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Repair diatom, phenol, Phormidium and phosphite causal claims (batch84) - #1702
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Source-based self-adversarial review at exact head 32423c9; not independent approval. Repairs1694-1697addressed;1698-1701remain unresolved.
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Preserve surface attachment while bounding EPS identity and mediation.; Retain amino-acid competition as a hypothesis while preserving controlled negative physiology.
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Preserve phenol conversion and qualify the inferred enzymatic route.; Preserve perturbation-supported sink directions and condition-specific dependence.; Preserve aromatic conversion without complete-mineralization or removal claims.
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Preserve photosynthetic carbon supply and the experimentally supported downstream direction.; Preserve major-population isotope uptake with explicit participants and no invented compound specificity.; Retain gene-supported polymer-use hypothesis with corrected donor and recipient.; Preserve alpha heterotrophic evidence without class-wide reciprocal services.
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Preserve phosphite-driven hydrogenogenesis and qualify the intracellular enzyme model.; Preserve H2 transfer while distinguishing physiological inhibition and net thermodynamics.; Correct methanogenic sink actor direction and preserve the positive methane endpoint.
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Before papers, fresh two-root baseline covered460records/921caches,1438nodes600arrows,47warnings0structural. Every original node/arrow and missing structure reviewed in four whole records:12retained nodes/6arrows and3removed nodes/2arrows have dispositions. No new node or downstream arrow.
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Diatom SEM attachment remains positive. Filamentous EPS identity/source and attachment-mediated physiological damage were not established. Amino-acid competition is an author hypothesis from nutrient/pigment observations, not measured amino-acid exchange. Medium-matched HAC supports negative coculture physiology; broth enrichment is not a demonstrated bacterial growth benefit.
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Late physiological controls exist, while day8axenic transcriptomics does not. Diel gene counts do not prove endogenous clock disruption; transcript-constrained biomass flux and ICA modules are model/association outputs. No competition-to-clock-to-flux path is invented. Additional physiological/diel structure remains1698research.
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All three phenol arrows retain positive perturbation/conversion support: BES and highH2block degradation in the methanogenic culture. Hydrogen is supported without excluding formate. AQDS enables acetate production under methanogenic inhibition, but axenic isolation failed. The alternative Desulfovibrio culture is not added to the canonical pair.
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Phenol intermediates support a proposed carboxylation/dehydroxylation route, not identified enzymes or aromatic-carbon transfer to the methanogen. Acetate remains an organic product and Table2has residual substrate at100days. Rename mineralization to conversion; do not downgrade the measured product phenotype. Existing CHEBI30746parent-acid grounding is explicitly labeled, not silently reassigned.
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Phormidium protein/SIP genuinely supports cyanobacterial carbon flow. Major heterotroph peptide coverage is WenzhouxiangellaMAG57andPhycisphaeralesMAG34; explicit canonical participants do not credit every member of their phyla. Lag supports a macromolecule-use interpretation, not identified protein/glycogen transfer or a trophic cascade. Do not assign all fermentation substrates to Wenzhouxiangella.
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Phormidium Figure3is explicitly gene-content inference. Verrucomicrobiota hydrolases/sulfatases support a polymer-use hypothesis, not Planctomycetota-to-Verruco transfer. MAG58isotope signal has lower peptide coverage, while alpha bacteriochlorophyll genes are capacity, not measured phototrophic flux. Canonical taxonomy is unchanged.
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Vitamin/cofactor delivery, ROS protection and nutrient return were unsupported exact-community nodes using general introductory examples. Their three nodes/two arrows are removed with rationale, not treated as negative experimental results. Unrelated tetrapyrrole nutrient-cycling GO and untested mutualism removed. Bacteroidota disconnection remains visible and tracked1699; no fabricated link for audit credit. Long-term crash-free culture does not establish static membership or redundancy mediation.
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Phosphite H2-mediated partnership and both donor-to-methane arrows survive. BES/highH2inhibition and G11rescue support lowH2sink dependence. HndABCD/Rnfdetails remain a metaproteomic/thermodynamic model, not an enzyme perturbation. Net oxidation is exergonic; the proposed bottleneck concerns intracellular energy conservation. Methanoculleus is the sink actor, not the donor. Acetate assimilation is distinct from methane carbon.
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Phosphite enrichment had seven taxa with acetate/sulfide and sixteen with cysteine, not a pure two-member culture. The physiology-supported sink-to-donor feedback candidate is recorded without adding unreviewed topology;1700remains research and1701tracks raw non-graph composition/identity claims.
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Three fresh full primary main texts and one cached phenol primary read, with actual access limits recorded. PhormidiumPDFpages8/11visually inspected for Figures3/4. Separate supplements/raw data and other original figures uninspected. Failed HTTP500/BioCNoresult/browser-check responses are not full text. Eleven graph quotations match fresh primary and seven use cached phenol; eight new discussion quotations also checked.
