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Bound coculture and living-host causal claims (batch63) - #1560
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Source-based self-adversarial review at exact head ba082c3; not independent approval.
Repairs #1556, #1557 and #1558 addressed; #1559 remains unresolved.
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Bound mangrove coculture outcomes to abstract-only assay and mediator evidence.
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Separate SC3 living-host preference, priority effects and invasion association.
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Separate lettuce compatibility screening, rhizosphere gene copies and plant outcomes.
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Read the three whole records and account for every original node/arrow. Complete Lotus and lettuce fresh main bodies, Methods, Results, Discussion and embedded captions read; mangrove complete primary abstract only. No original figure pixels, linked lettuce table cells, separate supplements or raw data audited. Numerical summaries are author-reported, not recomputed.
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Mangrove: retain both positive observations and zero arrows. Compare day6 coculture and day9 axenic maxima, not matched-time biomass. Full Methods do not establish partner-resolved measurement because they were unavailable. Metabolite production and physical association are not traced transfer, selective growth mediation, contact necessity or reciprocal benefit. Preserve earlier1154/1155 repairs.
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Lotus: distinguish SC3 living-host experiments from SC1 exudate and SC2 comparisons. Preserve mixed-community cognate-root preference and lack of preference in SC3 mono-associations. Neither implies that a specific member facilitates colonization or receives reciprocal benefit.
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Lotus: preserve four-week establishment plus two-week reciprocal challenge, higher early-arrival relative proportions and no significant total-load increase after secondary inoculation. These are not absolute exclusion, invariant abundance, equilibrium or selective niche-preemption/host-feedback tests.
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Lotus: preserve cognate-root invasion advantage and strain-index correlation, absent in rhizosphere. Remove the correlation and standing-community-context arrows without erasing the observed advantage. Causal mediator and later equilibrium remain unresolved.
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Lotus roster: do not silently certify three nodule isolates and unspecified family-associated bacterium IDs as16 SC3 members. Only canonical Lotus host is securely grounded for these nodes; missing comparator host and unverified microbial roster remain under1559. Public supplementaryFiles download ended with actual90s timeout and incomplete719804-byte archive; no contents certified and no access control bypassed.
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Lettuce: no inhibition zones establish assay-specific compatibility, not commensalism, universal non-antagonism or stable rhizosphere coexistence. Per-strain14L inoculum production is not a consortium-growth assay;543 already addressed that wording. Remove the preparation-to-establishment arrow.
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Lettuce: preserve amendment-conditioned nifH/phoD/BPP DNA-copy responses, not expression, nitrogen-fixation/phosphate flux, gene ownership or inoculant establishment. The paper expressly limits metabarcoding strain tracking. Four listed taxa are applied inoculants, not all rhizosphere members or missing host.
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Lettuce: preserve overall35% dry-biomass and average26% nutrient-content benefits with substrate/nutrient variation. Significant concentration increases onlyP/K and nonsignificant overall extracted-availability effect qualify the outcome. Remove IAA process assertion, mutualism and gene-copy-to-benefit mediation arrow. Earth greenhouse simulants are not lunar/Martian environments.
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Review full biological diff and focused tests.457 other records,920 caches and raw non-graph blocks unchanged. Canonical taxonomy preserved, not recertified. All37 baseline network warnings retained;9 explicit omitted-roster connectivity warnings tracked1559, with no structural defects or audit-rule change. Coarse roster/scope census unchanged; it does not certify within-community membership.
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Actual schema, strict, term, reference, snippet, history, 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:853 all-state issue titles/bodies and22 scoped ignored/hidden local matches; full matching1155/1154/1093/1082/595/543/497 bodies read, not every PR/comment/local match.1556-1558 addressed but OPEN until protected-main merge;1559 and existing unrelated issues remain OPEN. Exact-head self-review is COMMENT, never independent approval. No new structure or paid Edison submission.
579 passed in 206.57s (0:03:26); nine new focused tests. Actual schema, strict, terms, reference, snippet and history gates passed. 68 record snippets match selected caches; all12 graph excerpts independently match fresh primary text. All920 caches unchanged. MATCH does not certify historical provenance/non-graph claims;1559 remains unresolved. CLI Total checks counts reported issues, not executed checks;476/1091/1095 remain limitations.
All8 original nodes retained;4 to0 arrows. Remove correlation, experimental-context, screening and untested gene-copy mediation links while retaining positive observations. Mangrove different-day maxima and mediator limits are abstract-bounded. Lotus SC3 living-host preference, priority and root invasion remain distinct. Lettuce compatibility, conditional DNA-copy enrichment and plant treatment benefits do not prove strain establishment, flux, IAA mediation or reciprocal benefit. No new structure or paid Edison submission.
