997C2-2915-4370-87EE-E96826E51772/view-source"}],"url":"https://scicomp.stackexchange.com/questions/45391/quadrature-for-oscillatory-integral"},{"author":"L Maxime","author_url":"https://scicomp.stackexchange.com/users/46525/l-maxime","content_license":"CC BY-SA 4.0","context_id":"45393","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":"2026-03-04T09:40:44+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"90799FC5-F11A-4DBD-99A1-FFF984E63A91","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/90799FC5-F11A-4DBD-99A1-FFF984E63A91/view-source"}],"url":"https://scicomp.stackexchange.com/a/45393"}],"contexts":[{"context_id":"question","html":"<p>I have some integrals of the form:\n<span class=\"math-container\">$$\nI_{mn} = \\int_a^b \\cos{(nx)} \\sin{(mx)} P_l(x) dx\n$$</span>\nwhere <span class=\"math-container\">$P_l(x)$</span> is a polynomial of degree <span class=\"math-container\">$l$</span> and <span class=\"math-container\">$n,m$</span> are integers. I want to solve these integrals for lots of different <span class=\"math-container\">$n,m$</span> values as well as lots of different polynomials <span class=\"math-container\">$P_l(x)$</span>. I am looking for a fixed-point quadrature scheme to ensure rapid convergence in a finite number of steps. Unfortunately this type of integral does not seem to fit into any of the classical fixed-point quadrature methods.</p>\n<p>I thought of projecting <span class=\"math-container\">$P_l(x)$</span> onto the Chebyshev polynomial basis, then I would be left with an integral of 3 oscillatory terms which I could solve analytically, although its a bit messy because I would need to consider lots of special cases.</p>\n<p>Does anyone know of a simple fixed-point quadrature scheme which would help with this?</p>\n","text":"I have some integrals of the form:\n$$\nI_{mn} = \\int_a^b \\cos{(nx)} \\sin{(mx)} P_l(x) dx\n$$\nwhere $P_l(x)$ is a polynomial of degree $l$ and $n,m$ are integers. I want to solve these integrals for lots of different $n,m$ values as well as lots of different polynomials $P_l(x)$. I am looking for a fixed-point quadrature scheme to ensure rapid convergence in a finite number of steps. Unfortunately this type of integral does not seem to fit into any of the classical fixed-point quadrature methods.\n\n\n\n\nI thought of projecting $P_l(x)$ onto the Chebyshev polynomial basis, then I would be left with an integral of 3 oscillatory terms which I could solve analytically, although its a bit messy because I would need to consider lots of special cases.\n\n\n\n\nDoes anyone know of a simple fixed-point quadrature scheme which would help with this?"},{"context_id":"45393","html":"<p>I know that this answer is off topic, but I hope that this answer can help you in your implementation and that afterwards you can check your quadrature scheme.</p>\n<h1>Re-writing the integral with Euler formula</h1>\n<p>By exploiting Euler formula, we can write the cos and sin into an exponential form:\n<span class=\"math-container\">\\begin{align}\n   \\cos{(nx)} &amp;= \\frac{1}{2}(e^{inx}+e^{-inx})\\\\ \n   \\sin{(nx)} &amp;= \\frac{1}{2i}(e^{inx}-e^{-inx})\\\\ \n\\end{align}</span></p>\n<p>Inserting the formulas into the integral gives:\n<span class=\"math-container\">\\begin{align}\nI_{mn} &amp;= \\int_a^b \\frac{1}{2}(e^{inx}+e^{-inx})\\frac{1}{2i}(e^{imx}-e^{-imx})P_l(x)dx\n\\end{align}</span></p>\n<p>Four terms of the form:\n<span class=\"math-container\">$$\n\\hat{I}_{mn} = \\int_a^b e^{i(m+n)x}P_l(x)dx\n$$</span> will then appear. I'll focus on one of them and leave the evaluation of <span class=\"math-container\">$I_{mn}$</span> as an the first exercise. Without loss of generality, I set <span class=\"math-container\">$P_l(x)=x^l$</span>. The generalization to any polynomial is straighforward by linear combination.