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Bound wetland cross-feeding and magnetite claims (batch66) - #1576
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Source-based self-adversarial review at exact head 63b4be2; not independent approval.
Repairs #1571-#1573 addressed; #1574 and #1575 unresolved.
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Bound wetland co-occurrence and Methanoregula predictions to observational and genomic evidence.
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Qualify MWF001 cross-feeding and finite coexistence; keep causal extension research open.
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Separate magnetite methane response from unvalidated DIET and constrained model flux.
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Read all three whole records and every original node. Nine nodes and zero original arrows retained, with one MUCC rename and intact discussion anchors. Earlier MUCC workflow and magnetite backward-edge deletions preserved. All three primary main texts and captions read; no original figure-pixel, separate-supplement, raw-data or executable-model audit. Extracted table artifacts contain no main-table cells.
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MUCC: eight core genera concern five marsh/swamp sites, not occupancy in every sample or all nine wetland sites. JLA is a swamp despite marsh shorthand. Canonical whole-community and Archaea/Bacteria guild entries are contextual placeholders, not a resolved eight-genus roster.
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MUCC: 12 samples/site, positive Spearman genus associations, environmental covariates and genus-matched MAG potential do not demonstrate exchange, niche partitioning or syntrophy. Whole-community network structure did not have the methanogen-network association. Preserve observations, not a causal network from analytic workflow.
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MUCC: Methanoregula relative dominance and transcription are not selectively tested drivers or methane flux. Methods describe 2018 expression and 2015 modeled production; temporal alignment and source counts need reconciliation. Candidate methylated-sulfide/methoxylated-substrate machinery is not demonstrated methanol use; graph methanol grounding removed while genomic potential remains.
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MWF001: retain experimentally supported cross-feeding interpretation and explicit four source strains. Spent-medium growth plus carbon-source nonusers support the interpretation, but stationary OD does not chemically establish complete resource depletion. The residual-resource exclusion applies to simulated spent medium. Generic CRM species/resources and unequal affinities are not exact-strain pathways or measured exchanged compounds.
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MWF001: finite eight-cycle persistence in 31 carbon-supplied conditions is not universal stability. Preserve the additional 5X-malate Ct loss, no-carbon Ml loss, citrate/inosine dilution exceptions and separate four-day chemostats. Pair effects are condition dependent, not universal reciprocity. Existing exact-byproduct gap and #1127/#1128 corrections preserved.
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MWF001: the candidate PARTIAL cross-feeding-to-coexistence arrow is scientifically plausible and remains explicitly unfinished under #1575. Free one-target Edison dry run passed; no paid run/report was completed and no new structure added. needs_research prevents falsely declaring this sparse graph complete.
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Magnetite: the 19% effect is relative to SULF_0.6, not full CTRL recovery or rescue at 1.2 g/L. Separate abiotic sulfide removal, unresolved sulfur species and no detected abiotic H2 do not selectively establish the biotic mediator or DIET. Keep the supported bulk outcome without an unsupported syntrophy type.
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Magnetite: only one biological replicate per condition was sequenced. Relative abundance cannot establish replicated absolute growth. Four representative GEMs are not every MAG in four broad guilds; putative SRB status and #913 caveats remain. Gap filling, expected-role curation, reactor-output constraints, trade-off0.7 and nonunique solution sampling mean feasibility, not independent validation.
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Magnetite: keep computational CROSS_FEEDING on acetate and amino-acid/organic-acid model nodes, explicitly HYPOTHESIZED. Mean sampled fluxes are not measured extracellular exchange or necessary mutualism. Existing direct-DIET gap, #914 arrow removal and #915 MAGN_0.6 medium restriction remain intact.
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Review full biological diff and eight focused tests. Canonical taxonomy, pre-existing discussions and append-only curation events preserved semantically.457 other records,920 caches and all raw non-graph blocks unchanged. Coarse participant census unchanged; this does not verify identity or exact partner flux.46 baseline network findings retained exactly; no structural errors or audit-rule changes.
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Actual schema, strict, term, reference, snippet, history, network, deterministic render and regression outputs recorded. Exact descriptions parsed over456 pages, not browser screenshots. One primary match requires straight/curly apostrophe equivalence; no cache rewrite. Post-commit docs-current is a separate publication gate.
