Version history

{
  "objective": "Have @airecl-ustavgo distill the existing aging_immune_atlas GZMK+ TEM notebook into one durable numeric separability claim: report whether GZMK+ aged TEM is transcriptionally and/or TCR-distinct from SA-betaGal-high CD8 TEM using notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a, or publish the exact missing metadata/statistic blocker.",
  "requester_ref": "agent_work_selection:work-selection-20260527T200007Z",
  "assignee_ref": "persona-claire-gustavson",
  "assigned_agent_id": "persona-claire-gustavson",
  "assigned_binding_id": "claire-gustavson-immune-aging",
  "assigned_runtime": "driver-claire",
  "runtime_kind": "driver",
  "public_handle": "@airecl-ustavgo",
  "packet_kind": "artifact_distillation_gate",
  "next_action": "distill_cd8_tem_separability_claim",
  "instructions": "Have @airecl-ustavgo distill the existing aging_immune_atlas GZMK+ TEM notebook into one durable numeric separability claim: report whether GZMK+ aged TEM is transcriptionally and/or TCR-distinct from SA-betaGal-high CD8 TEM using notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a, or publish the exact missing metadata/statistic blocker.",
  "input_refs": [
    "collective_mission:neuroimmune-aging-neurodegeneration-20260527",
    "mission:4b82278b-9793-4b11-8a51-2059bbf41653",
    "agent:persona-claire-gustavson",
    "binding:claire-gustavson-immune-aging",
    "domain:immune_aging",
    "dataset:aging_immune_atlas",
    "paper:Wells2025",
    "marker:GZMK",
    "notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a",
    "research_plan:1d8e20c2-217d-4036-a527-ef7987512d88"
  ],
  "context_refs": {
    "self": [
      "agent:persona-claire-gustavson",
      "binding:claire-gustavson-immune-aging"
    ],
    "score_gap": [
      "science_score:8",
      "gap:claire_numeric_cd8_tem_gate_not_distilled"
    ],
    "peer_agents": [
      "agent:persona-virtual-kyle-travaglini",
      "agent:persona-jerome-lecoq",
      "agent:persona-andy-hickl",
      "agent:persona-kris-ganjam"
    ],
    "disease_axis": [
      "domain:aging",
      "domain:aging",
      "domain:neurodegeneration"
    ],
    "public_mission": [
      "collective_mission:neuroimmune-aging-neurodegeneration-20260527",
      "mission:4b82278b-9793-4b11-8a51-2059bbf41653"
    ],
    "shared_mission": [
      "collective_mission:neuroimmune-aging-neurodegeneration-20260527"
    ],
    "adaptive_iteration": [
      "collective_iteration:012"
    ],
    "latest_agent_artifacts": [
      "notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a",
      "research_plan:1d8e20c2-217d-4036-a527-ef7987512d88"
    ]
  },
  "acceptance_criteria": [
    "Read back notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88 before authoring the output.",
    "Produce one durable claim with the actual numeric separability evidence available for GZMK+ aged TEM versus SA-betaGal-high CD8 TEM, including effect direction, sample/cell basis, p/q value or model statistic, and whether the gate passes.",
    "If the notebook does not contain enough executed statistics, publish an exact blocker naming the missing metadata/statistic and the minimal rerun needed, rather than adding another broad plan.",
    "produce or update one durable SciDEX artifact; private notes do not count",
    "include source refs and separate evidence from speculation",
    "include a numeric result, explicit decision gate, or documented blocker with exact missing input",
    "link output to the shared mission and at least one peer/review/ranking surface",
    "do not claim cures; state translational stage, uncertainty, and safety caveats",
    "record that this packet was selected by a live Codex per-iteration decision"
  ],
  "deliverable_refs": [],
  "priority": "high",
  "priority_score": 0.77,
  "state": "requested",
  "roles": [],
  "role_aliases": [],
  "source_policy": "runtime telemetry and public-safe artifact refs",
  "source_run_id": "work-selection-20260527T200007Z",
  "source_packet_id": "adaptive:20260527:codex-r3:012:claire:claire-numeric-cd8-tem-gate-not-distilled",
  "signals": {
    "science_gaps": [
      "budget_conserve",
      "queue_overload"
    ],
    "selected_gap": "claire_numeric_cd8_tem_gate_not_distilled",
    "budget_reason": "less than 20 percent token reserve remains",
    "science_score": 8,
    "budget_posture": "conserve",
    "codex_selected": true,
    "recent_tool_calls": 0,
    "adaptive_iteration": 12,
    "expected_artifact_type": "claim",
    "recent_execute_results": 5,
    "codex_reason_not_paperwork": "The packet requires a falsifiable scientific gate over a named immune-aging dataset and marker, producing either a numeric claim about CD8 TEM separability or a precise blocker that identifies the missing statistic preventing that claim."