</p>\n<h1>Focus on <span class=\"math-container\">$\\hat{I}_{mn}^l =\\int_a^b e^{i(m+n)x}x^ldx$</span></h1>\n<p>By applying the integral by parts trick:\n<span class=\"math-container\">\\begin{align}\n\\hat{I}_{mn}^l &amp;=\\int_a^b e^{i(m+n)x}x^ldx\\\\\n&amp;= [\\frac{1}{i(m+n)}e^{i(m+n)x}x^l]_a^b-\\int_a^b \\frac{1}{i(m+n)}e^{i(m+n)x}lx^{l-1}dx\\\\\n\\end{align}</span></p>\n<h1>Last step</h1>\n<p>You may have notices that the last intregral of the RHS almost looks like the orignal integral and that you can write this last equation as some recurrence formulae giving you the value of <span class=\"math-container\">$\\hat{I}^l_{mn}$</span> depending on <span class=\"math-container\">$\\hat{I}^{l-1}_{mn}$</span> (last exercise).</p>\n<p>Good luck! If this post needs more details do not hesitate.</p>\n","text":"I know that this answer is off topic, but I hope that this answer can help you in your implementation and that afterwards you can check your quadrature scheme.\n\n\n\n\nRe-writing the integral with Euler formula\n\n\n\n\nBy exploiting Euler formula, we can write the cos and sin into an exponential form:\n\\begin{align}\n   \\cos{(nx)} &= \\frac{1}{2}(e^{inx}+e^{-inx})\\\\ \n   \\sin{(nx)} &= \\frac{1}{2i}(e^{inx}-e^{-inx})\\\\ \n\\end{align}\n\n\n\n\nInserting the formulas into the integral gives:\n\\begin{align}\nI_{mn} &= \\int_a^b \\frac{1}{2}(e^{inx}+e^{-inx})\\frac{1}{2i}(e^{imx}-e^{-imx})P_l(x)dx\n\\end{align}\n\n\n\n\nFour terms of the form:\n$$\n\\hat{I}_{mn} = \\int_a^b e^{i(m+n)x}P_l(x)dx\n$$ will then appear. I'll focus on one of them and leave the evaluation of $I_{mn}$ as an the first exercise. Without loss of generality, I set $P_l(x)=x^l$. The generalization to any polynomial is straighforward by linear combination.\n\n\n\n\nFocus on $\\hat{I}_{mn}^l =\\int_a^b e^{i(m+n)x}x^ldx$\n\n\n\n\nBy applying the integral by parts trick:\n\\begin{align}\n\\hat{I}_{mn}^l &=\\int_a^b e^{i(m+n)x}x^ldx\\\\\n&= [\\frac{1}{i(m+n)}e^{i(m+n)x}x^l]_a^b-\\int_a^b \\frac{1}{i(m+n)}e^{i(m+n)x}lx^{l-1}dx\\\\\n\\end{align}\n\n\n\n\nLast step\n\n\n\n\nYou may have notices that the last intregral of the RHS almost looks like the orignal integral and that you can write this last equation as some recurrence formulae giving you the value of $\\hat{I}^l_{mn}$ depending on $\\hat{I}^{l-1}_{mn}$ (last exercise).\n\n\n\n\nGood luck! If this post needs more details do not hesitate."}],"domain":"computational_science","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"b30713c077858e0fb346bb568cd553392adb6f6d31dfbf51091a074502bdcd3c","hard_case_family":["no_accepted_answer"],"id":"RHM-fdc98f9181e53944d2f4ddb0","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":"vibe","profile_url":"https://scicomp.stackexchange.com/users/28440/vibe","user_type":"registered"},"created_at":"2026-03-02T01:36:30+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"C62997C2-2915-4370-87EE-E96826E51772","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/C62997C2-2915-4370-87EE-E96826E51772/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":"45391","source_record_sha256":"9963bc23f954630aec036aa2c259beae2db7d875ef9ccd1890f6243096cb66a9","source_url":"https://scicomp.stackexchange.com/questions/45391/quadrature-for-oscillatory-integral","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Quadrature for oscillatory integral\nI have some integrals of the form:\n$$\nI_{mn} = \\int_a^b \\cos{(nx)} \\sin{(mx)} P_l(x) dx\n$$\nwhere $P_l(x)$ is a polynomial of degree $l$ and $n,m$ are integers. I want to solve these integrals for lots of different $n,m$ values as well as lots of different polynomials $P_l(x)$. I am looking for a fixed-point quadrature scheme to ensure rapid convergence in a finite number of steps. Unfortunately this type of integral does not seem to fit into any of the classical fixed-point quadrature methods.\n\n\n\n\nI thought of projecting $P_l(x)$ onto the Chebyshev polynomial basis, then I would be left with an integral of 3 oscillatory terms which I could solve analytically, although its a bit messy because I would need to consider lots of special cases.\n\n\n\n\nDoes anyone know of a simple fixed-point quadrature scheme which would help with this?