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Bound soil and mucin community causal claims (batch65) - #1570
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Source-based self-adversarial review at exact head e788ade; not independent approval.
Repairs #1566, #1567 and #1568 addressed; #1569 remains unresolved.
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Separate MSC1 persistence, early NAG growth and computational co-abundance from untested dependency.
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Qualify MSC2 chitin-sharing and Streptomyces induction arrows with assay and model limits.
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Separate MUC2 group-qPCR and extracellular acid endpoints from untested causal mediation.
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Read all three whole records and account for all8 original nodes and3 arrows. Three complete fresh primary main bodies and main text tables read; original figure pixels, separate supplements, raw data and executable models not audited. Numerical summaries remain author-reported, not independently recomputed.
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MSC1: retain compositional persistence with drift, not invariant membership or demonstrated codependency. Canonical nine-member roster is explicitly incomplete;31-versus-35 OTUs and Sect_C_4-versus-C2 source naming remain unresolved. Preserve prior workflow-arrow deletion and bacterial Bosea grounding.
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MSC1: positive comparisons concern early-exponential total OD on supplied10mM soluble NAG against the average of corresponding monocultures. The source reports no significant late-exponential difference. This is not partner-resolved biomass, reciprocal benefit, obligate syntrophy or chitin-polymer turnover. Four named canonical participants omit the unresolved Rhizobium isolate; V4 does not separate Ensifer OTUs.
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MSC1: pooled relative16S Pearson associations and betweenness hubs are computational, not experimentally demonstrated facilitation, niche partitioning or keystone necessity. Rhizobiales is an order. Soil chitin and liquid NAG assays must not be collapsed into one causal test. Source Table1 isolate mismatch, herbicide doses and conflicting Methods inequalities remain under1569.
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MSC2: preserve five monoculture chitin-growth phenotypes without assigning exclusive initial mixed-community donor roles. Distinguish100ppm monocultures from500ppm community growth, chitin+NAG preconditioning and18mM ammonium supply. Do not rewrite supported Sinorhizobium chitin use as nitrogen fixation merely because of its genus or existing497.
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MSC2: retain both existing biological arrows as HYPOTHESIZED. Primary Discussion proposes product sharing and resource-enablement of Streptomyces; lack of selective rescue/removal experiments limits certainty but does not justify deleting the source-supported model. Previously removed dangling outcome arrows stay absent.
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MSC2: GC-MS measured cell-pellet metabolites after supernatant removal, despite extracellular-pool wording in Introduction. NAG accumulation is not directly measured extracellular transfer. Mixed-bag FBA removes species boundaries and cannot establish actual partner exchange. Transcript comparisons are70vs118h within the community, not matched mono/community induction or direct enzyme activity.
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MSC2: preserve positive community-responsive Streptomyces observations and its approximately12% alignedRNA proportion at70h without treating RNA proportions as viable abundance or chitinase flux. NAG preconditioning can complicate repression/induction interpretation. Canonical source strain labels and genomes are preserved, not independently re-grounded.
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MUC2: preserve increased Akkermansia and decreased Prevotella qPCR estimates with no significant totalOD difference. Six group assays and calculatedCFU equivalents are not live colony counts or fourteen-strain resolution. Explicit participants are the inoculated roster, not proven endpoint survival. CAZy capacity classes summarize species-genome sets, not exact-strain enzyme measurements.
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MUC2: retain lower acetate and higher propionate/butyrate/formate as net72h extracellular concentrations. They are not production rates, traced mucin-carbon flux, identified producers or donor-recipient exchange. Remove the common-treatment composition-to-acid arrow without denying either positive endpoint. pH was not measured/controlled, daily medium replacement matters, and host effects were not tested.
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Review full biological diff and eight focused tests. Retarget both anchors of the existing MUC2 qPCR gap without altering its rationale/evidence. Preserve culture-accession safeguards805/806/808 and grounding statuses807; ambiguous labels remain a separate issue.457 other records,920 caches and raw non-graph blocks unchanged;46 baseline warnings retained exactly and no structural defects or auditor changes.
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Actual schema, strict, terms, references, snippets, histories, corpus audit, deterministic renders and regression outputs captured. Exact descriptions parsed across456 pages, not browser screenshots. Coarse roster/scope census unchanged and does not certify identity or flux. Post-commit docs-current remains a separate publication gate.
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Deduplication covered861 all-state issue titles/bodies and28 scoped ignored/hidden local files;8 matching bodies read along with prior MSC1 workflow and MUC2 curation histories, not every PR/comment/local artifact.1566-1568 addressed but OPEN until protected-main merge;1569 remains OPEN afterward. Exact-head self-review is COMMENT, not independent approval. No new causal structure or paid Edison submission.
595 passed in 208.89s (0:03:28); eight new focused tests. Actual schema, strict, term, reference, snippet and history gates passed. 48 record snippets match selected caches; all12 graph excerpts independently match fresh primary text. All920 caches unchanged. MATCH does not certify historical provenance or non-graph claims;1569 remains unresolved. CLI Total checks counts reported issues, not executed checks;476/1091/1095 remain limitations.
