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Bound LBNL plant gut and soil graph claims (batch61) - #1549
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Source-based self-adversarial review at exact head c56006a; not independent approval.
Repairs #1545, #1546 and #1547 addressed; #1548 remains unresolved.
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Bound Brachypodium persistence, recovery and member-function claims to primary assays.
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Preserve modeled gut coexistence feedback and remove unsupported acetate and inference-workflow claims.
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Separate soil SynCom assay variants and remove assembly/storage graph procedures.
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Read all three whole records and fresh open-access primary main bodies, Methods, Results, Discussion and embedded captions/table text. Account for all15 original nodes and2 arrows. Original figure pixels, separate supplements, raw data and executable models not audited; flattened matrices not used to recurate exact gene-by-strain assignments.
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Brachypodium design and five-phylum assembly are procedures, not ecological causal nodes. Remove both while retaining design metadata and positive biological results. Retain genomic potential and member assay phenotypes as bounded context, not traced expression, transfer or host mediation.
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Brachypodium abstract stability is qualified by Results: six strains undetectable or below0.1% after three weeks in vitro, with more balanced host-associated profiles. Do not equate relative detection with viable counts or uniform15-member stability.
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Adversarial diff review caught mixed host/liquid evidence classification after the initial candidate. Replace the broad stability excerpt with direct host Results labeled IN_VIVO and preserve separate IN_VITRO low-detection evidence. Retain the initial31 actual outputs/digests as superseded; rerun all31 final-state gates.
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Brachypodium significant plant outcomes occur after rewatering; sustained-drought endpoints were not significantly improved. Root-tip responses are strain/condition dependent; root exudate recruitment and metabolite return remain hypotheses. Correct live-host evidence classification without claiming universal tip preference or migration tracking.
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Gut model predictions and effective signed interactions are not universal acetate cross-feeding or demonstrated niche partitioning. The acetate passage is prior-literature context. Keep model/experimental evidence distinct, acknowledge imperfect prediction and higher-order/parameter uncertainty, and do not turn OD-scaled abundance into viable-cell counts.
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Drop the gut inference-to-topology workflow arrow only. Retain topology-to-coexistence: coupled positive and negative effects implement negative feedback in fitted pairwise gLV models over tested parameter ranges, with CH-ER as an experimentally coexisting example. Do not erase this positive model mechanism or generalize to every full-community condition.
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Soil nutrient tests used18 starting strains; ratio panels and EcoFAB17/18 differ from the final16. Keep nutrient/ratio diversity and plant colonization as positive observations with correct variants/time bounds. Pseudomonas in-vitro effects do not transfer automatically to EcoFAB. Single inoculum batch and relic-DNA/relative-abundance limits remain explicit.
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Remove soil automated assembly and storage nodes while preserving their valid methodological outcomes in discussion. Taxon-dropout results remain described as context; proposed facilitation/competition is not silently minted into new causal structure. No new nodes/arrows; no paid Edison calls.
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Canonical taxa remain unchanged domain-level aggregate placeholders, explicitly named on all11 retained nodes. This is not resolved experimental membership. Non-graph taxonomy, ingredient and protocol defects remain separately OPEN under1548; raw non-graph blocks preserved, not recertified.
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Full biological diffs, participant registry and focused tests reviewed.457 other records and920 caches unchanged. Both-root participant census unchanged; no audit-rule changes.36 baseline network warnings preserved, no structural defects, deterministic rerenders and456-page exact description parser, not browser screenshots.
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844 all-state issue titles/bodies plus41 scoped ignored/hidden local matches searched; all10 matching issue bodies read, not every comment/PR/local match.1545-1547 addressed but OPEN until protected-main merge. Exact-head self-review is COMMENT, not independent approval. Post-commit docs-current remains a separate publication gate.
561 passed in 356.77s (0:05:56); nine new focused tests. Actual final-revision schema, strict, term, reference, snippet and history gates passed. 39 record snippets match selected caches; every retained graph excerpt independently matches fresh primary text. All920 reference caches unchanged. MATCH does not certify all historical cache provenance or non-graph content;1548 remains unresolved. CLI Total checks counts reported issues, not executed checks; coverage476, Linux DOI lookup1091 and writer artifact1095 remain limitations.