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All921caches,456otherrecords and raw non-graph blocks hash-verified unchanged; four guarded curation events and append-only histories. Schema/strict/terms/references/snippets/history pass; actual broad regressions, deterministic renders and exact published descriptions recorded. HTML parser checks are not browser screenshots.47priorwarnings preserved plus one Bacteroidota disconnection; no structural defect or auditor-rule change.
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Dedup969all-state issue titles/bodies and hidden/ignored local search with declared exclusions; comments/PRs not exhaustive. Three scoped one-community Edison dry runs, no provider job/credits; questions unanswered and prior denials unchanged. Repairs1694-1697close only after protected-main merge;1698-1701remainOPEN. Self-adversarial COMMENT is not independent approval. Move dependents before deleting parents.
756 passed in 350.42s (0:05:50); ten new focused tests. Four schema/strict/term/reference/snippet/history gates passed. Four full-record reference validators exit0. CLI Total checks counts issues, not executed checks.18graph quotations match primary/cache content;11match independent fresh full text and7match the existing cached phenol primary. Literal matching is not entailment or whole-record certification. Original921caches and non-graph blocks preserved, not globally recertified.
15original nodes/8arrows reviewed;12nodes/6positive arrows retained,3unsupported Phormidium service nodes/2arrows removed. Positive SEM attachment, carbon transfer, phenol inhibition/conversion and phosphite syntrophy preserved. Missing structures #1698-#1700 and non-graph #1701 remain OPEN.
456otherrecords,921caches and raw non-graph blocks unchanged. Explicit major Phormidium SIP participants; no taxonomy/auditor-rule changes.47baseline warnings preserved plus one Bacteroidota disconnection exposing the removed unsupported role. Zero structural defects. Deterministic rendering and exact description parser checks across456pages, not browser screenshots. Full both-root audit-snippets executed with actual counts, not a clean-corpus assertion.
Postcommit check-docs-current passed clean, logSHA256 0ed6f1b6ee19c27155c551b47dbf22ee8ed36ba041e23b91a2e97291e7923d82. Decision ledger,41actual check outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch84. Corpus260reviewed/156pending/44needs_research. Three one-community Edison dry runs, zero paid jobs/credits; scoped questions unanswered. Not independent approval or corpus completion.
Protected-main merge pending.
Network integrity findingsWarnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build. The full report is attached to the workflow run as an artifact. |
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Self-adversarial integration review at exact head 345eedc71e173c75dff8d5692ef946aeb3c908de. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 32423c9184e490bd3692026a337c63a33ec02d19, the only changes are the canonical schema pin, shared schema and generated datamodel from that main commit. Every other tracked file is identical; the batch-owned binary patch remains byte-identical (SHA-256 27abfa92a59f403e7e6c94fc1fc485f7a13b71661e4a8d93701f0f943bdc46dc). All 60 published batch patches were checked this way. No scientific assertion, reference cache, history, decision ledger or generated page was edited by this integration.
Adversarial checks: no inherited schema-file edits lost; generated CrossCorpusLink remains standalone and does not add a causal claim; normal strict validation passed all 460 records; required CrossCorpusLink fields enforced. Fresh broad regression runs on both ends of the stack: 302 passed in 172.77s (0:02:52); 756 passed in 255.55s (0:04:15). Docs-current passed clean at batches25/84, and vendored-sync passed. The 58 intermediate combinations were not independently retested. Existing primary-source review limitations and unresolved research issues remain applicable; historic validation receipts are not rewritten as new scientific reviews.
An additional generated-datamodel loading check FAILED and is retained in the integration receipt. Differential testing found exactly the same failures on all 460 paths before and after this integration:417 unhashable TaxonDescriptor and43 unhashable CultureCollectionEnum exceptions, with linkml-runtime1.11.1. Existing tests explicitly use plain YAML instead of this loader. Pre-existing defect #1703 remains OPEN; no datamodel-loader success is claimed. Normal strict schema validation is a separate passing path, not a relabeling of that failure.
Required CI must pass on this exact head and the protected merge-queue candidate. No manual workflow dispatch, artificial status, administrative merge or protection bypass. Dependents stay draft until their parent is confirmed merged; move dependents before branch deletion.
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Self-adversarial review refreshed at exact head 2f46f9b49b0f9c368621554ff34afccc57ff5dc3
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 0c0a274b883e5ead55f62ef8f9a578564d934423.
The batch-owned binary patch is byte-identical
(SHA-256 27abfa92a59f403e7e6c94fc1fc485f7a13b71661e4a8d93701f0f943bdc46dc); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.
The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.