All8 original nodes retained;3 original arrows reviewed. Two MSC2 biological arrows retained as hypotheses; one MUC2 common-treatment mediation arrow removed. MSC1 storage persistence, early NAG totalOD and computational soil co-abundance remain distinct. MSC2 cell-pellet metabolomics is not extracellular transfer; temporal community transcripts are not matched induction and mixed-bag FBA removes species boundaries. MUC2 group-qPCR and net supernatant concentrations do not establish viable counts, partner flux or composition-mediated effects. No new structure or paid Edison submission.
Zero structural errors;46 baseline network warnings preserved exactly, none added or removed.457 other records and raw non-graph blocks unchanged. Canonical taxonomy preserved, not recertified. Explicit participants identify partial or input rosters and assay/focal subsets, not necessarily final abundance or assigned partner activity. Measured coarse roster/scope census:{"community_level_only": 267, "credited_solely_by_the_rule": 1238, "mixed": 124, "records": 460, "taxa": 1507, "with_community_level": 391}. This does not resolve incomplete rosters, culture identities or flux.
Repeat renders deterministic and exact descriptions parsed across456 pages, not browser screenshots. Three complete fresh primary bodies and main text tables read; original figure pixels, separate supplements, raw data and executable models not audited. Author-reported numerical summaries were not recomputed. Source protocol and identity inconsistencies remain explicit. Post-commit just check-docs-current exited0 with clean tree; log SHA256 c1e8bea36af781816112aca5a18f3c871e419607046929b50e7161d85958f514.
Every-node/arrow decisions,32 command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch65. Not independent approval. Corpus209 reviewed /230 pending /21 needs_research; corpus-wide work is unfinished.
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 7d8b624fc0b4fb4f5d8b6830694f62a51acdd6e9. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head e788ade71f030cd1c482ac279b5a6c554aa1f467, 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 4bfbd2986b4b136dbb20071f33b8035e9a0831fa4a564d94b5cf1c43fc60a424). 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 daf2f1d591e6e1901c47eb9f9b8caffdfa43896d
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 504f7efeff7a6e9ad6b165f1ff4514fae0eec98c.
The batch-owned binary patch is byte-identical
(SHA-256 4bfbd2986b4b136dbb20071f33b8035e9a0831fa4a564d94b5cf1c43fc60a424); 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 924dffab6b2459c45c45c090461027d5bb1c0896. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head daf2f1d591e6e1901c47eb9f9b8caffdfa43896d, 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 4bfbd2986b4b136dbb20071f33b8035e9a0831fa4a564d94b5cf1c43fc60a424). 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 a0b1fae032a8c970dd3eb67d837c782c97384b39.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 4bfbd2986b4b136dbb20071f33b8035e9a0831fa4a564d94b5cf1c43fc60a424.
Tree 8b0c03ff95bf635015b301c0e8e3e74e72eb50fd matches the independently computed clean merge.
Compared with historical tree a6374209d58abbe314e471bed9c57a1659e3f4a6, 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 #1566.
Closes #1567.
Closes #1568.
Related #1569 remains OPEN for incomplete/ambiguous identities, role and protocol metadata, and primary-source reporting inconsistencies.
Adversarial Review
Verification And Output Records
595 passed in 208.89s (0:03:28); eight new focused tests. Actual schema, strict, term, reference, snippet and history gates passed. 48 record snippets match selected caches; all12 graph excerpts independently match fresh primary text. All920 caches unchanged. MATCH does not certify historical provenance or non-graph claims;1569 remains unresolved. CLI Total checks counts reported issues, not executed checks;476/1091/1095 remain limitations.
All8 original nodes retained;3 original arrows reviewed. Two MSC2 biological arrows retained as hypotheses; one MUC2 common-treatment mediation arrow removed. MSC1 storage persistence, early NAG totalOD and computational soil co-abundance remain distinct. MSC2 cell-pellet metabolomics is not extracellular transfer; temporal community transcripts are not matched induction and mixed-bag FBA removes species boundaries. MUC2 group-qPCR and net supernatant concentrations do not establish viable counts, partner flux or composition-mediated effects. No new structure or paid Edison submission.
Zero structural errors;46 baseline network warnings preserved exactly, none added or removed.457 other records and raw non-graph blocks unchanged. Canonical taxonomy preserved, not recertified. Explicit participants identify partial or input rosters and assay/focal subsets, not necessarily final abundance or assigned partner activity. Measured coarse roster/scope census:{"community_level_only": 267, "credited_solely_by_the_rule": 1238, "mixed": 124, "records": 460, "taxa": 1507, "with_community_level": 391}. This does not resolve incomplete rosters, culture identities or flux.
Repeat renders deterministic and exact descriptions parsed across456 pages, not browser screenshots. Three complete fresh primary bodies and main text tables read; original figure pixels, separate supplements, raw data and executable models not audited. Author-reported numerical summaries were not recomputed. Source protocol and identity inconsistencies remain explicit. Post-commit just check-docs-current exited0 with clean tree; log SHA256 c1e8bea36af781816112aca5a18f3c871e419607046929b50e7161d85958f514.
Every-node/arrow decisions,32 command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch65. Not independent approval. Corpus209 reviewed /230 pending /21 needs_research; corpus-wide work is unfinished.
Dependency
Draft depends on #1565. 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.