Zero structural errors;37 baseline network warnings preserved plus9 exposed Lotus roster-connectivity warnings under1559. Only the securely grounded canonical Lotus host is credited; uncertain microbial entries are not silently validated.457 other records and raw non-graph blocks unchanged. Canonical taxonomy preserved, not recertified. 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 within-community membership.
Repeat renders deterministic and exact descriptions parsed across456 pages, not browser screenshots. Complete Lotus/lettuce main bodies and embedded captions read; mangrove complete abstract only. No original figure pixels, linked lettuce table cells, separate supplements or raw data audited. Public Lotus supplement download timed out after90s with an incomplete archive; no contents certified. Author-reported numerical summaries were not recomputed. Post-commit just check-docs-current exited0 with clean tree; log SHA256 6b9365047ce5a45f0ca0d83be4e3b369cda17a0bd2c46be5b487793904805a2a.
Every-node/arrow decisions,32 command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch63. Not independent approval. Corpus203 reviewed /236 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 88e4b34b556d367e2e53ba377ef3355c24edaaa5. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head ba082c3e8c3f34f78e3f9dc32b35f57cc303bc7f, 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 56628353d3e70b18578634ddfd3923ba93d2c410f2f0ea78dccb66dadbcdf9b8). 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 e9ce314e5fe582bcc8089bcfcdd39ff2a9816709
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree d1a028f4cbbf74d50dda25651b6f5c5d3492e1e6.
The batch-owned binary patch is byte-identical
(SHA-256 56628353d3e70b18578634ddfd3923ba93d2c410f2f0ea78dccb66dadbcdf9b8); 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 1b9fab538c3a45d3376bf1a120ab2896b63722aa. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head e9ce314e5fe582bcc8089bcfcdd39ff2a9816709, 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 56628353d3e70b18578634ddfd3923ba93d2c410f2f0ea78dccb66dadbcdf9b8). 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 7d0f9a57c1433d5a441d9d9534ef0aae38f069b2.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 56628353d3e70b18578634ddfd3923ba93d2c410f2f0ea78dccb66dadbcdf9b8.
Tree 8bc4ab90176319708d7082eef8b9f5b3230b0ac1 matches the independently computed clean merge.
Compared with historical tree 245cf0a548a2617557e873493da9ed1e6c2e8aff, 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 #1556.
Closes #1557.
Closes #1558.
Related #1559 remains OPEN for unresolved taxonomy, protocol and non-graph metadata; existing #497/#1082 remain separate.
Adversarial Review
Verification And Output Records
579 passed in 206.57s (0:03:26); nine new focused tests. Actual schema, strict, terms, reference, snippet and history gates passed. 68 record snippets match selected caches; all12 graph excerpts independently match fresh primary text. All920 caches unchanged. MATCH does not certify historical provenance/non-graph claims;1559 remains unresolved. CLI Total checks counts reported issues, not executed checks;476/1091/1095 remain limitations.
All8 original nodes retained;4 to0 arrows. Remove correlation, experimental-context, screening and untested gene-copy mediation links while retaining positive observations. Mangrove different-day maxima and mediator limits are abstract-bounded. Lotus SC3 living-host preference, priority and root invasion remain distinct. Lettuce compatibility, conditional DNA-copy enrichment and plant treatment benefits do not prove strain establishment, flux, IAA mediation or reciprocal benefit. No new structure or paid Edison submission.
Zero structural errors;37 baseline network warnings preserved plus9 exposed Lotus roster-connectivity warnings under1559. Only the securely grounded canonical Lotus host is credited; uncertain microbial entries are not silently validated.457 other records and raw non-graph blocks unchanged. Canonical taxonomy preserved, not recertified. 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 within-community membership.
Repeat renders deterministic and exact descriptions parsed across456 pages, not browser screenshots. Complete Lotus/lettuce main bodies and embedded captions read; mangrove complete abstract only. No original figure pixels, linked lettuce table cells, separate supplements or raw data audited. Public Lotus supplement download timed out after90s with an incomplete archive; no contents certified. Author-reported numerical summaries were not recomputed. Post-commit just check-docs-current exited0 with clean tree; log SHA256 6b9365047ce5a45f0ca0d83be4e3b369cda17a0bd2c46be5b487793904805a2a.
Every-node/arrow decisions,32 command outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch63. Not independent approval. Corpus203 reviewed /236 pending /21 needs_research; corpus-wide work is unfinished.
Dependency
Draft depends on #1555. 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.