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Bound lake and Mars-simulant causal claims (batch62) - #1555
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Source-based self-adversarial review at exact head e17817e; not independent approval.
Repairs #1550, #1551 and #1552 addressed; #1553 and #1554 remain unresolved.
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Bound Lac Pavin depth-associated genetic potential and remove common-gradient arrows.
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Separate oxygen guild selection from the conditional Methylomonas-to-Methylobacter model.
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Separate living-host nodulation, nifH promoter activity and substrate phenotypes.
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Read whole three records and all four fresh primary main bodies, Methods, Results, Discussion and embedded captions/table text. Account for all9 original nodes and6 arrows. Original figure pixels, separate supplements, raw data and executable models not audited; no invented supplementary-cell or reproduced-flux claims.
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Lac Pavin: preserve depth-associated genomic potential, not measured flux or expression. Drop both common-gradient arrows; oxygen co-varies with other geochemistry and is not isolated experimentally. Retain low-abundance anoxic methane oxidizers and anoxic mcr occurrence, without absolute spatial exclusion or absence inferred from incomplete genome recovery.
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Lac Pavin: distinguish CPR/DPANN II/III and III RuBisCO nucleotide-associated incorporation from complete Calvin-cycle autotrophy. Weak CPR gene-repertoire differentiation and host-selection hypothesis remain explicit. Canonical Archaea/CPR/DPANN participants are a partial roster, not a substitute for missing non-CPR bacterial lineages.
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Washington: positive guild carbon coupling is retained as inferred family-level CROSS_FEEDING with PARTIAL support. Remove untraced methanol assignment; supplied methane is external context, not direct donor transfer. Prior isotope findings are not newly measured in the 2015 experiment, and reciprocal benefit/mechanism is unresolved.
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Washington: retain oxygen-feeding-regime selection of relative guild composition, including hypoxic periods, intermediate mixtures and replicate exceptions. Drop the bridge to a separate two-methanotroph model; those partners are not the two different functional guilds. Relative 16S does not prove absolute viable abundance.
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Washington model: correct reported formaldehyde direction to Methylomonas -> Methylobacter. Preserve conditional synthetic uptake and lack of uptake under sediment constraints. MB:ML ratios0.05:1 and9.3:1 are imposed, not recovered predictions. CO2 is environmental export; borrowed parameters, optimization and inhibition constraints bound interpretation.
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Washington source contradictions are not silently resolved: nutrient-rich dominance and formaldehyde-export wording conflict. Keep reported conditional transfer with PARTIAL support and source uncertainty;1554 requests S4/SBML/solution or author clarification. Public supplemental HTTP500 and blocked web access do not justify bypass or a claim that supplements were inspected.
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Mars: living-host IN_VIVO evidence, alternative S. meliloti2011/S. medicaeWSM419 inoculations and S. meliloti1021-only reporter are distinct. Preserve nodule count exceptions, promoter activity and plant mass/lateral-root observations. Remove N2/ammonia mediator assignment and both anatomical/conclusion arrows; neither establishes flux, delivery, mutual benefit or causal induction.
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Mars: Results lateral-root reductions qualify the abstract. Earth greenhouse and simulants without perchlorates are not Mars atmosphere experiments. Chemical mediation is hypothetical; host identity remains missing from the canonical roster and1553 tracks non-graph repairs.
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Full biological diffs, participant registry and focused tests reviewed.457 other records and raw non-graph blocks,920 caches unchanged. Canonical roster/scope census unchanged; one newly exposed Methylosarcina connectivity warning is expected from omitting the misgrounded species, tracked1553. All36 prior warnings remain, no structural defects and no auditor-rule changes.
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Actual final-state schema, strict, terms, references, snippets, history, corpus audit, deterministic render and regression outputs captured. Exact descriptions parsed across456 pages, not browser screenshots. Post-commit docs-current is a separate publication gate.
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Deduplication:848 all-state issue titles/bodies and35 scoped ignored/hidden local matches.497 and related301 issue bodies read, not every comment/PR/local file.1550-1552 addressed but OPEN until protected-main merge;1553/1554 remain unresolved afterward. Exact-head self-review is COMMENT, never independent approval. No new causal structure or paid Edison job.
570 passed in 294.68s (0:04:54); nine new focused tests. Actual schema, strict, terms, reference, snippet and history gates passed. 73 record snippets match selected caches; all16 retained graph excerpts independently match four fresh primary main bodies. All920 caches unchanged. MATCH does not certify historical provenance or non-graph content;1553 and source discrepancy1554 remain unresolved. CLI Total checks counts reported issues, not executed checks;476/1091/1095 remain limitations.