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45393,"score":3}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":45413,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>While I'm not familiar with the OMP_DYNAMIC, for a scaling test you want to ensure that you know with how many cores you are running. The whole point is to say how your performance changes with the number of cores you are running, i.e. (going by the answer in the linked SO question), what OMP_DYNAMIC tries to guess by running with possibly less than the maximum number of threads. If for a particular run you cannot say with how many cores you ran(*), how would you even make a scaling plot?</p>\n<p>Going by the latest <a href=\"https://www.openmp.org/wp-content/uploads/OpenMP-API-Specification-6-0.pdf\" rel=\"nofollow noreferrer\">OpenMP spec</a> the initial value of <code>dyn_var</code> (which is set by <code>OMP_DYNAMIC</code> and the respective OMP routine) is implementation-defined (3.2 ICV Initialization), which I would say is a very bad choice on part of the standard, since prior to the introduction of this the behaviour was static and so now you can get behavioural changes by a version upgrade.</p>\n<p>What you can use it for however is for comparing runs at the same maximum/nominal core count. Depending on all computational details it might offer a benefit or not.</p>\n<p>* Ok you could record the dynamic count, but that may differ between different parallel regions, so how do you report that?</p>\n","answer_id":45413,"answer_text":"While I'm not familiar with the OMP_DYNAMIC, for a scaling test you want to ensure that you know with how many cores you are running. The whole point is to say how your performance changes with the number of cores you are running, i.e. (going by the answer in the linked SO question), what OMP_DYNAMIC tries to guess by running with possibly less than the maximum number of threads. If for a particular run you cannot say with how many cores you ran(*), how would you even make a scaling plot?\n\n\n\n\nGoing by the latest OpenMP spec (https://www.openmp.org/wp-content/uploads/OpenMP-API-Specification-6-0.pdf) the initial value of dyn_var (which is set by OMP_DYNAMIC and the respective OMP routine) is implementation-defined (3.2 ICV Initialization), which I would say is a very bad choice on part of the standard, since prior to the introduction of this the behaviour was static and so now you can get behavioural changes by a version upgrade.\n\n\n\n\nWhat you can use it for however is for comparing runs at the same maximum/nominal core count. Depending on all computational details it might offer a benefit or not.\n\n\n\n\n* Ok you could record the dynamic count, but that may differ between different parallel regions, so how do you report that?","answer_url":"https://scicomp.stackexchange.com/a/45413","author":"niemc","author_url":"https://scicomp.stackexchange.com/users/50632/niemc","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-03-19T00:07:33+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":45410,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"niemc","profile_url":"https://scicomp.stackexchange.com/users/50632/niemc","user_type":"registered"},"created_at":"2026-03-19T00:07:33+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"5372F3AB-7410-43D7-8F1B-DE58216730F2","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/5372F3AB-7410-43D7-8F1B-DE58216730F2/view-source"}],"score":3,"updated_at":"2026-03-19T00:07:33+00:00"}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"Jared","author_url":"https://scicomp.stackexchange.com/users/44117/jared","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Jared","profile_url":"https://scicomp.stackexchange.com/users/44117/jared","user_type":"registered"},"created_at":"2026-03-17T22:14:06+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"1C284D3D-A99E-4907-9487-D4A530808265","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/1C284D3D-A99E-4907-9487-D4A530808265/view-source"}],"url":"https://scicomp.stackexchange.com/questions/45410/omp-dynamic-and-scaling-tests"},{"author":"niemc","author_url":"https://scicomp.stackexchange.com/users/50632/niemc","content_license":"CC BY-SA 4.0","context_id":"45413","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"niemc","profile_url":"https://scicomp.stackexchange.com/users/50632/niemc","user_type":"registered"},"created_at":"2026-03-19T00:07:33+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"5372F3AB-7410-43D7-8F1B-DE58216730F2","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/5372F3AB-7410-43D7-8F1B-DE58216730F2/view-source"}],"url":"https://scicomp.stackexchange.com/a/45413"}],"contexts":[{"context_id":"question","html":"<p>When