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Dedup865 all-state issue titles/bodies and24 scoped ignored/hidden local matches; five relevant full issue bodies and prior graph histories read, not every PR/comment/artifact. #1571-#1573 addressed but OPEN until protected-main merge; #1574 metadata and #1575 research stay OPEN. Exact-head COMMENT self-review is not independent approval; corpus work remains unfinished.
603 passed in 214.64s (0:03:34); eight new focused tests. Actual schema, strict, term, reference, snippet and history gates passed. 69 record snippets match selected caches.16 graph excerpts independently match fresh primary text:15 after whitespace normalization and1 with straight/curly apostrophe equivalence.920 caches unchanged. CLI Total checks counts reported issues, not executed checks. MATCH is not scientific entailment or historical provenance certification. All920 caches unchanged;16 graph excerpts match fresh primary text (15 whitespace-only,1 apostrophe rendering equivalence). #1574 remains unresolved; broader #476/#1091/#1095 limitations persist.
Nine existing nodes retained, zero arrows; no new structure or provider spend. MWF001 candidate extension remains needs_research under #1575; its successful free dry run is not a completed report. Canonical taxonomy and raw non-graph blocks preserved, not recertified.457 other records unchanged. Zero structural errors;46 baseline network findings preserved exactly. Coarse roster/scope census unchanged and does not certify strain identity or actual flux.
Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots. Post-commit just check-docs-current passed with clean tree; log SHA256 73c37d210e54071479172f22fa5690a72d1d9c8176f2c5a9337593eab5144183. Every-node decisions,32 command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch66. Corpus211 reviewed /227 pending /22 needs_research: unfinished, not independent approval.
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 d6c0e3557de895ec1d10a726f72187473f2386c1. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 63b4be276f32559964d8dfa48d98c3186713926f, 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 4a2f7adc48919591cdba85221317fc5189e82e7f0cf6385adfc60a007d53be72). 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 15219376fd11758b7fc1cc4c4401ca1dfeff9906
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree a8a64105aa64b395a8b864cdeeda146948d77323.
The batch-owned binary patch is byte-identical
(SHA-256 4a2f7adc48919591cdba85221317fc5189e82e7f0cf6385adfc60a007d53be72); 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 215b84d05f677f6910c82b9ae7c817ba6e082017. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 15219376fd11758b7fc1cc4c4401ca1dfeff9906, 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 4a2f7adc48919591cdba85221317fc5189e82e7f0cf6385adfc60a007d53be72). 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 e2ffcfa67919230d0bf3acae7cd2e77032547c1c.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 4a2f7adc48919591cdba85221317fc5189e82e7f0cf6385adfc60a007d53be72.
Tree 930c844e5a181d81f9ccd6f179e3cb4505ed6630 matches the independently computed clean merge.
Compared with historical tree 84c3b3e67864739536508d32371cc5d7e9d725b1, 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 #1571.
Closes #1572.
Closes #1573.
Related #1574 (metadata) and #1575 (MWF001 causal extension) remain OPEN after graph repair merge.
Adversarial Review
Verification And Output Records
603 passed in 214.64s (0:03:34); eight new focused tests. Actual schema, strict, term, reference, snippet and history gates passed. 69 record snippets match selected caches.16 graph excerpts independently match fresh primary text:15 after whitespace normalization and1 with straight/curly apostrophe equivalence.920 caches unchanged. CLI Total checks counts reported issues, not executed checks. MATCH is not scientific entailment or historical provenance certification. All920 caches unchanged;16 graph excerpts match fresh primary text (15 whitespace-only,1 apostrophe rendering equivalence). #1574 remains unresolved; broader #476/#1091/#1095 limitations persist.
Nine existing nodes retained, zero arrows; no new structure or provider spend. MWF001 candidate extension remains needs_research under #1575; its successful free dry run is not a completed report. Canonical taxonomy and raw non-graph blocks preserved, not recertified.457 other records unchanged. Zero structural errors;46 baseline network findings preserved exactly. Coarse roster/scope census unchanged and does not certify strain identity or actual flux.
Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots. Post-commit just check-docs-current passed with clean tree; log SHA256 73c37d210e54071479172f22fa5690a72d1d9c8176f2c5a9337593eab5144183. Every-node decisions,32 command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch66. Corpus211 reviewed /227 pending /22 needs_research: unfinished, not independent approval.
Source Limits
Dependency
Draft depends on #1570. Do not merge into the topic parent. Require eligible exact-head CI and protected main queue after the parent merges. Move dependents before deleting parent branches.