{
  "slug": "microbiome-causality",
  "edition": "consensus_consistency_audit_2026-10-09 revised",
  "round": 2,
  "date": "2026-10-14",
  "authoring_model": "Sol 6.1",
  "adversarial_reviewer": "Claude Opus 5.5 (Anthropic)",
  "canonical_path": "consensus_consistency_audit_2026-10-09\\revised\\microbiome-causality\\microbiome-causality.review.md",
  "divergent_copies_not_touched": [
    "hsef_v53_popularity_ranks_41_45_2026-10-08\\microbiome-causality\\microbiome-causality.review.md"
  ],
  "revision_regression_check": "Diffed against the earlier edition: the revision added only the 'Consensus provenance reconciliation - 9 October 2026' block and changed nothing else. ONE regression was introduced by the revision - finding C3, the false 'earlier adversarial approval' clause spliced in unconditionally. The Momentum defect (C1) and the rendering defects (C2) were inherited from the original edition.",
  "level_before": "Γ",
  "level_after": "Γ",
  "confidence_before": "Moderate",
  "confidence_after": "Moderate",
  "role_before": "reinforcing / stabilizing factor",
  "role_after": "reinforcing / stabilizing factor",
  "momentum_before": "Decisive work underway",
  "momentum_after": "Mechanistic only",
  "subclaims_before_and_after": "SC1 Β, SC2 Ζ, SC3 Ε, SC4 Γ - unchanged",
  "pmids_checked": 67,
  "pmids_failed": 0,
  "retractions_or_eoc_found": 0,
  "load_bearing_claims_spotchecked": 15,
  "validator": "PASS - 0 fail, 0 warn, 30 pass (archived v5.3 validator)",
  "findings": [
    {
      "id": "C1",
      "severity": "Minor",
      "category": "momentum boilerplate / internal consistency",
      "location": "AT A GLANCE table; Final score Momentum paragraph; scorecard extended_scoring_MSD.momentum",
      "original": "Decisive work underway. THEMATIC and recent placebo-controlled PD/ALS/defined-L.reuteri studies test functional human boundaries (PMID39800192,39073834,39617896,38113884); no claim of a currently recruiting trial.",
      "corrected": "Mechanistic only, with the artifact expanded to state that the named work is clinical rather than boundary-addressing, that no currently recruiting trial is claimed, and that none of these designs is the before-disease factor manipulation SC4's next threshold requires.",
      "evidence": "The artifact's own closing clause and the Stability entry both contradict the framework definition of 'Decisive work underway' ('Someone is running an experiment that could cross the next threshold'). The four named studies are completed trials in established disease. Momentum modifies no letter, so level, confidence and role are unchanged. Recurring upstream defect flagged in the round-2 brief.",
      "level_impact": "none"
    },
    {
      "id": "C2",
      "severity": "Editorial",
      "category": "rendering defects",
      "location": "throughout review.md (13 instances)",
      "original": "'Universal cap5'; 'phase2 placebo-controlled' (x2); 'ErratumIn:' (x8), two reading 'PMIDnot supplied'",
      "corrected": "'Universal cap 5'; 'phase 2 placebo-controlled'; 'Erratum in:'; 'PMID not supplied'",
      "evidence": "Known upstream rendering defects (round-2 brief item 4). No numeric value, letter or attribution altered.",
      "level_impact": "none"
    },
    {
      "id": "C3",
      "severity": "Minor",
      "category": "false provenance clause / revision regression",
      "location": "Consensus provenance reconciliation block, final paragraph; consensus-addendum.md",
      "original": "The earlier adversarial approval refers to its original edition; this provenance supplement is not a new independent or blinded adjudication.",
      "corrected": "No earlier adversarial approval is attached to this case; this provenance supplement is not a new independent or blinded adjudication.",
      "evidence": "Inserted unconditionally by the 9 October revision script. Verified before changing: the earlier edition at hsef_v53_popularity_ranks_41_45_2026-10-08 carries no approval section, reviews/microbiome-causality/ carries no redteam record, and this slug is not among the thirty reviews that carry a 2026-10-06 approval. Revision-introduced regression.",
      "level_impact": "none"
    },
    {
      "id": "C4",
      "severity": "Minor",
      "category": "framework conformance (confidence rationale) - lead policy 2026-10-14",
      "location": "scorecard final_score.confidence_rationale and consensus_validation.score_before/score_after.confidence_rationale",
      "original": "... density, heterogeneous controls and incomplete access set the confidence, not correctness.",
      "corrected": "Rationale rewritten to strike reviewer access as a determinant and to name only evidence density, replication and heterogeneity, with an explicit statement that access depth is recorded per ledger row and is not a determinant of the band.",
      "evidence": "Lead policy of 2026-10-14, step 1: how much of a paper the reviewer could read is neither evidence density nor reproducibility and never justifies a band. Step 2 re-derivation: What remains is substantive and is documented in the review's own text: defined rodent perturbations replicate across distinct mechanisms, but the human record is mixed and the transfer literature shows demonstrated rather than hypothetical reproducibility problems - engraftment without functional effect, and housing- and diet-dependent reversals - with heterogeneous products, comparators and endpoints across the 67 reports. Reproducibility is demonstrably not well established, which is what the High text requires.",
      "band_before": "Moderate",
      "band_after": "Moderate",
      "level_impact": "none"
    }
  ],
  "rejected_findings": [
    {
      "id": "R1",
      "issue": "Headline could be Δ on the THEMATIC result",
      "reasoning": "The HE recurrence contrast is a secondary endpoint whose pooled any-FMT comparison is post hoc, in patients who already had cirrhosis on lactulose and rifaximin. Treating established disease does not test whether composition is the primary upstream cause of the registered disease scope."