conducting scaling experiments on a code accelerated with OpenMP, is it standard practice to set OMP_DYNAMIC to false so that the number of threads spawned per parallel region is deterministic? I cannot find any references (e.g., papers, tutorials, etc.) that explicitly mention how they handle this variable. It does seem typical to adjust the scheduling (dynamic and static, though this is different than OMP_DYNAMIC), but as far as I can tell there is never mention of dynamic adjustment of threads in parallel regions and if this <em>should</em> be disabled during performance experiments.</p>\n<p>Refefences:</p>\n<p><a href=\"https://apps.fz-juelich.de/jsc-pubsystem/aigaion/attachments/HowManyThreadsWillBeTooMany.pdf-6a09560d6a1206fe8e302a30c53024f3.pdf\" rel=\"nofollow noreferrer\">https://apps.fz-juelich.de/jsc-pubsystem/aigaion/attachments/HowManyThreadsWillBeTooMany.pdf-6a09560d6a1206fe8e302a30c53024f3.pdf</a></p>\n<p><a href=\"https://stackoverflow.com/questions/61831001/omp-set-dynamic-less-helpful-than-what-i-expect\">https://stackoverflow.com/questions/61831001/omp-set-dynamic-less-helpful-than-what-i-expect</a></p>\n","text":"When conducting scaling experiments on a code accelerated with OpenMP, is it standard practice to set OMP_DYNAMIC to false so that the number of threads spawned per parallel region is deterministic? I cannot find any references (e.g., papers, tutorials, etc.) that explicitly mention how they handle this variable. It does seem typical to adjust the scheduling (dynamic and static, though this is different than OMP_DYNAMIC), but as far as I can tell there is never mention of dynamic adjustment of threads in parallel regions and if this should be disabled during performance experiments.\n\n\n\n\nRefefences:\n\n\n\n\nhttps://apps.fz-juelich.de/jsc-pubsystem/aigaion/attachments/HowManyThreadsWillBeTooMany.pdf-6a09560d6a1206fe8e302a30c53024f3.pdf (https://apps.fz-juelich.de/jsc-pubsystem/aigaion/attachments/HowManyThreadsWillBeTooMany.pdf-6a09560d6a1206fe8e302a30c53024f3.pdf)\n\n\n\n\nhttps://stackoverflow.com/questions/61831001/omp-set-dynamic-less-helpful-than-what-i-expect (https://stackoverflow.com/questions/61831001/omp-set-dynamic-less-helpful-than-what-i-expect)"},{"context_id":"45413","html":"<p>While I'm not familiar with the OMP_DYNAMIC, for a scaling test you want to ensure that you know with how many cores you are running. The whole point is to say how your performance changes with the number of cores you are running, i.e. (going by the answer in the linked SO question), what OMP_DYNAMIC tries to guess by running with possibly less than the maximum number of threads. If for a particular run you cannot say with how many cores you ran(*), how would you even make a scaling plot?</p>\n<p>Going by the latest <a href=\"https://www.openmp.org/wp-content/uploads/OpenMP-API-Specification-6-0.pdf\" rel=\"nofollow noreferrer\">OpenMP spec</a> the initial value of <code>dyn_var</code> (which is set by <code>OMP_DYNAMIC</code> and the respective OMP routine) is implementation-defined (3.2 ICV Initialization), which I would say is a very bad choice on part of the standard, since prior to the introduction of this the behaviour was static and so now you can get behavioural changes by a version upgrade.</p>\n<p>What you can use it for however is for comparing runs at the same maximum/nominal core count. Depending on all computational details it might offer a benefit or not.</p>\n<p>* Ok you could record the dynamic count, but that may differ between different parallel regions, so how do you report that?</p>\n","text":"While I'm not familiar with the OMP_DYNAMIC, for a scaling test you want to ensure that you know with how many cores you are running. The whole point is to say how your performance changes with the number of cores you are running, i.e. (going by the answer in the linked SO question), what OMP_DYNAMIC tries to guess by running with possibly less than the maximum number of threads. If for a particular run you cannot say with how many cores you ran(*), how would you even make a scaling plot?