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Review degradation, competition and diatom graph scope (batch90) - #1743
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Source-based self-adversarial review at exact head c12b1dc; not independent approval. Repairs1738-1741addressed; metadata1742remains unfinished.
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Preserve chemically supported upstream transformation with transfer limits.; Remove the reverse-feeding implication while retaining downstream degradation.; Preserve conditional mineralization without treating the outcome as evidence of product-removal feedback.
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Add reported metabolic-perturbation evidence rather than treating dominance alone as mechanism.; Preserve reported contact inhibition and relative-kinetics attribution with source-access limits.; Preserve the measured dominance outcome separately from its explanatory mechanisms.
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Retain the authors qualified syntrophic electron-transfer model without an obligacy requirement.; Represent the composite circuit collectively with explicit canonical participants.; Preserve reported removal and mineralization without conflating endpoints with a specific interaction type.
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Preserve reported bacterial synthesis without claiming individual-process mutualism.; Preserve the reported signaling response and existing causal direction.; Preserve nutrient-exchange interpretation with exact-pair and flux limits.
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Fresh both-root baseline preceded papers. All14originalnodes7arrows have dispositions:12biologicalnodes and all7directions retained; two out-of-scope diatom nodes removed. No new node or direction and no arrow endpoint changes.
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Chloronitro preserves chemical identification, sequential transformations and reported conditional mineralization. The downstream Rhodococcus process no longer asserts metabolite provision back to Pseudomonas. Both original causal directions remain.
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Conditional mineralization is not silently downgraded to disappearance. The endpoint alone does not establish product-removal feedback making upstream metabolism favourable, so it is untyped. Local SYNTROPHY does not require obligacy. Full carbon balances were not inspected; unavailable methods do not prove absent controls.
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TPA retains all three competition nodes and both arrows. Dominance alone is not evidence for resource competition; the source-reported metabolism-loss comparison is added. Positive contact inhibition and relative-kinetics attribution remain; separate effect sizes are not invented.
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Naphthalene retains the authors DIET/circuit interpretation as PARTIAL SYNTROPHY on the first two nodes, electrochemical and multi-omics findings and separate untyped removal/mineralization endpoints. Specific interspecies route and mediator necessity remain qualified. Collective nodes use canonical participants.
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Diatom consortium resolution is a workflow, while coastal prevalence is broader environmental evidence already retained outside the pair graph. Removing those nodes does not erase the three signal/exchange nodes or existing positive causal arrow.
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Individual diatom signal/exchange processes are not categorical reciprocal fitness measurements. Canonical participants are preserved. H3 taxonomic evidence and another-system background citation do not certify the exact SA11 cultivation fields; metadata1742remains open.
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Four exact-system primary abstracts and two attribution abstracts read. No complete primary main text retrieved. Chloronitro XML500/PMC challenge/OA metadata404 and Nature redirect/subscription preview disclosed. Cached secondary background paragraphs are not independent fresh primary evidence. No figures, supplements or raw data audited.
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Adversarial schema reading caught an incorrect obligacy premise after the initial816-test pass. That report and tested inputs are archived as superseded with verified digests. Two appended correction histories preserve the original four histories. A schema-contract regression and fresh full validation bind the corrected state.
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All921caches456otherrecords and raw non-graph blocks preserved. Six append-only histories and eleven focused tests. Two new explicit-participant users, measured legacy census unchanged, all56oldwarnings retained and zero structural defects. No taxonomy or auditor-rule changes.
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No new genetic designs, resistance-selection details, harmful-algal optimization, toxin guidance or experimental protocols. No Edison dry run or provider submission. Executed gates and deterministic HTML checks are not browser screenshots or generated-model loader certification. Loader1703remains open. Repairs1738-1741await protected-main merge;1742remains open. Self-review is not independent approval or corpus completion.
817 passed in 280.29s (0:04:40); eleven new focused tests. Four per-record schema/strict/term/reference/snippet gates and six append-only history gates passed. Four full-record reference-validator runs passed. CLI Total checks counts issues, not executed checks. Sixteen graph and eight discussion quotations match independent fresh-primary abstract and cache text. Literal matching is not entailment or full-text certification.
All14originalnodes7arrows reviewed;12biologicalnodes and all7directions retained. Two out-of-scope diatom nodes removed; environmental evidence remains outside the pair graph. No new node or direction, and no arrow endpoint changes. Reported degradation, competition and signaling findings remain distinct from reverse-feeding implications, model-specific mediation and reciprocal fitness classification.