All15 original nodes and2 arrows reviewed: retain11 bounded biological/model nodes and1 model-feedback arrow; remove4 procedure nodes and1 inference-workflow arrow. Brachypodium host/liquid persistence, drought/rewatering and spatial response limits are explicit. Gut negative feedback remains a positive model result. Soil nutrient18, EcoFAB17/18 and final16 are distinguished. No new causal structure or paid Edison submissions.
Adversarial review corrected a remaining mixed host/liquid evidence classification. Initial31 gate outputs remain preserved as superseded, and all31 final-state gates were rerun before the separate primary-proof check. Zero structural errors; all36 baseline network warnings unchanged.457 other records and raw non-graph blocks unchanged. Canonical Bacteria entries remain aggregate placeholders, not resolved strain rosters. Measured unchanged census:{"community_level_only": 267, "credited_solely_by_the_rule": 1238, "mixed": 124, "records": 460, "taxa": 1507, "with_community_level": 391}.
Repeat renders deterministic and descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 5f1d6e7f2994991397c05f3c9e04e14c7f1fc8ff98b3a57e458dba5826e72235.
Every-node/every-arrow decisions,32 final command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch61. Not independent approval. Corpus197 reviewed /242 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 32820d08831611b6d9927f9ba8be6aba2d11c143. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head c56006a21ada62691625b6513f72f781cd5f8a18, 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 fb38821c6bdae6ef43123d9706a1ae2f0f3770464a624658da6a8a72771904e8). 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 6c7d556546a1a71a4bab4305e8ced1302814d60b
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 9e4692f3b1103f73de752cc38ddb15c303c5ad35.
The batch-owned binary patch is byte-identical
(SHA-256 fb38821c6bdae6ef43123d9706a1ae2f0f3770464a624658da6a8a72771904e8); 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 c381bf41bd3e0de4893f6f74c06005823fed4131. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 6c7d556546a1a71a4bab4305e8ced1302814d60b, 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 fb38821c6bdae6ef43123d9706a1ae2f0f3770464a624658da6a8a72771904e8). 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 2966431109afb2803c4d9acfe8b38ffcb37cf1fd.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 fb38821c6bdae6ef43123d9706a1ae2f0f3770464a624658da6a8a72771904e8.
Tree 22ca96583ea77edf7762ec6152d18911d654c0a9 matches the independently computed clean merge.
Compared with historical tree 7c0172caef108ad6609798f17db3e3b3eacbc326, 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 #1545.
Closes #1546.
Closes #1547.
Related #1548 remains OPEN: unresolved LBNL strain rosters and non-graph mechanism/protocol metadata.
Adversarial Review
Verification And Output Records
561 passed in 356.77s (0:05:56); nine new focused tests. Actual final-revision schema, strict, term, reference, snippet and history gates passed. 39 record snippets match selected caches; every retained graph excerpt independently matches fresh primary text. All920 reference caches unchanged. MATCH does not certify all historical cache provenance or non-graph content;1548 remains unresolved. CLI Total checks counts reported issues, not executed checks; coverage476, Linux DOI lookup1091 and writer artifact1095 remain limitations.
All15 original nodes and2 arrows reviewed: retain11 bounded biological/model nodes and1 model-feedback arrow; remove4 procedure nodes and1 inference-workflow arrow. Brachypodium host/liquid persistence, drought/rewatering and spatial response limits are explicit. Gut negative feedback remains a positive model result. Soil nutrient18, EcoFAB17/18 and final16 are distinguished. No new causal structure or paid Edison submissions.
Adversarial review corrected a remaining mixed host/liquid evidence classification. Initial31 gate outputs remain preserved as superseded, and all31 final-state gates were rerun before the separate primary-proof check. Zero structural errors; all36 baseline network warnings unchanged.457 other records and raw non-graph blocks unchanged. Canonical Bacteria entries remain aggregate placeholders, not resolved strain rosters. Measured unchanged census:{"community_level_only": 267, "credited_solely_by_the_rule": 1238, "mixed": 124, "records": 460, "taxa": 1507, "with_community_level": 391}.
Repeat renders deterministic and descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 5f1d6e7f2994991397c05f3c9e04e14c7f1fc8ff98b3a57e458dba5826e72235.
Every-node/every-arrow decisions,32 final command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch61. Not independent approval. Corpus197 reviewed /242 pending /21 needs_research; corpus-wide work is not complete.
Dependency
Draft depends on #1544. 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.