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S1.jsonl

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+{"record_kind": "run_header", "run_id": "pearl-manuscript-s1-20260916", "seq": 1, "trace_sequence": 1, "timestamp": "2026-09-16T10:24:12+00:00", "logged_at": "2026-09-16T10:24:12.350000+00:00", "source_agent": null, "scenario_id": "S1", "provenance": "manuscript-aligned-case-log-v1", "not_wet_lab": false, "world_contract": "manuscript-case-S1", "config": {"communication_mode": "typed_events", "ir_schema_version": 4}, "user_command": "Create a rainbow in the well-plate.", "sources": [{"well": "A1", "label": "Colored dye", "volume_ul": 15000}, {"well": "A2", "label": "Colored dye", "volume_ul": 15000}, {"well": "A3", "label": "Colored dye", "volume_ul": 15000}, {"well": "A4", "label": "Colored dye", "volume_ul": 15000}, {"well": "A5", "label": "Water", "volume_ul": 15000}], "constraints": ["The instruction names neither target colours, well assignments, dye identities, nor a mixing procedure.", "The reservoir holds colored dyes and water."]}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 2, "trace_sequence": 2, "timestamp": "2026-09-16T10:24:24+00:00", "logged_at": "2026-09-16T10:24:24.350000+00:00", "source_agent": null, "event_id": "obs-s1-sources", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s1-sources", "wells": {"reservoir:A1": {"hex": "#E10600"}, "reservoir:A2": {"hex": "#2E8B3A"}, "reservoir:A3": {"hex": "#1E4FD6"}, "reservoir:A4": {"hex": "#FFD400"}, "reservoir:A5": {"hex": "#F4F7F8"}}, "note": "Camera read of the reservoir. The instruction did not name these colours."}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 3, "trace_sequence": 3, "timestamp": "2026-09-16T10:24:36+00:00", "logged_at": "2026-09-16T10:24:36.350000+00:00", "source_agent": "planner", "event_id": "msg-0003", "event_type": "ir_proposed", "rationale": "The instruction is only to make a rainbow. I will choose seven wells, B1 through B7, and build red, orange, yellow, green, blue, indigo, and violet from the colours I just saw.", "message": "The instruction is only to make a rainbow. I will choose seven wells, B1 through B7, and build red, orange, yellow, green, blue, indigo, and violet from the colours I just saw."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 4, "trace_sequence": 4, "timestamp": "2026-09-16T10:24:48+00:00", "logged_at": "2026-09-16T10:24:48.350000+00:00", "source_agent": "planner", "event_id": "plan-plan-s1", "event_type": "plan", "plan_id": "plan-s1", "revision_id": "rev_0", "rationale": "Place a rainbow in B1-B7. Those wells are my choice, not part of the instruction.", "canonical_operations": [{"action_id": "s1-b1", "tool_name": "transfer", "source": "reservoir:A1", "dest": "plate:B1", "volume_ul": 80}, {"action_id": "s1-b2r", "tool_name": "transfer", "source": "reservoir:A1", "dest": "plate:B2", "volume_ul": 40}, {"action_id": "s1-b2y", "tool_name": "transfer", "source": "reservoir:A4", "dest": "plate:B2", "volume_ul": 40}, {"action_id": "s1-b3", "tool_name": "transfer", "source": "reservoir:A4", "dest": "plate:B3", "volume_ul": 80}, {"action_id": "s1-b4", "tool_name": "transfer", "source": "reservoir:A2", "dest": "plate:B4", "volume_ul": 80}, {"action_id": "s1-b5", "tool_name": "transfer", "source": "reservoir:A3", "dest": "plate:B5", "volume_ul": 80}, {"action_id": "s1-b6b", "tool_name": "transfer", "source": "reservoir:A3", "dest": "plate:B6", "volume_ul": 50}, {"action_id": "s1-b6r", "tool_name": "transfer", "source": "reservoir:A1", "dest": "plate:B6", "volume_ul": 30}, {"action_id": "s1-b7b", "tool_name": "transfer", "source": "reservoir:A3", "dest": "plate:B7", "volume_ul": 40}, {"action_id": "s1-b7r", "tool_name": "transfer", "source": "reservoir:A1", "dest": "plate:B7", "volume_ul": 40}]}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 5, "trace_sequence": 5, "timestamp": "2026-09-16T10:25:00+00:00", "logged_at": "2026-09-16T10:25:00.350000+00:00", "source_agent": null, "event_id": "appr-appr-s1", "event_type": "proceed_signal", "plan_id": "plan-s1", "revision_id": "rev_0", "approval_id": "appr-s1", "approved_action_ids": ["s1-b1", "s1-b2r", "s1-b2y", "s1-b3", "s1-b4", "s1-b5", "s1-b6b", "s1-b6r", "s1-b7b", "s1-b7r"], "message": "Approved against the public deck and the stated instruction."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 6, "trace_sequence": 6, "timestamp": "2026-09-16T10:25:12+00:00", "logged_at": "2026-09-16T10:25:12.350000+00:00", "source_agent": "actor", "event_id": "act-s1-b1", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "s1-b1", "plan_id": "plan-s1", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s1-b1", "action_params": {"source": "A1", "dest": "B1", "volume_ul": 80}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B1"}}, "result_observation_ids": ["obs-s1-b1"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 7, "trace_sequence": 7, "timestamp": "2026-09-16T10:25:24+00:00", "logged_at": "2026-09-16T10:25:24.350000+00:00", "source_agent": "actor", "event_id": "act-s1-b2r", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "s1-b2r", "plan_id": "plan-s1", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s1-b2r", "action_params": {"source": "A1", "dest": "B2", "volume_ul": 40}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B2"}}, "result_observation_ids": ["obs-s1-b2r"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 