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Bound cinnamate causal graph to supported products and syntrophic evidence #1313

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@realmarcin

Source-based self-adversarial review of kb/communities/Cinnamate_Degradation_Consortium.yaml (CommunityMech:000018), current SHA-256 e0c1766f30e1d6225d8dede3b2944ca9193c45610ca6aaa194c07ecacec25edc.

The primary abstract supports Papillibacter conversion of cinnamate to benzoate, subsequent syntrophic benzoate degradation, and acetate/methane/carbon dioxide products. It does not establish complete mineralization of all carbon or identify the interspecies electron carrier experimentally. The graph currently presents H2 transfer as directly measured and types the initial conversion as commensalism; neither follows from the accessible source. GO:0006635 is fatty-acid beta oxidation, not a demonstrated fatty-acid pathway in this aromatic-substrate assay.

Fix within graph/discussion/history scope: preserve the three nodes and two causal links; retain the supported benzoate substrate link; qualify the hydrogen/CO2 methanogenesis model as HYPOTHESIZED/PARTIAL; avoid unqualified hydrogen metabolite assertions and complete mineralization; remove unsupported commensalism and fatty-acid-process typing; document the exact-system electron-carrier and carbon-balance evidence gap. Preserve reported syntrophic dependence and measured products.

Primary source: https://pubmed.ncbi.nlm.nih.gov/12432464/ and https://link.springer.com/article/10.1007/s00284-002-3759-9 . Publisher full body is subscription content and was not read. No new nodes/arrows or Edison spend needed.

Deduplication: all 657 existing all-state issue titles/bodies and ignored-inclusive local reports/history/research/tests searched; no matching graph issue found. Issue comments were not exhaustively searched. This is a self-adversarial review, not independent approval.

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  1. realmarcin commented on Oct 5, 2026

    @realmarcin
    ContributorAuthor

    Implemented and locally verified in PR #1315, exact head 0910d16. All 22 recorded gates passed, including 233 regression tests, 36 MATCH snippets, unchanged network warnings, deterministic rendering and a post-commit docs-current check. The decision ledger, adversarial review, validation JSON and append-only record history are committed. This issue remains open until the PR reaches main through the protected queue. Non-graph metadata remains separately tracked in #1314.

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