| {"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."} | |