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Self-adversarial governance integration review at exact head eee0b8153a257f7557b33dc8eea78351b75d6a94. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 2f46f9b49b0f9c368621554ff34afccc57ff5dc3, exactly two files changed: scripts/.vendored_canon_ref and tests/test_id_label_empty_adapter.py. Each resulting tree differs from its old tree by the exact binary patch from main, and each batch-owned binary patch remains byte-identical (SHA-256 27abfa92a59f403e7e6c94fc1fc485f7a13b71661e4a8d93701f0f943bdc46dc). These invariants passed on all 74 published branches. Original heads are retained in local archive refs/archive/communitymech-pre-governance-20261007. No scientific record, source cache, history, decision ledger, schema, runtime code or generated page changed in this integration.
Adversarial inspection: the adapter regression still checks the empty sentinel and case-insensitive caching, now with an isolated fake oaklib module and a one-call selector assertion. No validation threshold or runtime behavior was relaxed. Fresh regressions at both stack ends: 337 passed in 214.19s (0:03:34); 917 passed in 402.58s (0:06:42). Docs-current and pinned vendored-sync passed at batches26/99. The 72 intermediate combinations were checked by tree/patch hashes, not independently retested. Historical source-review limitations and unresolved issues, including loader #1703 and cache #1091, remain applicable. This is not new paper review, independent approval, or a claim that those outstanding issues are fixed.
Digest-bound integration receipt/logs: /private/tmp/communitymech-governance-integration-20261007/receipt.json. Prior output/review records in reports/causal_graph_review/ remain unchanged. The prior lifecycle receipt is archived and will be updated only after all exact-head comments are verified.
Required CI and independent review must pass for the exact head and protected merge-queue candidate. No CI rerun, manual dispatch, fabricated status, admin merge or protection bypass. Dependents remain draft; move them before deleting a merged parent branch.
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Exact-head self-adversarial restack review at c93ffc2cbaa872a7356ab25defcaca4bf5207abf.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 27abfa92a59f403e7e6c94fc1fc485f7a13b71661e4a8d93701f0f943bdc46dc.
Tree ccc970db20db932f512f5aff0d441fc048bef0fc matches the independently computed clean merge.
Compared with historical tree ed5df561cb34b371df45ef974aa43be349364c2f, only scripts/.vendored_canon_ref
changes, incorporating main PR #1834's pin 849f336e025510316a5f235eb0af8547b8bd50cc.
All curated records, source caches, review outputs, histories, regression tests, and rendered
pages remain unchanged. No new primary-source review or local scientific-test rerun is claimed.
This PR is now part of native stack #1973, rooted at #1363 on main. No protected merge
has occurred. Fresh eligible PR/merge-group CI remains mandatory. No rule bypass, fabricated
status, merge into a topic parent, or premature branch deletion.
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Superseded by the protected cumulative merge #1975 at Patch-inclusion receipt. Existing issue-closing links were transferred to #1975; unresolved research and non-graph gaps are not closed by this action. This PR is being closed as superseded, not represented as individually merged. Archival provenance tags retain source commits; cleanup removes branch refs only and preserves worktree files. |
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Scope
Closes #1694.
Closes #1695.
Closes #1696.
Closes #1697.
Research #1698/#1699/#1700 and non-graph #1701 stay OPEN after repair merge.
Adversarial Review
Verification And Output Records
756 passed in 350.42s (0:05:50); ten new focused tests. Four schema/strict/term/reference/snippet/history gates passed. Four full-record reference validators exit0. CLI Total checks counts issues, not executed checks.18graph quotations match primary/cache content;11match independent fresh full text and7match the existing cached phenol primary. Literal matching is not entailment or whole-record certification. Original921caches and non-graph blocks preserved, not globally recertified.
15original nodes/8arrows reviewed;12nodes/6positive arrows retained,3unsupported Phormidium service nodes/2arrows removed. Positive SEM attachment, carbon transfer, phenol inhibition/conversion and phosphite syntrophy preserved. Missing structures #1698-#1700 and non-graph #1701 remain OPEN.
456otherrecords,921caches and raw non-graph blocks unchanged. Explicit major Phormidium SIP participants; no taxonomy/auditor-rule changes.47baseline warnings preserved plus one Bacteroidota disconnection exposing the removed unsupported role. Zero structural defects. Deterministic rendering and exact description parser checks across456pages, not browser screenshots. Full both-root audit-snippets executed with actual counts, not a clean-corpus assertion.
Postcommit check-docs-current passed clean, logSHA256 0ed6f1b6ee19c27155c551b47dbf22ee8ed36ba041e23b91a2e97291e7923d82. Decision ledger,41actual check outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch84. Corpus260reviewed/156pending/44needs_research. Three one-community Edison dry runs, zero paid jobs/credits; scoped questions unanswered. Not independent approval or corpus completion.
Source Limits
Dependency
Draft depends on #1693. Do not merge into the topic parent. Require exact-head CI and protected-main queue after parent merge. Move dependents before deleting parent branches.