8, "trace_sequence": 8, "timestamp": "2026-09-16T10:25:36+00:00", "logged_at": "2026-09-16T10:25:36.350000+00:00", "source_agent": "actor", "event_id": "act-s1-b2y", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "s1-b2y", "plan_id": "plan-s1", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s1-b2y", "action_params": {"source": "A4", "dest": "B2", "volume_ul": 40}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B2"}}, "result_observation_ids": ["obs-s1-b2y"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 9, "trace_sequence": 9, "timestamp": "2026-09-16T10:25:48+00:00", "logged_at": "2026-09-16T10:25:48.350000+00:00", "source_agent": "actor", "event_id": "act-s1-b3", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "s1-b3", "plan_id": "plan-s1", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s1-b3", "action_params": {"source": "A4", "dest": "B3", "volume_ul": 80}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B3"}}, "result_observation_ids": ["obs-s1-b3"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 10, "trace_sequence": 10, "timestamp": "2026-09-16T10:26:00+00:00", "logged_at": "2026-09-16T10:26:00.350000+00:00", "source_agent": "actor", "event_id": "act-s1-b4", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "s1-b4", "plan_id": "plan-s1", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s1-b4", "action_params": {"source": "A2", "dest": "B4", "volume_ul": 80}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B4"}}, "result_observation_ids": ["obs-s1-b4"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 11, "trace_sequence": 11, "timestamp": "2026-09-16T10:26:12+00:00", "logged_at": "2026-09-16T10:26:12.350000+00:00", "source_agent": "actor", "event_id": "act-s1-b5", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "s1-b5", "plan_id": "plan-s1", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s1-b5", "action_params": {"source": "A3", "dest": "B5", "volume_ul": 80}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B5"}}, "result_observation_ids": ["obs-s1-b5"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 12, "trace_sequence": 12, "timestamp": "2026-09-16T10:26:24+00:00", "logged_at": "2026-09-16T10:26:24.350000+00:00", "source_agent": "actor", "event_id": "act-s1-b6b", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "s1-b6b", "plan_id": "plan-s1", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s1-b6b", "action_params": {"source": "A3", "dest": "B6", "volume_ul": 50}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B6"}}, "result_observation_ids": ["obs-s1-b6b"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 13, "trace_sequence": 13, "timestamp": "2026-09-16T10:26:36+00:00", "logged_at": "2026-09-16T10:26:36.350000+00:00", "source_agent": "actor", "event_id": "act-s1-b6r", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "s1-b6r", "plan_id": "plan-s1", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s1-b6r", "action_params": {"source": "A1", "dest": "B6", "volume_ul": 30}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B6"}}, "result_observation_ids": ["obs-s1-b6r"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 14, "trace_sequence": 14, "timestamp": "2026-09-16T10:26:48+00:00", "logged_at": "2026-09-16T10:26:48.350000+00:00", "source_agent": "actor", "event_id": "act-s1-b7b", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "s1-b7b", "plan_id": "plan-s1", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s1-b7b", "action_params": {"source": "A3", "dest": "B7", "volume_ul": 40}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B7"}}, "result_observation_ids": ["obs-s1-b7b"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 15, "trace_sequence": 15, "timestamp": "2026-09-16T10:27:00+00:00", "logged_at": "2026-09-16T10:27:00.350000+00:00", "source_agent": "actor", "event_id": "act-s1-b7r", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "s1-b7r", "plan_id": "plan-s1", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s1-b7r", "action_params": {"source": "A1", "dest": "B7", "volume_ul": 40}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B7"}}, "result_observation_ids": ["obs-s1-b7r"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 16, "trace_sequence": 16, "timestamp": "2026-09-16T10:27:12+00:00", "logged_at": "2026-09-16T10:27:12.350000+00:00", "source_agent": null, "event_id": "appr-appr-s1-mix-b2", "event_type": "proceed_signal", "plan_id": "plan-s1", "revision_id": "rev_0", "approval_id": "appr-s1-mix-b2", "approved_action_ids": ["s1-mix-b2"], "message": "Approved against the public deck and the stated instruction."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 17, "trace_sequence": 17, "timestamp": "2026-09-16T10:27:24+00:00", "logged_at": "2026-09-16T10:27:24.350000+00:00", "source_agent": "actor", "event_id": "act-s1-mix-b2", "event_type": "tool_call", "tool_name": "mix_well", "tool_call_id": "s1-mix-b2", "plan_id": "plan-s1", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s1-mix-b2", "action_params": {"well": "B2"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B2"}}, "result_observation_ids": ["obs-s1-mix-b2"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 18, "trace_sequence": 18, "timestamp": "2026-09-16T10:27:36+00:00", "logged_at": "2026-09-16T10:27:36.350000+00:00", "source_agent": null, "event_id": "appr-appr-s1-mix-b6", "event_type": "proceed_signal", "plan_id": "plan-s1", "revision_id": "rev_0", "approval_id": "appr-s1-mix-b6", "approved_action_ids": ["s1-mix-b6"], "message": "Approved against the public deck and the stated instruction."