\n\n\n\n\nGoing by the latest OpenMP spec (https://www.openmp.org/wp-content/uploads/OpenMP-API-Specification-6-0.pdf) the initial value of dyn_var (which is set by OMP_DYNAMIC and the respective OMP routine) is implementation-defined (3.2 ICV Initialization), which I would say is a very bad choice on part of the standard, since prior to the introduction of this the behaviour was static and so now you can get behavioural changes by a version upgrade.\n\n\n\n\nWhat you can use it for however is for comparing runs at the same maximum/nominal core count. Depending on all computational details it might offer a benefit or not.\n\n\n\n\n* Ok you could record the dynamic count, but that may differ between different parallel regions, so how do you report that?"}],"domain":"computational_science","external_citations":["https://apps.fz-juelich.de/jsc-pubsystem/aigaion/attachments/HowManyThreadsWillBeTooMany.pdf-6a09560d6a1206fe8e302a30c53024f3.pdf","https://stackoverflow.com/questions/61831001/omp-set-dynamic-less-helpful-than-what-i-expect","https://www.openmp.org/wp-content/uploads/OpenMP-API-Specification-6-0.pdf"],"ground_truth_type":"metadata_grounded","group_id":"9eb41d8b4c911a7d7e095fda16bd9dd13dabff250c18abde35f31466b66c7bef","hard_case_family":["multiple_sources"],"id":"RHM-f5270f970df296d26ca0a63e","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":"Jared","profile_url":"https://scicomp.stackexchange.com/users/44117/jared","user_type":"registered"},"created_at":"2026-03-17T22:14:06+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"1C284D3D-A99E-4907-9487-D4A530808265","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/1C284D3D-A99E-4907-9487-D4A530808265/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":"45410","source_record_sha256":"bc58d2987b704b2555402ef830381330d88f2171d0dcc32c1ba09fdd23081de1","source_url":"https://scicomp.stackexchange.com/questions/45410/omp-dynamic-and-scaling-tests","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"OMP_DYNAMIC and scaling tests\nWhen conducting scaling experiments on a code accelerated with OpenMP, is it standard practice to set OMP_DYNAMIC to false so that the number of threads spawned per parallel region is deterministic? I cannot find any references (e.g., papers, tutorials, etc.) that explicitly mention how they handle this variable. It does seem typical to adjust the scheduling (dynamic and static, though this is different than OMP_DYNAMIC), but as far as I can tell there is never mention of dynamic adjustment of threads in parallel regions and if this should be disabled during performance experiments.\n\n\n\n\nRefefences:\n\n\n\n\nhttps://apps.fz-juelich.de/jsc-pubsystem/aigaion/attachments/HowManyThreadsWillBeTooMany.pdf-6a09560d6a1206fe8e302a30c53024f3.pdf (https://apps.fz-juelich.de/jsc-pubsystem/aigaion/attachments/HowManyThreadsWillBeTooMany.pdf-6a09560d6a1206fe8e302a30c53024f3.pdf)\n\n\n\n\nhttps://stackoverflow.com/questions/61831001/omp-set-dynamic-less-helpful-than-what-i-expect (https://stackoverflow.com/questions/61831001/omp-set-dynamic-less-helpful-than-what-i-expect)","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45413,"score":3}],"split":"validation"}
{"accepted_status":{"accepted_answer_id":null,"scientific_correctness_verified":false},"candidate_answers":[{"answer_html":"<p>This method appears to be simply Implicit Euler but with broken error control and without any actual ability to measure or ensure convergence to the correct solution.