{"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."}