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 19, "trace_sequence": 19, "timestamp": "2026-09-16T10:27:48+00:00", "logged_at": "2026-09-16T10:27:48.350000+00:00", "source_agent": "actor", "event_id": "act-s1-mix-b6", "event_type": "tool_call", "tool_name": "mix_well", "tool_call_id": "s1-mix-b6", "plan_id": "plan-s1", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s1-mix-b6", "action_params": {"well": "B6"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B6"}}, "result_observation_ids": ["obs-s1-mix-b6"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 20, "trace_sequence": 20, "timestamp": "2026-09-16T10:28:00+00:00", "logged_at": "2026-09-16T10:28:00.350000+00:00", "source_agent": null, "event_id": "appr-appr-s1-mix-b7", "event_type": "proceed_signal", "plan_id": "plan-s1", "revision_id": "rev_0", "approval_id": "appr-s1-mix-b7", "approved_action_ids": ["s1-mix-b7"], "message": "Approved against the public deck and the stated instruction."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 21, "trace_sequence": 21, "timestamp": "2026-09-16T10:28:12+00:00", "logged_at": "2026-09-16T10:28:12.350000+00:00", "source_agent": "actor", "event_id": "act-s1-mix-b7", "event_type": "tool_call", "tool_name": "mix_well", "tool_call_id": "s1-mix-b7", "plan_id": "plan-s1", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s1-mix-b7", "action_params": {"well": "B7"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B7"}}, "result_observation_ids": ["obs-s1-mix-b7"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 22, "trace_sequence": 22, "timestamp": "2026-09-16T10:28:24+00:00", "logged_at": "2026-09-16T10:28:24.350000+00:00", "source_agent": null, "event_id": "obs-s1-final", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s1-final", "wells": {"plate:B1": {"hex": "#E10600"}, "plate:B2": {"hex": "#FF8C00"}, "plate:B3": {"hex": "#FFD400"}, "plate:B4": {"hex": "#2E8B3A"}, "plate:B5": {"hex": "#1E4FD6"}, "plate:B6": {"hex": "#3F2A8C"}, "plate:B7": {"hex": "#7B2CBF"}}, "note": "Seven wells show a rainbow. Well choice and colour order came from the camera reads."}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 23, "trace_sequence": 23, "timestamp": "2026-09-16T10:28:36+00:00", "logged_at": "2026-09-16T10:28:36.350000+00:00", "source_agent": "planner", "event_id": "msg-0023", "event_type": "recovery_decision", "rationale": "B1 through B7 now show a rainbow. I stop here.", "message": "B1 through B7 now show a rainbow. I stop here."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s1-20260916", "seq": 24, "trace_sequence": 24, "timestamp": "2026-09-16T10:28:48+00:00", "logged_at": "2026-09-16T10:28:48.350000+00:00", "source_agent": "planner", "event_id": "done-S1", "event_type": "completion_decision", "plan_id": "plan-s1", "revision_id": "rev_0", "adopted": {"summary": "Rainbow in B1-B7, wells chosen after the camera read.", "wells": ["B1", "B2", "B3", "B4", "B5", "B6", "B7"]}, "discarded": [], "message": "Rainbow in B1-B7, wells chosen after the camera read."}
+{"record_kind": "trial", "run_id": "pearl-manuscript-s1-20260916", "seq": 25, "trace_sequence": 25, "timestamp": "2026-09-16T10:29:00+00:00", "logged_at": "2026-09-16T10:29:00.350000+00:00", "source_agent": null, "scenario_id": "S1", "termination": "completed", "not_wet_lab": false, "adopted": {"summary": "Rainbow in B1-B7, wells chosen after the camera read.", "wells": ["B1", "B2", "B3", "B4", "B5", "B6", "B7"]}, "discarded": [], "commentary": "The instruction was only to create a rainbow. Dye identities and the destination wells were not in that instruction."}

S2.jsonl

@@ -0,0 +1,11 @@
+{"record_kind": "run_header", "run_id": "pearl-manuscript-s2-20260916", "seq": 1, "trace_sequence": 1, "timestamp": "2026-09-16T10:24:12+00:00", "logged_at": "2026-09-16T10:24:12.350000+00:00", "source_agent": null, "scenario_id": "S2", "provenance": "manuscript-aligned-case-log-v1", "not_wet_lab": false, "world_contract": "manuscript-case-S2", "config": {"communication_mode": "typed_events", "ir_schema_version": 4}, "user_command": "Make purple using only red and green.", "sources": [{"well": "A1", "label": "Dye 1", "volume_ul": 15000}, {"well": "A2", "label": "Dye 2", "volume_ul": 15000}, {"well": "A3", "label": "Dye 3", "volume_ul": 15000}, {"well": "A4", "label": "Dye 4", "volume_ul": 15000}, {"well": "A5", "label": "Water", "volume_ul": 15000}], "constraints": ["Use only the liquids the instruction allows.", "No mixing procedure is prescribed."]}
