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Bound regolith, lupin and MAMC causal claims (batch64) - #1565
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Source-based self-adversarial review at exact head 5b6301d; not independent approval.
Repairs #1561, #1562 and #1563 addressed; #1564 remains unresolved.
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Separate regolith attachment, phosphorus and living-host outcomes from proposed mediation.
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Scope SC-7 growth, transcription and assembly observations to the tested assays and input roster.
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Remove MAMC procedure nodes and bound the retained M48 FTIR endpoint.
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Read all three whole records and account for9 original nodes and2 arrows. Three complete fresh primary main bodies and complete Nicotiana2026 correction read; embedded text tables inspected. MAMC image-only Table1 cells, original figure pixels, separate supplements and raw data were not audited. Numerical endpoints are author-reported, not independently recomputed.
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Nicotiana: separate five individual-strain flask treatments from the three-strain1:1:1 plant inoculum. Attached microbial biomass phosphorus is an operational pool, not direct biofilm imaging. Its regression with inferred dissociation and pH correlation do not selectively prove attachment or named-acid mediation. Retain these hypotheses in prose, not asserted arrows or GO biofilm activity.
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Nicotiana: preserve increased phosphorus endpoints for three effective strains and limited activity of two comparators. Total available phosphorus pools include dissolved, biomass and adsorbed fractions and are not all freely dissolved inorganic phosphate. Remove unmeasured oxalate/citrate and CROSS_FEEDING assertions while retaining phosphate context.
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Nicotiana: retain the18-day conditioning benefit, percentages of control rather than percent increases, and adverse day6 seedling response without pretreatment. Controls were not pre-cultured and MS supplied phosphorus from day6. Correct living-host evidence; these outcomes do not isolate exclusive phosphorus mediation or lunar-environment performance. The2026 correction only fixes particle-size labels.
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Lupin: preserve positive SC7 growth in both systems and existing richness-versus-membership confounding. Main Table1 confirms twelve input strain codes; keep both Streptomyces strain names despite their shared genus CURIE. Input membership is not dominance, equal harvest abundance, complete host/background membership or independently verified genome identity.
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Lupin: distinguish FlowPot root RNA-seq from non-sterile CAS-soil microbiome measurements. Expression/enrichment, leghemoglobin and genomic annotations are not hormone secretion, nitrogen-fixation rate or a demonstrated growth mediator. No transcription-to-growth or assembly-to-growth arrow is introduced.
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Lupin: relative genus profiles are not absolute exclusion or exact inoculant persistence. In-silico ASV removal is not a biological knockout. Disclose conflicting PERMANOVA wording/p=.001 and preserve observational conclusions without certifying blanket significance. Source timing contradiction and missing-host/dominance metadata remain under1564.
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MAMC: remove enrichment and reductive screening nodes as procedures; preserve earlier workflow-arrow deletion. Retain M48 study isolate IDs13/18/25/29/68 and its positive performance. FTIR estimates43.01/39.65/69.18% average50.6%, not50.6% each, gravimetric mass loss, mineralization or partner-resolved flux.
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MAMC: metabolic functional groups and isolate secretome assays do not establish niche partitioning, directed exchange or division of labor in M48. Keep source-reported16S identification labels with identity caveats; canonical labels are not independently certified culture-strain equivalents. Approximately3e4 cells/mL per strain is stated for the18-strain control; separate non-graph metadata repair stays open.
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Review full biological diff and eight focused tests.457 other records,920 caches and raw non-graph blocks unchanged. Canonical taxonomy preserved, not recertified.46 baseline network warnings retained exactly with zero structural defects or auditor-rule changes. Coarse roster/scope census unchanged and does not resolve missing hosts or strain identity.
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Actual schema, strict, terms, references, snippets, histories, corpus audit, deterministic render and regression outputs captured. Exact descriptions parsed across456 pages, not browser screenshots. Post-commit docs-current remains a separate publication gate.
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Deduplication covered857 all-state issue titles/bodies with no exact matches and21 scoped ignored/hidden local files. Existing Lupinus review and MAMC workflow history read, not every PR/comment/local match.1561-1563 addressed but OPEN until protected-main merge;1564 remains OPEN afterward. Exact-head self-review is COMMENT, not independent approval. No new graph structure or paid Edison submission.
587 passed in 201.44s (0:03:21); eight new focused tests. Actual schema, strict, terms, reference, snippet and history gates passed. 67 record snippets match selected caches; all9 graph excerpts independently match fresh primary text. All920 caches unchanged. MATCH does not certify historical provenance/non-graph claims;1564 remains unresolved. CLI Total checks counts reported issues, not executed checks;476/1091/1095 remain limitations.