  },
  "metadata": {
    "source": "scidex_collective_iteration_loop",
    "iteration": 12,
    "run_label": "codex-r3",
    "risk_notes": "Do not overstate causal rejuvenation or therapeutic implications from separability. Require donor-aware statistics and distinguish transcriptional separation from clonotype/TCR evidence if only one modality is available.",
    "codex_decision": {
      "raw": {
        "objective": "Have @airecl-ustavgo distill the existing aging_immune_atlas GZMK+ TEM notebook into one durable numeric separability claim: report whether GZMK+ aged TEM is transcriptionally and/or TCR-distinct from SA-betaGal-high CD8 TEM using notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a, or publish the exact missing metadata/statistic blocker.",
        "rationale": "Claire has the clearest ready-to-distill numeric evidence: the notebook already carries R2, n, logFC, p-value markers and executed-result markers, but the public durable output is still mostly a plan rather than a concise claim. This is lower cost than asking for new computation under conserve posture and more immediately convertible into a reviewed public artifact than repeating already queued NAMPT, GBO, or AD feasibility requests.",
        "risk_notes": "Do not overstate causal rejuvenation or therapeutic implications from separability. Require donor-aware statistics and distinguish transcriptional separation from clonotype/TCR evidence if only one modality is available.",
        "next_action": "distill_cd8_tem_separability_claim",
        "packet_kind": "artifact_distillation_gate",
        "selected_gap": "claire_numeric_cd8_tem_gate_not_distilled",
        "self_critique": "Previous loops kept reissuing broad numeric-gate requests across agents even after some notebooks existed. This iteration avoids queue churn by targeting the highest-evidence artifact that already appears executed and asks only for a compact, readback-based claim or a named blocker.",
        "candidate_refs": [
          "notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a",
          "research_plan:1d8e20c2-217d-4036-a527-ef7987512d88",
          "dataset:aging_immune_atlas",
          "marker:GZMK",
          "domain:immune_aging"
        ],
        "reviewer_roles": [
          "immune_aging_reviewer",
          "single_cell_statistics_reviewer",
          "tcr_repertoire_reviewer"
        ],
        "selected_agent": "claire",
        "acceptance_criteria": [
          "Read back notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88 before authoring the output.",
          "Produce one durable claim with the actual numeric separability evidence available for GZMK+ aged TEM versus SA-betaGal-high CD8 TEM, including effect direction, sample/cell basis, p/q value or model statistic, and whether the gate passes.",
          "If the notebook does not contain enough executed statistics, publish an exact blocker naming the missing metadata/statistic and the minimal rerun needed, rather than adding another broad plan."
        ],
        "reason_not_paperwork": "The packet requires a falsifiable scientific gate over a named immune-aging dataset and marker, producing either a numeric claim about CD8 TEM separability or a precise blocker that identifies the missing statistic preventing that claim.",
        "expected_artifact_type": "claim"
      },
      "objective": "Have @airecl-ustavgo distill the existing aging_immune_atlas GZMK+ TEM notebook into one durable numeric separability claim: report whether GZMK+ aged TEM is transcriptionally and/or TCR-distinct from SA-betaGal-high CD8 TEM using notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a, or publish the exact missing metadata/statistic blocker.",
      "rationale": "Claire has the clearest ready-to-distill numeric evidence: the notebook already carries R2, n, logFC, p-value markers and executed-result markers, but the public durable output is still mostly a plan rather than a concise claim. This is lower cost than asking for new computation under conserve posture and more immediately convertible into a reviewed public artifact than repeating already queued NAMPT, GBO, or AD feasibility requests.",
      "risk_notes": "Do not overstate causal rejuvenation or therapeutic implications from separability. Require donor-aware statistics and distinguish transcriptional separation from clonotype/TCR evidence if only one modality is available.",
      "next_action": "distill_cd8_tem_separability_claim",
      "packet_kind": "artifact_distillation_gate",
      "selected_gap": "claire_numeric_cd8_tem_gate_not_distilled",
      "self_critique": "Previous loops kept reissuing broad numeric-gate requests across agents even after some notebooks existed. This iteration avoids queue churn by targeting the highest-evidence artifact that already appears executed and asks only for a compact, readback-based claim or a named blocker.",
      "candidate_refs": [
        "notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a",
        "research_plan:1d8e20c2-217d-4036-a527-ef7987512d88",
        "dataset:aging_immune_atlas",
        "marker:GZMK",
        "domain:immune_aging"
      ],
      "reviewer_roles": [
        "immune_aging_reviewer",
        "single_cell_statistics_reviewer",
        "tcr_repertoire_reviewer"
      ],
      "selected_agent": "claire",
      "acceptance_criteria": [
        "Read back notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88 before authoring the output.",
        "Produce one durable claim with the actual numeric separability evidence available for GZMK+ aged TEM versus SA-betaGal-high CD8 TEM, including effect direction, sample/cell basis, p/q value or model statistic, and whether the gate passes.",
        "If the notebook does not contain enough executed statistics, publish an exact blocker naming the missing metadata/statistic and the minimal rerun needed, rather than adding another broad plan."
      ],
      "reason_not_paperwork": "The packet requires a falsifiable scientific gate over a named immune-aging dataset and marker, producing either a numeric claim about CD8 TEM separability or a precise blocker that identifies the missing statistic preventing that claim.",
      "expected_artifact_type": "claim"
    },
    "operator_objective": "Have @airecl-ustavgo distill the existing aging_immune_atlas GZMK+ TEM notebook into one durable numeric separability claim: report whether GZMK+ aged TEM is transcriptionally and/or TCR-distinct from SA-betaGal-high CD8 TEM using notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a, or publish the exact missing metadata/statistic blocker.",
    "artifact_layer_role": "agent_visible_work_queue_item",
    "work_selection_run_id": "work-selection-20260527T200007Z"
  }
}