+{"record_kind": "event", "run_id": "pearl-manuscript-s2-20260916", "seq": 2, "trace_sequence": 2, "timestamp": "2026-09-16T10:24:24+00:00", "logged_at": "2026-09-16T10:24:24.350000+00:00", "source_agent": null, "event_id": "obs-s2-sources", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s2-sources", "wells": {"reservoir:A1": {"hex": "#E10600", "identified": "red"}, "reservoir:A2": {"hex": "#2E8B3A", "identified": "green"}, "reservoir:A3": {"hex": "#1E4FD6", "identified": "blue"}, "reservoir:A4": {"hex": "#FFD400", "identified": "yellow"}, "reservoir:A5": {"hex": "#F4F7F8", "identified": "water"}}, "note": "Camera read of Dye 1 through Dye 4 and water. The reservoir labels do not name these colours."}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s2-20260916", "seq": 3, "trace_sequence": 3, "timestamp": "2026-09-16T10:24:36+00:00", "logged_at": "2026-09-16T10:24:36.350000+00:00", "source_agent": "planner", "event_id": "msg-0003", "event_type": "ir_proposed", "rationale": "The camera reads Dye 1 as red, Dye 2 as green, Dye 3 as blue, and Dye 4 as yellow.", "message": "The camera reads Dye 1 as red, Dye 2 as green, Dye 3 as blue, and Dye 4 as yellow."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s2-20260916", "seq": 4, "trace_sequence": 4, "timestamp": "2026-09-16T10:24:48+00:00", "logged_at": "2026-09-16T10:24:48.350000+00:00", "source_agent": "knowledge", "event_id": "know-color-mix-card-v1", "event_type": "observation", "observation_type": "knowledge_response", "payload": {"source_id": "color-mix-card-v1", "text": "Purple is a red-blue mixture. Red and green do not produce purple."}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s2-20260916", "seq": 5, "trace_sequence": 5, "timestamp": "2026-09-16T10:25:00+00:00", "logged_at": "2026-09-16T10:25:00.350000+00:00", "source_agent": "planner", "event_id": "msg-0005", "event_type": "recovery_decision", "rationale": "The instruction asks for purple from only red and green. Dye 1 and Dye 2 are those two colours, and they do not make purple. The instruction does not allow Dye 3, which reads blue. I will not dispense.", "message": "The instruction asks for purple from only red and green. Dye 1 and Dye 2 are those two colours, and they do not make purple. The instruction does not allow Dye 3, which reads blue. I will not dispense."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s2-20260916", "seq": 6, "trace_sequence": 6, "timestamp": "2026-09-16T10:25:12+00:00", "logged_at": "2026-09-16T10:25:12.350000+00:00", "source_agent": "planner", "event_id": "msg-0006", "event_type": "recovery_decision", "rationale": "This instruction is not feasible. I withhold physical execution and ask for an instruction that can produce purple.", "message": "This instruction is not feasible. I withhold physical execution and ask for an instruction that can produce purple."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s2-20260916", "seq": 7, "trace_sequence": 7, "timestamp": "2026-09-16T10:25:24+00:00", "logged_at": "2026-09-16T10:25:24.350000+00:00", "source_agent": "planner", "event_id": "plan-plan-s2-withhold", "event_type": "plan", "plan_id": "plan-s2-withhold", "revision_id": "rev_0", "rationale": "Dispatch the next approved action.", "canonical_operations": [{"action_id": "s2-withhold", "tool_name": "refuse", "reason": "infeasible_instruction", "liquids_dispensed": false}]}
+{"record_kind": "event", "run_id": "pearl-manuscript-s2-20260916", "seq": 8, "trace_sequence": 8, "timestamp": "2026-09-16T10:25:36+00:00", "logged_at": "2026-09-16T10:25:36.350000+00:00", "source_agent": null, "event_id": "appr-appr-s2-withhold", "event_type": "proceed_signal", "plan_id": "plan-s2-withhold", "revision_id": "rev_0", "approval_id": "appr-s2-withhold", "approved_action_ids": ["s2-withhold"], "message": "Approved against the public deck and the stated instruction."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s2-20260916", "seq": 9, "trace_sequence": 9, "timestamp": "2026-09-16T10:25:48+00:00", "logged_at": "2026-09-16T10:25:48.350000+00:00", "source_agent": "actor", "event_id": "act-s2-withhold", "event_type": "tool_call", "tool_name": "refuse", "tool_call_id": "s2-withhold", "plan_id": "plan-s2-withhold", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s2-withhold", "action_params": {"reason": "infeasible_instruction", "liquids_dispensed": false}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"actions_executed": 0, "transfers": 0}}, "result_observation_ids": ["obs-s2-withhold"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s2-20260916", "seq": 10, "trace_sequence": 10, "timestamp": "2026-09-16T10:26:00+00:00", "logged_at": "2026-09-16T10:26:00.350000+00:00", "source_agent": "planner", "event_id": "done-S2", "event_type": "completion_decision", "plan_id": "plan-s2-withhold", "revision_id": "rev_0", "adopted": {"summary": "No liquid was dispensed. A feasible instruction was requested.", "actions_executed": 0, "transfers": 0}, "discarded": ["any transfer"], "message": "No liquid was dispensed. A feasible instruction was requested."}
+{"record_kind": "trial", "run_id": "pearl-manuscript-s2-20260916", "seq": 11, "trace_sequence": 11, "timestamp": "2026-09-16T10:26:12+00:00", "logged_at": "2026-09-16T10:26:12.350000+00:00", "source_agent": null, "scenario_id": "S2", "termination": "completed", "not_wet_lab": false, "adopted": {"summary": "No liquid was dispensed. A feasible instruction was requested.", "actions_executed": 0, "transfers": 0}, "discarded": ["any transfer"], "commentary": "Withhold happens before any liquid move. The camera, not the reservoir labels, identified Dye 1 as red and Dye 2 as green. The conflict is recognized from the instruction and the mix card, and it is not pre-loaded as a conflict record."}

S3.jsonl

@@ -0,0 +1,21 @@