All9 original nodes reviewed:7 retained observations,2 removed MAMC procedure nodes and2 to0 Nicotiana mediation arrows. Regolith attachment and phosphorus pools are not demonstrated biofilm/named-acid mediators. Preserve positive plant responses, adverse early unconditioned-treatment effects and subsequent MS supplementation. Lupin growth, FlowPot transcription and CAS-soil relative profiles remain distinct. MAMC's50.6% mean of three FTIR fraction estimates is not50.6% each or direct mass loss. 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 tested panels/inoculants, not missing hosts or whole background communities. MAMC strain-like16S labels are not independently verified culture identities. 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 missing hosts or strain identity.
Repeat renders deterministic and exact descriptions parsed across456 pages, not browser screenshots. Three complete fresh primary bodies, embedded text tables and the complete2026 Nicotiana correction read; the correction changes particle-size labels only. MAMC image-only Table1 cells, original figure pixels, separate supplements and raw data were not audited. Author-reported numerical summaries were not recomputed. Lupin statistical/timing inconsistencies remain explicit. Post-commit just check-docs-current exited0 with clean tree; log SHA256 725ae9eab0f5650a3aeae7918ec6179037982400ab8c3864cc6f08231e276ef7.
Every-node/arrow decisions,32 command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch64. Not independent approval. Corpus206 reviewed /233 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 4e8a272baad535a87bc2f0a71ce62824683412f9. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 5b6301d3c4c61bbc12df8d7b7dd4f0e55d444e7e, 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 08cc1f76a101e897ee1ccb1040a875de62d2db0d4085b9e7b3c81709b6850c91). 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 73b589d0d8a13139035638a04f2d9e53227dc9c8
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 3ff1576f047673d255293d285e23156fd57ad1e3.
The batch-owned binary patch is byte-identical
(SHA-256 08cc1f76a101e897ee1ccb1040a875de62d2db0d4085b9e7b3c81709b6850c91); 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 99ae2a2bd8724662f4725f0450c2fe5d05373399. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 73b589d0d8a13139035638a04f2d9e53227dc9c8, 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 08cc1f76a101e897ee1ccb1040a875de62d2db0d4085b9e7b3c81709b6850c91). 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 1851f6296906ea6e3ecd2c2838579cc3c26fe2b2.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 08cc1f76a101e897ee1ccb1040a875de62d2db0d4085b9e7b3c81709b6850c91.
Tree ba2f5b18a86d468a189b6b6eb890c37ea52a9bbb matches the independently computed clean merge.
Compared with historical tree 299e27af667f68861d59a5b6ee0002e32ee85757, 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 #1561.
Closes #1562.
Closes #1563.
Related #1564 remains OPEN for host/strain/role identities, assay metadata, non-graph mechanisms and primary-source reporting inconsistencies.
Adversarial Review
Verification And Output Records
587 passed in 201.44s (0:03:21); eight new focused tests. Actual schema, strict, terms, reference, snippet and history gates passed. 67 record snippets match selected caches; all9 graph excerpts independently match fresh primary text. All920 caches unchanged. MATCH does not certify historical provenance/non-graph claims;1564 remains unresolved. CLI Total checks counts reported issues, not executed checks;476/1091/1095 remain limitations.
All9 original nodes reviewed:7 retained observations,2 removed MAMC procedure nodes and2 to0 Nicotiana mediation arrows. Regolith attachment and phosphorus pools are not demonstrated biofilm/named-acid mediators. Preserve positive plant responses, adverse early unconditioned-treatment effects and subsequent MS supplementation. Lupin growth, FlowPot transcription and CAS-soil relative profiles remain distinct. MAMC's50.6% mean of three FTIR fraction estimates is not50.6% each or direct mass loss. 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 tested panels/inoculants, not missing hosts or whole background communities. MAMC strain-like16S labels are not independently verified culture identities. 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 missing hosts or strain identity.
Repeat renders deterministic and exact descriptions parsed across456 pages, not browser screenshots. Three complete fresh primary bodies, embedded text tables and the complete2026 Nicotiana correction read; the correction changes particle-size labels only. MAMC image-only Table1 cells, original figure pixels, separate supplements and raw data were not audited. Author-reported numerical summaries were not recomputed. Lupin statistical/timing inconsistencies remain explicit. Post-commit just check-docs-current exited0 with clean tree; log SHA256 725ae9eab0f5650a3aeae7918ec6179037982400ab8c3864cc6f08231e276ef7.
Every-node/arrow decisions,32 command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch64. Not independent approval. Corpus206 reviewed /233 pending /21 needs_research; corpus-wide work is unfinished.
Dependency
Draft depends on #1560. 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.