456otherrecords, all921caches and raw non-graph blocks unchanged. All56existing network warnings preserved, zero structural defects. Two explicit participant users added; legacy census measured unchanged. Deterministic rendering and exact HTML-description parsing, not browser screenshots. Informational full-corpus snippet audit is not clean-corpus certification. Loader #1703 and metadata #1742 remain unresolved.
Adversarial review caught an incorrect obligacy premise after the initial816-test pass. That validation is archived as superseded. The first two naphthalene nodes retain qualified SYNTROPHY under the actual schema; two correction histories and a new schema-contract regression record the correction. All current gates were rerun.
Postcommit check-docs-current passed clean, SHA256 53728b911f3b8fa07db3882d791ae29c452702cf2d2994623549369af9737b07. Decision ledger,44actual output records/digests and self-adversarial review committed under reports/causal_graph_review for batch90. Corpus280reviewed/132pending/48needs_research. Four exact-system primary abstracts, not complete main texts; source-access failures documented. No paid Edison submission, new genetic designs, harmful-algal optimization, toxin guidance or experimental protocols. 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 review refreshed at exact head f4a68018066be667fcfd152c3db9863a1b3af9fe
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 83d7e5364b4698afcc8d350c0ee6dbef29f59092.
The batch-owned binary patch is byte-identical
(SHA-256 8da1e259325e83807db8908b56ecbde4a11dd0287621c2c32fb24f7e03859205); 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 6aa7e37deeca703f7a6ffc3a5e104e1f757eb3b5. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head f4a68018066be667fcfd152c3db9863a1b3af9fe, 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 8da1e259325e83807db8908b56ecbde4a11dd0287621c2c32fb24f7e03859205). 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 8e1982ef53e1b48315e2675e1808194ddf6add34.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 8da1e259325e83807db8908b56ecbde4a11dd0287621c2c32fb24f7e03859205.
Tree cc180cc05e4048b1e274266ac948000d318abb3a matches the independently computed clean merge.
Compared with historical tree 52674cee4b61ccd314c329ad6b9af577bc74d06f, 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. |
1 participant
Scope
Closes #1738.
Closes #1739.
Closes #1740.
Closes #1741.
Metadata #1742 remains OPEN after graph-repair merge.
Adversarial Review
Verification And Output Records
817 passed in 280.29s (0:04:40); eleven new focused tests. Four per-record schema/strict/term/reference/snippet gates and six append-only history gates passed. Four full-record reference-validator runs passed. CLI Total checks counts issues, not executed checks. Sixteen graph and eight discussion quotations match independent fresh-primary abstract and cache text. Literal matching is not entailment or full-text certification.
All14originalnodes7arrows reviewed;12biologicalnodes and all7directions retained. Two out-of-scope diatom nodes removed; environmental evidence remains outside the pair graph. No new node or direction, and no arrow endpoint changes. Reported degradation, competition and signaling findings remain distinct from reverse-feeding implications, model-specific mediation and reciprocal fitness classification.
456otherrecords, all921caches and raw non-graph blocks unchanged. All56existing network warnings preserved, zero structural defects. Two explicit participant users added; legacy census measured unchanged. Deterministic rendering and exact HTML-description parsing, not browser screenshots. Informational full-corpus snippet audit is not clean-corpus certification. Loader #1703 and metadata #1742 remain unresolved.
Adversarial review caught an incorrect obligacy premise after the initial816-test pass. That validation is archived as superseded. The first two naphthalene nodes retain qualified SYNTROPHY under the actual schema; two correction histories and a new schema-contract regression record the correction. All current gates were rerun.
Postcommit check-docs-current passed clean, SHA256 53728b911f3b8fa07db3882d791ae29c452702cf2d2994623549369af9737b07. Decision ledger,44actual output records/digests and self-adversarial review committed under reports/causal_graph_review for batch90. Corpus280reviewed/132pending/48needs_research. Four exact-system primary abstracts, not complete main texts; source-access failures documented. No paid Edison submission, new genetic designs, harmful-algal optimization, toxin guidance or experimental protocols. Not independent approval or corpus completion.
Source Limits
Dependency
Draft depends on #1737. Do not merge into the topic parent. Require exact-head CI and protected-main queue after parent merge. Move dependents before deleting parent branches.