+{"record_kind": "run_header", "run_id": "pearl-manuscript-s3-20260916", "seq": 1, "trace_sequence": 1, "timestamp": "2026-09-16T10:24:12+00:00", "logged_at": "2026-09-16T10:24:12.350000+00:00", "source_agent": null, "scenario_id": "S3", "provenance": "manuscript-aligned-case-log-v1", "not_wet_lab": false, "world_contract": "manuscript-case-S3", "config": {"communication_mode": "typed_events", "ir_schema_version": 4}, "user_command": "Make purple.", "sources": [{"well": "A1", "label": "Dye 1", "volume_ul": 15000}, {"well": "A2", "label": "Dye 2", "volume_ul": 15000}, {"well": "A3", "label": "Dye 3", "volume_ul": 15000}, {"well": "A4", "label": "Dye 4", "volume_ul": 15000}, {"well": "A5", "label": "Water", "volume_ul": 15000}], "constraints": ["96-well plate.", "The instruction does not mention a rotation."]}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 2, "trace_sequence": 2, "timestamp": "2026-09-16T10:24:24+00:00", "logged_at": "2026-09-16T10:24:24.350000+00:00", "source_agent": null, "event_id": "obs-s3-dyes", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s3-dyes", "wells": {"reservoir:A1": {"hex": "#E10600", "identified": "red"}, "reservoir:A2": {"hex": "#2E8B3A", "identified": "green"}, "reservoir:A3": {"hex": "#1E4FD6", "identified": "blue"}, "reservoir:A4": {"hex": "#FFD400", "identified": "yellow"}, "reservoir:A5": {"hex": "#F4F7F8", "identified": "water"}}, "note": "Camera read of Dye 1 through Dye 4. The labels do not name the colours."}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 3, "trace_sequence": 3, "timestamp": "2026-09-16T10:24:36+00:00", "logged_at": "2026-09-16T10:24:36.350000+00:00", "source_agent": "planner", "event_id": "msg-0003", "event_type": "ir_proposed", "rationale": "Dye 1 reads red and Dye 3 reads blue. Purple is a red-blue mixture. I will dispense Dye 1 into A1, then add Dye 3 to the same well.", "message": "Dye 1 reads red and Dye 3 reads blue. Purple is a red-blue mixture. I will dispense Dye 1 into A1, then add Dye 3 to the same well."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 4, "trace_sequence": 4, "timestamp": "2026-09-16T10:24:48+00:00", "logged_at": "2026-09-16T10:24:48.350000+00:00", "source_agent": null, "event_id": "obs-s3-before", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s3-before", "wells": {"plate:A1": {"empty": true}, "plate:H12": {"empty": true}}, "note": "A1 and H12 are empty before the first transfer."}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 5, "trace_sequence": 5, "timestamp": "2026-09-16T10:25:00+00:00", "logged_at": "2026-09-16T10:25:00.350000+00:00", "source_agent": "planner", "event_id": "plan-plan-s3-red", "event_type": "plan", "plan_id": "plan-s3-red", "revision_id": "rev_0", "rationale": "Dispense the red the camera found in Dye 1 into A1, then add the blue found in Dye 3.", "canonical_operations": [{"action_id": "s3-red", "tool_name": "transfer", "source": "reservoir:A1", "dest": "plate:A1", "volume_ul": 40}]}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 6, "trace_sequence": 6, "timestamp": "2026-09-16T10:25:12+00:00", "logged_at": "2026-09-16T10:25:12.350000+00:00", "source_agent": null, "event_id": "appr-appr-s3-red", "event_type": "proceed_signal", "plan_id": "plan-s3-red", "revision_id": "rev_0", "approval_id": "appr-s3-red", "approved_action_ids": ["s3-red"], "message": "Approved against the public deck and the stated instruction."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 7, "trace_sequence": 7, "timestamp": "2026-09-16T10:25:24+00:00", "logged_at": "2026-09-16T10:25:24.350000+00:00", "source_agent": "actor", "event_id": "act-s3-red", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "s3-red", "plan_id": "plan-s3-red", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s3-red", "action_params": {"source": "A1", "dest": "A1", "volume_ul": 40, "substance": "red"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"commanded_well": "A1", "substance": "red"}}, "result_observation_ids": ["obs-s3-red"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 8, "trace_sequence": 8, "timestamp": "2026-09-16T10:25:36+00:00", "logged_at": "2026-09-16T10:25:36.350000+00:00", "source_agent": "human", "event_id": "s3-rotate", "event_type": "external_perturbation", "message": "A person rotated the plate 180 degrees. The rotation was not announced.", "rationale": "A person rotated the plate 180 degrees. The rotation was not announced.", "payload": {"rotation_deg": 180, "announced": false, "liquid_moved": {"from": "plate:A1", "to": "plate:H12", "substance": "red"}}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 9, "trace_sequence": 9, "timestamp": "2026-09-16T10:25:48+00:00", "logged_at": "2026-09-16T10:25:48.350000+00:00", "source_agent": "planner", "event_id": "msg-0009", "event_type": "ir_proposed", "rationale": "I continue the purple mix and dispense blue into A1.", "message": "I continue the purple mix and dispense blue into A1."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 10, "trace_sequence": 10, "timestamp": "2026-09-16T10:26:00+00:00", "logged_at": "2026-09-16T10:26:00.350000+00:00", "source_agent": null, "event_id": "appr-appr-s3-blue-a1", "event_type": "proceed_signal", "plan_id": "plan-s3-red", "revision_id": "rev_0", "approval_id": "appr-s3-blue-a1", "approved_action_ids": ["s3-blue-a1"], "message": "Approved against the public deck and the stated instruction."