{"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."}