    },
    {
      "id": "R2",
      "issue": "Scope-matched aggregation possibly misread",
      "reasoning": "Checked against the known misreading. SC2 (rodent) and SC3 (prespecified diagnoses under intervention) are scope-restricted relative to the registered broad-primacy claim, so only SC4 matches and the letter is Γ. Both declared alternatives (weakest-link Β, primary-subclaim Γ) are correct. The derivation's 'preregistered human-primacy gate' wording reads like primary-subclaim language but both rules return the same letter."
    },
    {
      "id": "R3",
      "issue": "Ζ on SC2 without an independence basis",
      "reasoning": "Independence is recorded as the framework requires, naming three lines (defined colonization under host-immune epistasis; non-lethal microbial enzyme inhibition in conventional animals; host intestinal-pathway interruption under matched community change) and the distinct systematic error each excludes."
    },
    {
      "id": "R4",
      "issue": "Cap 5 cited for SC4 while the quoted rationale discusses diet, genotype and engraftment",
      "reasoning": "The cap-precedence paragraph states the binding inference explicitly, resolving the collision in writing rather than silently."
    },
    {
      "id": "R5",
      "issue": "Multiple PMIDs printed as comma runs",
      "reasoning": "Used consistently throughout this document as its citation convention rather than as a sporadic rendering failure; house style is outside the correction remit."
    },
    {
      "id": "R6",
      "issue": "'remains Gamma' spelled out in prose",
      "reasoning": "The normative descriptor rule governs the letter and descriptor fields, which are correct; 'Gamma hard-rule audit' is a section label used across this corpus."
    },
    {
      "id": "R7",
      "issue": "Collective authors dropped by the reference builder",
      "reasoning": "Checked all 67 reference rows; none has a blank author or leading comma."
    },
    {
      "id": "R8",
      "issue": "Divergence 'Contested' carries no rung arithmetic",
      "reasoning": "Contested is defined as the value for which no single field-implied level applies."
    },
    {
      "id": "R9",
      "issue": "Eighteen PMIDs shared with the separately registered gut-microbiome-systemic-causality review",
      "reasoning": "The two reviews register different claims and each is scored against its own. Shared records are used at the same scopes in both. Neither lets the recurrent C. difficile literature carry a systemic claim: this review names it an out-of-scope calibration comparator and the other scores it as an explicitly out-of-scope subclaim. Neither borrows the other's evidence to clear a threshold."
    },
    {
      "id": "R10",
      "issue": "Confidence band Moderate justified partly by reviewer access depth",
      "reasoning": "The scorecard confidence_rationale names 'incomplete access' as a confidence input although the framework defines confidence by evidence density and reproducibility. The band was independently re-derived against the High text and Moderate is correct: this review documents demonstrated reproducibility failures in the transfer literature and a mixed human trial record. Not edited per case because the sentence is a corpus-wide template; recommended as a template fix."
    }
  ],
  "files_changed": [
    "microbiome-causality.review.md",
    "microbiome-causality.scorecard.json",
    "consensus-addendum.md",
    "validator-adversarial-2026-10-14.txt",
    "SHA256.txt",
    "ADVERSARIAL_REVIEW.md",
    "adversarial-findings.json"
  ],
  "package_level_files_not_edited": [
    "README.md",
    "COMPLETION.json",
    "FINAL_VERIFICATION.json"
  ],
  "approval": "Approved as revised. - Claude Opus 5.5 (Anthropic), 2026-10-14.",
  "systematic_artifacts_checked": {
    "reviewer_notes_consensus_contradiction": "absent - the preserved METHODS AND CONSENSUS CONTRIBUTION and REVIEWER NOTES sections both affirm Consensus use, so nothing contradicts the spliced validation block; no scoping edit needed",
    "false_approval_boilerplate": "present - corrected as finding C3",
    "best_supported_rival_renderer_bug": "absent - models_evaluated[0] is 'Diet/substrate-dependent microbial contribution' with is_nominal false; the nominal 'Primary gut-microbiome driver' is the fifth entry, so the prose names the correct rank-1 rival",
    "confidence_set_from_access_depth": "CORRECTED under lead policy 2026-10-14 as finding C4: access depth struck from the rationale; band re-derived from the remaining substantive evidence-quality and reproducibility concerns and stands at Moderate.",
    "scorecard_reviewer_field": "left as issued ('Codex'); corpus-wide house provenance",
    "momentum_decisive_work_underway": "this was finding C1, corrected from \"Decisive work underway\" to \"Mechanistic only\" earlier in this pass on exactly that reasoning - the four named studies are completed placebo-controlled trials. The lead's clarification confirms the correction."
  },
  "note_on_historical_snapshots": "consensus_validation.score_before and score_after carry the same confidence_rationale string and were updated in step with final_score so that the block's 'no change by this reconciliation' assertion stays true and no artifact disagrees with another. The pre-correction wording is preserved in sol61-original/."
}