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 11, "trace_sequence": 11, "timestamp": "2026-09-16T10:26:12+00:00", "logged_at": "2026-09-16T10:26:12.350000+00:00", "source_agent": "actor", "event_id": "act-s3-blue-a1", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "s3-blue-a1", "plan_id": "plan-s3-red", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s3-blue-a1", "action_params": {"source": "A3", "dest": "A1", "volume_ul": 40, "substance": "blue"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"commanded_well": "A1", "substance": "blue"}}, "result_observation_ids": ["obs-s3-blue-a1"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 12, "trace_sequence": 12, "timestamp": "2026-09-16T10:26:24+00:00", "logged_at": "2026-09-16T10:26:24.350000+00:00", "source_agent": null, "event_id": "obs-s3-separated", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s3-separated", "wells": {"plate:A1": {"hex": "#1E4FD6", "substance_seen": "blue", "empty": false}, "plate:H12": {"hex": "#E10600", "substance_seen": "red", "empty": false}}, "note": "A1 holds blue and is not mixed. The red aliquot is at H12. The two colours are separated."}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 13, "trace_sequence": 13, "timestamp": "2026-09-16T10:26:36+00:00", "logged_at": "2026-09-16T10:26:36.350000+00:00", "source_agent": "planner", "event_id": "msg-0013", "event_type": "recovery_decision", "rationale": "A 180-degree rotation maps A1 to H12. The red I dispensed is the liquid now at H12. I update the well mapping and add blue there.", "message": "A 180-degree rotation maps A1 to H12. The red I dispensed is the liquid now at H12. I update the well mapping and add blue there."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 14, "trace_sequence": 14, "timestamp": "2026-09-16T10:26:48+00:00", "logged_at": "2026-09-16T10:26:48.350000+00:00", "source_agent": "planner", "event_id": "plan-plan-s3-h12", "event_type": "plan", "plan_id": "plan-s3-h12", "revision_id": "rev_0", "rationale": "Add blue to the displaced red well at H12.", "canonical_operations": [{"action_id": "s3-blue-h12", "tool_name": "transfer", "source": "reservoir:A3", "dest": "plate:H12", "volume_ul": 40}]}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 15, "trace_sequence": 15, "timestamp": "2026-09-16T10:27:00+00:00", "logged_at": "2026-09-16T10:27:00.350000+00:00", "source_agent": null, "event_id": "appr-appr-s3-h12", "event_type": "proceed_signal", "plan_id": "plan-s3-h12", "revision_id": "rev_0", "approval_id": "appr-s3-h12", "approved_action_ids": ["s3-blue-h12"], "message": "Approved against the public deck and the stated instruction."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 16, "trace_sequence": 16, "timestamp": "2026-09-16T10:27:12+00:00", "logged_at": "2026-09-16T10:27:12.350000+00:00", "source_agent": "actor", "event_id": "act-s3-blue-h12", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "s3-blue-h12", "plan_id": "plan-s3-h12", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s3-blue-h12", "action_params": {"source": "A3", "dest": "H12", "volume_ul": 40, "substance": "blue"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:H12"}}, "result_observation_ids": ["obs-s3-blue-h12"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 17, "trace_sequence": 17, "timestamp": "2026-09-16T10:27:24+00:00", "logged_at": "2026-09-16T10:27:24.350000+00:00", "source_agent": null, "event_id": "appr-appr-s3-mix-h12", "event_type": "proceed_signal", "plan_id": "plan-s3-h12", "revision_id": "rev_0", "approval_id": "appr-s3-mix-h12", "approved_action_ids": ["s3-mix-h12"], "message": "Approved against the public deck and the stated instruction."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 18, "trace_sequence": 18, "timestamp": "2026-09-16T10:27:36+00:00", "logged_at": "2026-09-16T10:27:36.350000+00:00", "source_agent": "actor", "event_id": "act-s3-mix-h12", "event_type": "tool_call", "tool_name": "mix_well", "tool_call_id": "s3-mix-h12", "plan_id": "plan-s3-h12", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s3-mix-h12", "action_params": {"well": "H12"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:H12"}}, "result_observation_ids": ["obs-s3-mix-h12"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 19, "trace_sequence": 19, "timestamp": "2026-09-16T10:27:48+00:00", "logged_at": "2026-09-16T10:27:48.350000+00:00", "source_agent": null, "event_id": "obs-s3-final", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s3-final", "wells": {"plate:H12": {"hex": "#7B2CBF", "colour": "purple"}}, "note": "Purple is confirmed at H12."}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s3-20260916", "seq": 20, "trace_sequence": 20, "timestamp": "2026-09-16T10:28:00+00:00", "logged_at": "2026-09-16T10:28:00.350000+00:00", "source_agent": "planner", "event_id": "done-S3", "event_type": "completion_decision", "plan_id": "plan-s3-h12", "revision_id": "rev_0", "adopted": {"summary": "Purple confirmed at H12 after the 180-degree remap.", "physical_well": "H12", "colour": "purple"}, "discarded": ["leave the separated blue at A1 as the product"], "message": "Purple confirmed at H12 after the 180-degree remap."}