</p>\n","answer_id":45429,"answer_text":"This method appears to be simply Implicit Euler but with broken error control and without any actual ability to measure or ensure convergence to the correct solution.","answer_url":"https://scicomp.stackexchange.com/a/45429","author":"Oscar Smith","author_url":"https://scicomp.stackexchange.com/users/33841/oscar-smith","author_user_type":"registered","content_license":"CC BY-SA 4.0","created_at":"2026-04-05T17:38:55+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":45422,"revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Oscar Smith","profile_url":"https://scicomp.stackexchange.com/users/33841/oscar-smith","user_type":"registered"},"created_at":"2026-04-05T17:38:55+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"FF7D6040-9711-407E-AD44-F933FEAD971C","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/FF7D6040-9711-407E-AD44-F933FEAD971C/view-source"}],"score":3,"updated_at":"2026-04-05T17:38:55+00:00"}],"content_license":"CC BY-SA 4.0","context_sources":[{"author":"fethi gaouer","author_url":"https://scicomp.stackexchange.com/users/56574/fethi-gaouer","content_license":"CC BY-SA 4.0","context_id":"question","revision_attribution":[{"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":"2026-04-01T19:04:02+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"C2B7F1EE-558E-4597-AEC8-AB9AD9D0D121","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/C2B7F1EE-558E-4597-AEC8-AB9AD9D0D121/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":"2026-04-05T08:48:09+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"EB6BC856-36CA-4681-8A08-B0FD3EB4B53F","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/EB6BC856-36CA-4681-8A08-B0FD3EB4B53F/view-source"}],"url":"https://scicomp.stackexchange.com/questions/45422/stability-analysis-for-a-derivative-free-ode-solver-based-on-local-geodesic-inte"},{"author":"Oscar Smith","author_url":"https://scicomp.stackexchange.com/users/33841/oscar-smith","content_license":"CC BY-SA 4.0","context_id":"45429","revision_attribution":[{"content_license":"CC BY-SA 4.0","contributor":{"display_name":"Oscar Smith","profile_url":"https://scicomp.stackexchange.com/users/33841/oscar-smith","user_type":"registered"},"created_at":"2026-04-05T17:38:55+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"FF7D6040-9711-407E-AD44-F933FEAD971C","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/FF7D6040-9711-407E-AD44-F933FEAD971C/view-source"}],"url":"https://scicomp.stackexchange.com/a/45429"}],"contexts":[{"context_id":"question","html":"<p>We propose a numerical method for stiff ordinary differential equations (ODEs) based on a geometric transformation. The key ideas are:</p>\n<p><strong>1-Local geodesic approximation</strong> – On a short interval [t1,t2] the solution is approximated by a geodesic in a non‑Euclidean metric space. This geodesic depends on a single free parameter: the value y2=y(t2).</p>\n<p><strong>2-Calibration</strong> – For a given y2,the geodesic provides the midpoint</p>\n<p>(tm,ym). We then compute the derivative from the geodesic:</p>\n<pre><code>                       ym′ = (ym−y1)/(tm-t1)\n</code></pre>\n<p>​</p>\n<p>and evaluate the ODE at the midpoint:</p>\n<p>fm =f(tm,ym).\nThe residual is\nR(y2 )=∣ ym′−fm ∣.</p>\n<p><strong>3-Adjustment</strong> – Because the interval is short,</p>\n<p>R is nearly linear in y2 . A few secant iterations (or a simple manual search) suffice to make R negligible.</p>\n<p><strong>4-Systems –</strong> For a system of ODEs we select one component (e.g.y2) as the only free parameter. The geodesic gives (tm,ym). The other components at the midpoint, as well as their derivatives, are then deduced from the equations and the initial conditions. The residual is built on the remaining equations.</p>\n<p><strong>5-Long intervals</strong> – The total time interval is split into short segments where the curvature remains small. Each segment is treated independently using the same single‑parameter calibration.</p>\n<p><strong>6-Spectral pre‑processing</strong> – A coarse scan of the ODE’s right‑hand side estimates the local curvature and detects stiff regions or fast oscillations. This helps choose an optimal segmentation without trial and error.</p>\n<p><strong>Why this method differs from classical ones:</strong></p>\n<p>No implicit solver, no Jacobian.</p>\n<p>Stability is controlled by curvature, not by a CFL condition.</p>\n<p>Only one scalar parameter is adjusted per segment, regardless of the system size.