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Bound the biochar electron-transfer model separately from removal endpoints #1740

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@realmarcin

CommunityMech:000291; PMID42139785. Preserve all three nodes, both directions and reported removal/mineralization outcomes. Electrochemical and multi-omics findings support the authors electron-transfer and circuit interpretation, with the route and individual mediators qualified by abstract-only access. Retain PARTIAL SYNTROPHY on the two mechanism nodes: the local enum explicitly does not assert obligacy. Keep the measurement endpoint distinct and untyped; use canonical collective participants for the circuit and endpoint. No new genetic design or optimization. Close only after protected-main merge.

Precommit correction: adversarial reading of the schema caught the original issue rationale wrongly requiring obligacy. The initial 816-test report is archived as superseded. Append-only correction histories, a schema-contract regression and a fresh full validation record the correction.

Dedup:1006 all-state issue titles/bodies searched by IDs, PMIDs, names and broad substrate/taxon aliases. All nine matching bodies read; none is this graph repair. Explicitly read529/573/605 for general source/panel/membership scope.49 local matching files found with ignored/hidden included; .git/docs/site/references_cache excluded, relevant caches separately inspected. Comments and PRs not exhaustive. Self-adversarial review, not independent approval.

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  1. realmarcin commented on Oct 7, 2026

    @realmarcin
    ContributorAuthor

    Precommit adversarial correction: the actual SYNTROPHY enum explicitly does not require obligacy. The naphthalene transfer/circuit nodes retain the authors qualified SYNTROPHY model. The chloronitro endpoint remains untyped because pathway completion alone does not establish product-removal feedback, not because obligacy is unproven. Original histories and the initial 816-test validation are preserved as superseded; two correction histories and a schema-contract test have been added. Fresh full validation is in progress. No new causal direction or Edison job. Keep repairs open until protected-main merge.

  2. realmarcin commented on Oct 7, 2026

    @realmarcin
    ContributorAuthor

    Addressed in #1743 at c12b1dc; exact-head self-review: #1743 (review). 817 passed in 280.29s (0:04:40); postcommit docs-current passed. Decisions and actual output digests committed. Not independent approval; close only after protected-main merge. Metadata1742remains unfinished.

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