+{"record_kind": "trial", "run_id": "pearl-manuscript-s3-20260916", "seq": 21, "trace_sequence": 21, "timestamp": "2026-09-16T10:28:12+00:00", "logged_at": "2026-09-16T10:28:12.350000+00:00", "source_agent": null, "scenario_id": "S3", "termination": "completed", "not_wet_lab": false, "adopted": {"summary": "Purple confirmed at H12 after the 180-degree remap.", "physical_well": "H12", "colour": "purple"}, "discarded": ["leave the separated blue at A1 as the product"], "commentary": "Red was dispensed at A1, the plate was rotated, blue landed in the empty A1, and the remap put blue into the red well at H12."}

S4.jsonl

@@ -0,0 +1,17 @@
+{"record_kind": "run_header", "run_id": "pearl-manuscript-s4-20260916", "seq": 1, "trace_sequence": 1, "timestamp": "2026-09-16T10:24:12+00:00", "logged_at": "2026-09-16T10:24:12.350000+00:00", "source_agent": null, "scenario_id": "S4", "provenance": "manuscript-aligned-case-log-v1", "not_wet_lab": false, "world_contract": "manuscript-case-S4", "config": {"communication_mode": "typed_events", "ir_schema_version": 4}, "user_command": "Make a bright orange.", "sources": [{"well": "A1", "label": "Colored dye", "volume_ul": 10000}, {"well": "A2", "label": "Colored dye", "volume_ul": 10000}, {"well": "A3", "label": "Colored dye", "volume_ul": 10000}, {"well": "A4", "label": "Colored dye", "volume_ul": 10000}, {"well": "A5", "label": "Water", "volume_ul": 10000}], "constraints": ["Source labels do not name a colour.", "No dilution factor is given in the instruction."]}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 2, "trace_sequence": 2, "timestamp": "2026-09-16T10:24:24+00:00", "logged_at": "2026-09-16T10:24:24.350000+00:00", "source_agent": "human", "event_id": "s4-stocks", "event_type": "external_perturbation", "message": "The dye reservoirs were prepared before the run. Water was left as declared.", "rationale": "The dye reservoirs were prepared before the run. Water was left as declared.", "payload": {"dye_wells": ["A1", "A2", "A3", "A4"], "relative_concentration_vs_nominal": 5, "water_unchanged": true, "disclosed_to_agents": false}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 3, "trace_sequence": 3, "timestamp": "2026-09-16T10:24:36+00:00", "logged_at": "2026-09-16T10:24:36.350000+00:00", "source_agent": null, "event_id": "obs-s4-dark", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s4-dark", "wells": {"reservoir:A1": {"hex": "#140000", "appearance": "nearly black"}, "reservoir:A2": {"hex": "#001408", "appearance": "nearly black"}, "reservoir:A3": {"hex": "#000814", "appearance": "nearly black"}, "reservoir:A4": {"hex": "#141000", "appearance": "nearly black"}}, "note": "Neat stocks are too dark to identify."}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 4, "trace_sequence": 4, "timestamp": "2026-09-16T10:24:48+00:00", "logged_at": "2026-09-16T10:24:48.350000+00:00", "source_agent": "planner", "event_id": "msg-0004", "event_type": "ir_proposed", "rationale": "I cannot tell these colours neat. I will dilute each source and read the aliquot before I mix a product.", "message": "I cannot tell these colours neat. I will dilute each source and read the aliquot before I mix a product."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 5, "trace_sequence": 5, "timestamp": "2026-09-16T10:25:00+00:00", "logged_at": "2026-09-16T10:25:00.350000+00:00", "source_agent": "planner", "event_id": "plan-plan-s4-id", "event_type": "plan", "plan_id": "plan-s4-id", "revision_id": "rev_0", "rationale": "Dilute each original dye so its colour can be read.", "canonical_operations": [{"action_id": "s4-dilute-a1", "tool_name": "dilute", "source": "reservoir:A1", "dest": "plate:C1", "stock_ul": 20, "water_ul": 80}, {"action_id": "s4-dilute-a2", "tool_name": "dilute", "source": "reservoir:A2", "dest": "plate:C2", "stock_ul": 20, "water_ul": 80}, {"action_id": "s4-dilute-a3", "tool_name": "dilute", "source": "reservoir:A3", "dest": "plate:C3", "stock_ul": 20, "water_ul": 80}, {"action_id": "s4-dilute-a4", "tool_name": "dilute", "source": "reservoir:A4", "dest": "plate:C4", "stock_ul": 20, "water_ul": 80}]}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 6, "trace_sequence": 6, "timestamp": "2026-09-16T10:25:12+00:00", "logged_at": "2026-09-16T10:25:12.350000+00:00", "source_agent": null, "event_id": "appr-appr-s4-id", "event_type": "proceed_signal", "plan_id": "plan-s4-id", "revision_id": "rev_0", "approval_id": "appr-s4-id", "approved_action_ids": ["s4-dilute-a1", "s4-dilute-a2", "s4-dilute-a3", "s4-dilute-a4"], "message": "Approved against the public deck and the stated instruction."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 7, "trace_sequence": 7, "timestamp": "2026-09-16T10:25:24+00:00", "logged_at": "2026-09-16T10:25:24.350000+00:00", "source_agent": "actor", "event_id": "act-s4-dilute-a1", "event_type": "tool_call", "tool_name": "dilute", "tool_call_id": "s4-dilute-a1", "plan_id": "plan-s4-id", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s4-dilute-a1", "action_params": {"source": "A1", "dest": "C1", "stock_ul": 20, "water_ul": 80}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:C1"}}, "result_observation_ids": ["obs-s4-dilute-a1"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 8, "trace_sequence": 8, "timestamp": "2026-09-16T10:25:36+00:00", "logged_at": "2026-09-16T10:25:36.350000+00:00", "source_agent": "actor", "event_id": "act-s4-dilute-a2", "event_type": "tool_call", "tool_name": "dilute", "tool_call_id": "s4-dilute-a2", "plan_id": "plan-s4-id", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s4-dilute-a2", "action_params": {"source": "A2", "dest": "C2", "stock_ul": 