</p>\n<p><strong><strong>Benchmarks (performed in double precision, reference: Radau</strong> with tolerance 1e-12):</strong></p>\n<p><strong>Prothero–Robinson</strong></p>\n<p>y′ =−1000y+1000sint+cost with  y(0.1)=sin(0.1)<br />\nResult: y(0.101)≈0.10083089255<br />\nError:   1e-6</p>\n<p><strong>Van der Pol,</strong></p>\n<p>ε=1000, 8 segments from<br />\nResult: y(0.248583)≈0.2477211<br />\nError: 0.7% (finner subdivision gives 1e-7)</p>\n<p><strong>Lorenz system</strong> (single\nshort segment)</p>\n<p>Result: error on all variables<br />\nError≈1e-7</p>\n<p><strong>Brusselator</strong> (single segment)</p>\n<p>Result:  residual on second equation<br />\nerror:  &lt;1e-7</p>\n<p><strong>Questions to the community:</strong></p>\n<p>Are there other stiff or multi‑scale benchmarks that you would recommend to test this approach further?</p>\n<p>Has a similar curvature‑based step control been studied elsewhere?</p>\n<p>What theoretical tools could help analyse the stability of such a method?</p>\n","text":"We propose a numerical method for stiff ordinary differential equations (ODEs) based on a geometric transformation. The key ideas are:\n\n\n\n\n1-Local geodesic approximation – On a short interval [t1,t2] the solution is approximated by a geodesic in a non‑Euclidean metric space. This geodesic depends on a single free parameter: the value y2=y(t2).\n\n\n\n\n2-Calibration – For a given y2,the geodesic provides the midpoint\n\n\n\n\n(tm,ym). We then compute the derivative from the geodesic:\n\n\n\n\n                       ym′ = (ym−y1)/(tm-t1)\n\n\n\n\n\n​\n\n\n\n\nand evaluate the ODE at the midpoint:\n\n\n\n\nfm =f(tm,ym).\nThe residual is\nR(y2 )=∣ ym′−fm ∣.\n\n\n\n\n3-Adjustment – Because the interval is short,\n\n\n\n\nR is nearly linear in y2 . A few secant iterations (or a simple manual search) suffice to make R negligible.\n\n\n\n\n4-Systems – For a system of ODEs we select one component (e.g.y2) as the only free parameter. The geodesic gives (tm,ym). The other components at the midpoint, as well as their derivatives, are then deduced from the equations and the initial conditions. The residual is built on the remaining equations.\n\n\n\n\n5-Long intervals – The total time interval is split into short segments where the curvature remains small. Each segment is treated independently using the same single‑parameter calibration.\n\n\n\n\n6-Spectral pre‑processing – A coarse scan of the ODE’s right‑hand side estimates the local curvature and detects stiff regions or fast oscillations. This helps choose an optimal segmentation without trial and error.\n\n\n\n\nWhy this method differs from classical ones:\n\n\n\n\nNo implicit solver, no Jacobian.\n\n\n\n\nStability is controlled by curvature, not by a CFL condition.\n\n\n\n\nOnly one scalar parameter is adjusted per segment, regardless of the system size.\n\n\n\n\nBenchmarks (performed in double precision, reference: Radau with tolerance 1e-12):\n\n\n\n\nProthero–Robinson\n\n\n\n\ny′ =−1000y+1000sint+cost with  y(0.1)=sin(0.1)\n\nResult: y(0.101)≈0.10083089255\n\nError:   1e-6\n\n\n\n\nVan der Pol,\n\n\n\n\nε=1000, 8 segments from\n\nResult: y(0.248583)≈0.2477211\n\nError: 0.7% (finner subdivision gives 1e-7)\n\n\n\n\nLorenz system (single\nshort segment)\n\n\n\n\nResult: error on all variables\n\nError≈1e-7\n\n\n\n\nBrusselator (single segment)\n\n\n\n\nResult:  residual on second equation\n\nerror:  <1e-7\n\n\n\n\nQuestions to the community:\n\n\n\n\nAre there other stiff or multi‑scale benchmarks that you would recommend to test this approach further?\n\n\n\n\nHas a similar curvature‑based step control been studied elsewhere?\n\n\n\n\nWhat theoretical tools could help analyse the stability of such a method?"},{"context_id":"45429","html":"<p>This method appears to be simply Implicit Euler but with broken error control and without any actual ability to measure or ensure convergence to the correct solution.</p>\n","text":"This method appears to be simply Implicit Euler but with broken error control and without any actual ability to measure or ensure convergence to the correct solution."