All9 original nodes retained;6 to1 arrows. Drop common-driver, cross-study and anatomical/conclusion links; preserve oxygen-regime selection of relative guild composition. Lac Pavin is genomic potential, Washington formaldehyde transfer is a qualified conditional model result with corrected direction and imposed ratios, and Mars host reporter activity is not measured N2 flux or causal plant benefit. No new causal structure or paid Edison submissions.
Zero structural errors;36 baseline network warnings preserved plus1 exposed Methylosarcina connectivity warning tracked1553, from excluding a misgrounded species.457 other records and raw non-graph blocks unchanged. Canonical taxonomy preserved, not recertified. Measured roster/scope census:{"community_level_only": 267, "credited_solely_by_the_rule": 1238, "mixed": 124, "records": 460, "taxa": 1507, "with_community_level": 391}. This coarse census does not resolve missing/incorrect participants.
Repeat renders deterministic and exact descriptions parsed across456 pages, not browser screenshots. Original figure pixels, separate supplements, raw data and executable models were not audited. Public supplemental retrieval failed HTTP500; conflicting source wording is not guessed away. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 c4ba8a07ab5b8a17f74cede5c2a5e7a864446809023f1c3720070489952d4708.
Every-node/every-arrow decisions,32 command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch62. Not independent approval. Corpus200 reviewed /239 pending /21 needs_research; corpus-wide work is not complete.
Protected-main merge remains 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 772e10578c5eaeceaf10ac4f4a23f500daf6b847. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head e17817eb1d2af1655b83324f81854020205c7f29, 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 7b52721705316e2866a515b3817bfdb105567525abdddcd8042c836178a719df). 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 6a755e1f8b8846690ba3e16cf91b93e2cb48c6b0
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 3d6b5fbb945453e831a84a4703e1a5dbf3d3b725.
The batch-owned binary patch is byte-identical
(SHA-256 7b52721705316e2866a515b3817bfdb105567525abdddcd8042c836178a719df); 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 1e1cbb5577416006cdce461c39256d5740034d70. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 6a755e1f8b8846690ba3e16cf91b93e2cb48c6b0, 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 7b52721705316e2866a515b3817bfdb105567525abdddcd8042c836178a719df). 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 ab85be2e4e649fb6342bcc78a355552db7aeeef2.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 7b52721705316e2866a515b3817bfdb105567525abdddcd8042c836178a719df.
Tree b2d9b9bdc05d60862d5592cf4b2433d65f9a9953 matches the independently computed clean merge.
Compared with historical tree 837dc39c1f92dcddf39849b1a56899ac32c0d42d, 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 #1550.
Closes #1551.
Closes #1552.
Related #1553 and #1554 remain OPEN: unresolved taxonomy/non-graph metadata and contradictory model-paper wording.
Adversarial Review
Verification And Output Records
570 passed in 294.68s (0:04:54); nine new focused tests. Actual schema, strict, terms, reference, snippet and history gates passed. 73 record snippets match selected caches; all16 retained graph excerpts independently match four fresh primary main bodies. All920 caches unchanged. MATCH does not certify historical provenance or non-graph content;1553 and source discrepancy1554 remain unresolved. CLI Total checks counts reported issues, not executed checks;476/1091/1095 remain limitations.
All9 original nodes retained;6 to1 arrows. Drop common-driver, cross-study and anatomical/conclusion links; preserve oxygen-regime selection of relative guild composition. Lac Pavin is genomic potential, Washington formaldehyde transfer is a qualified conditional model result with corrected direction and imposed ratios, and Mars host reporter activity is not measured N2 flux or causal plant benefit. No new causal structure or paid Edison submissions.
Zero structural errors;36 baseline network warnings preserved plus1 exposed Methylosarcina connectivity warning tracked1553, from excluding a misgrounded species.457 other records and raw non-graph blocks unchanged. Canonical taxonomy preserved, not recertified. Measured roster/scope census:{"community_level_only": 267, "credited_solely_by_the_rule": 1238, "mixed": 124, "records": 460, "taxa": 1507, "with_community_level": 391}. This coarse census does not resolve missing/incorrect participants.
Repeat renders deterministic and exact descriptions parsed across456 pages, not browser screenshots. Original figure pixels, separate supplements, raw data and executable models were not audited. Public supplemental retrieval failed HTTP500; conflicting source wording is not guessed away. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 c4ba8a07ab5b8a17f74cede5c2a5e7a864446809023f1c3720070489952d4708.
Every-node/every-arrow decisions,32 command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch62. Not independent approval. Corpus200 reviewed /239 pending /21 needs_research; corpus-wide work is not complete.
Dependency
Draft depends on #1549. Do not merge into the topic parent. Require eligible exact-head CI and protected main queue after parent merges. Move dependent PRs before deleting parent branches.