20, "water_ul": 80}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:C2"}}, "result_observation_ids": ["obs-s4-dilute-a2"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 9, "trace_sequence": 9, "timestamp": "2026-09-16T10:25:48+00:00", "logged_at": "2026-09-16T10:25:48.350000+00:00", "source_agent": "actor", "event_id": "act-s4-dilute-a3", "event_type": "tool_call", "tool_name": "dilute", "tool_call_id": "s4-dilute-a3", "plan_id": "plan-s4-id", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s4-dilute-a3", "action_params": {"source": "A3", "dest": "C3", "stock_ul": 20, "water_ul": 80}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:C3"}}, "result_observation_ids": ["obs-s4-dilute-a3"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 10, "trace_sequence": 10, "timestamp": "2026-09-16T10:26:00+00:00", "logged_at": "2026-09-16T10:26:00.350000+00:00", "source_agent": "actor", "event_id": "act-s4-dilute-a4", "event_type": "tool_call", "tool_name": "dilute", "tool_call_id": "s4-dilute-a4", "plan_id": "plan-s4-id", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s4-dilute-a4", "action_params": {"source": "A4", "dest": "C4", "stock_ul": 20, "water_ul": 80}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:C4"}}, "result_observation_ids": ["obs-s4-dilute-a4"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 11, "trace_sequence": 11, "timestamp": "2026-09-16T10:26:12+00:00", "logged_at": "2026-09-16T10:26:12.350000+00:00", "source_agent": null, "event_id": "obs-s4-identified", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s4-identified", "wells": {"plate:C1": {"hex": "#E10600", "identified": "red"}, "plate:C2": {"hex": "#2E8B3A", "identified": "green"}, "plate:C3": {"hex": "#1E4FD6", "identified": "blue"}, "plate:C4": {"hex": "#FFD400", "identified": "yellow"}}, "note": "The diluted aliquots are red, green, blue, and yellow. Identity comes from these reads."}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 12, "trace_sequence": 12, "timestamp": "2026-09-16T10:26:24+00:00", "logged_at": "2026-09-16T10:26:24.350000+00:00", "source_agent": "planner", "event_id": "msg-0012", "event_type": "recovery_decision", "rationale": "Bright orange needs the red and yellow aliquots, with water. I will not dispense the neat stocks.", "message": "Bright orange needs the red and yellow aliquots, with water. I will not dispense the neat stocks."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 13, "trace_sequence": 13, "timestamp": "2026-09-16T10:26:36+00:00", "logged_at": "2026-09-16T10:26:36.350000+00:00", "source_agent": null, "event_id": "appr-appr-s4-orange", "event_type": "proceed_signal", "plan_id": "plan-s4-id", "revision_id": "rev_0", "approval_id": "appr-s4-orange", "approved_action_ids": ["s4-orange"], "message": "Approved against the public deck and the stated instruction."}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 14, "trace_sequence": 14, "timestamp": "2026-09-16T10:26:48+00:00", "logged_at": "2026-09-16T10:26:48.350000+00:00", "source_agent": "actor", "event_id": "act-s4-orange", "event_type": "tool_call", "tool_name": "mix_well", "tool_call_id": "s4-orange", "plan_id": "plan-s4-id", "revision_id": "rev_0", "executed": true, "params": {"action_id": "s4-orange", "action_params": {"dest": "B1", "red_well": "C1", "red_ul": 15, "yellow_well": "C4", "yellow_ul": 15, "water_ul": 50}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B1", "hex": "#FF8C00"}}, "result_observation_ids": ["obs-s4-orange"], "state_delta": {"execution_disposition": "dispatched"}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 15, "trace_sequence": 15, "timestamp": "2026-09-16T10:27:00+00:00", "logged_at": "2026-09-16T10:27:00.350000+00:00", "source_agent": null, "event_id": "obs-s4-final", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s4-final", "wells": {"plate:B1": {"hex": "#FF8C00", "colour": "bright orange"}}, "note": "Bright orange after the identity dilutions."}}
+{"record_kind": "event", "run_id": "pearl-manuscript-s4-20260916", "seq": 16, "trace_sequence": 16, "timestamp": "2026-09-16T10:27:12+00:00", "logged_at": "2026-09-16T10:27:12.350000+00:00", "source_agent": "planner", "event_id": "done-S4", "event_type": "completion_decision", "plan_id": "plan-s4-id", "revision_id": "rev_0", "adopted": {"summary": "Bright orange from red and yellow identified by diluting the original dyes.", "product_well": "B1", "identified": {"C1": "red", "C4": "yellow"}}, "discarded": ["mix the neat stocks before identifying them"], "message": "Bright orange from red and yellow identified by diluting the original dyes."}
+{"record_kind": "trial", "run_id": "pearl-manuscript-s4-20260916", "seq": 17, "trace_sequence": 17, "timestamp": "2026-09-16T10:27:24+00:00", "logged_at": "2026-09-16T10:27:24.350000+00:00", "source_agent": null, "scenario_id": "S4", "termination": "completed", "not_wet_lab": false, "adopted": {"summary": "Bright orange from red and yellow identified by diluting the original dyes.", "product_well": "B1", "identified": {"C1": "red", "C4": "yellow"}}, "discarded": ["mix the neat stocks before identifying them"], "commentary": "Each source was diluted and read before the orange mix. The labels did not provide the colour names."}