}],"domain":"computational_science","external_citations":[],"ground_truth_type":"metadata_grounded","group_id":"3014f47fb8200d2bcf83ca0d38d8f9cf3c3d59b0ac10e380d1c170975f9bb81b","hard_case_family":["no_accepted_answer"],"id":"RHM-b8e5514c6c9934e2a912d0f2","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":"fethi gaouer","profile_url":"https://scicomp.stackexchange.com/users/56574/fethi-gaouer","user_type":"registered"},"created_at":"2026-04-01T19:04:02+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"C2B7F1EE-558E-4597-AEC8-AB9AD9D0D121","revision_number":1,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/C2B7F1EE-558E-4597-AEC8-AB9AD9D0D121/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":"2026-04-05T08:48:09+00:00","raw_file":"raw/codex_api_v1/09cbe10ae05462240864407122b451f89c4541eb0ee757adda70c0629772d57a_1790825351806992800_0.json","raw_sha256":"34f3f34325937951c51090d8305fb513e1e88ef2ed40dcec5c0fe96d5710ba75","revision_guid":"EB6BC856-36CA-4681-8A08-B0FD3EB4B53F","revision_number":2,"revision_type":"single_user","revision_url":"https://scicomp.stackexchange.com/revisions/EB6BC856-36CA-4681-8A08-B0FD3EB4B53F/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":"45422","source_record_sha256":"7674d5bad612f19d4312ae4fee5c49dbe6db34cc7c64096e6c1b5eadad06c56b","source_url":"https://scicomp.stackexchange.com/questions/45422/stability-analysis-for-a-derivative-free-ode-solver-based-on-local-geodesic-inte","transformation":"RegalFire V3 deterministic transformation; no LLM truth labels"},"query":"Stability analysis for a derivative‑free ODE solver based on local geodesic interpolation\nWe propose a numerical method for stiff ordinary differential equations (ODEs) based on a geometric transformation. The key ideas are:\n\n\n\n\n1-Local geodesic approximation – On a short interval [t1,t2] the solution is approximated by a geodesic in a non‑Euclidean metric space. This geodesic depends on a single free parameter: the value y2=y(t2).\n\n\n\n\n2-Calibration – For a given y2,the geodesic provides the midpoint\n\n\n\n\n(tm,ym). We then compute the derivative from the geodesic:\n\n\n\n\n                       ym′ = (ym−y1)/(tm-t1)\n\n\n\n\n\n​\n\n\n\n\nand evaluate the ODE at the midpoint:\n\n\n\n\nfm =f(tm,ym).\nThe residual is\nR(y2 )=∣ ym′−fm ∣.\n\n\n\n\n3-Adjustment – Because the interval is short,\n\n\n\n\nR is nearly linear in y2 . A few secant iterations (or a simple manual search) suffice to make R negligible.\n\n\n\n\n4-Systems – For a system of ODEs we select one component (e.g.y2) as the only free parameter. The geodesic gives (tm,ym). The other components at the midpoint, as well as their derivatives, are then deduced from the equations and the initial conditions. The residual is built on the remaining equations.\n\n\n\n\n5-Long intervals – The total time interval is split into short segments where the curvature remains small. Each segment is treated independently using the same single‑parameter calibration.\n\n\n\n\n6-Spectral pre‑processing – A coarse scan of the ODE’s right‑hand side estimates the local curvature and detects stiff regions or fast oscillations. This helps choose an optimal segmentation without trial and error.\n\n\n\n\nWhy this method differs from classical ones:\n\n\n\n\nNo implicit solver, no Jacobian.\n\n\n\n\nStability is controlled by curvature, not by a CFL condition.\n\n\n\n\nOnly one scalar parameter is adjusted per segment, regardless of the system size.\n\n\n\n\nBenchmarks (performed in double precision, reference: Radau with tolerance 1e-12):\n\n\n\n\nProthero–Robinson\n\n\n\n\ny′ =−1000y+1000sint+cost with  y(0.1)=sin(0.1)\n\nResult: y(0.101)≈0.10083089255\n\nError:   1e-6\n\n\n\n\nVan der Pol,\n\n\n\n\nε=1000, 8 segments from\n\nResult: y(0.248583)≈0.2477211\n\nError: 0.7% (finner subdivision gives 1e-7)\n\n\n\n\nLorenz system (single\nshort segment)\n\n\n\n\nResult: error on all variables\n\nError≈1e-7\n\n\n\n\nBrusselator (single segment)\n\n\n\n\nResult:  residual on second equation\n\nerror:  <1e-7\n\n\n\n\nQuestions to the community:\n\n\n\n\nAre there other stiff or multi‑scale benchmarks that you would recommend to test this approach further?\n\n\n\n\nHas a similar curvature‑based step control been studied elsewhere?\n\n\n\n\nWhat theoretical tools could help analyse the stability of such a method?","retrieval_challenge":"Metadata-grounded challenge flags; semantic conflict and scientific correctness are not asserted","scores":[{"answer_id":45429,"score":3}],"split":"validation"}