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Bound nutrient exchange and rice SynCom causal claims (batch94) - #1760
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Source-based self-adversarial review at exact head 1b17429; not independent approval.
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Retain positive ammonium CROSS_FEEDING and its existing arrow with donor/recipient scope.; Retain positive organic-acid CROSS_FEEDING and its arrow, excluding unsupported ethanol/formate carbon transfer.; Retain reciprocal exchange, distinguishing engineered donor and adapted recipient contexts.
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Retain mineral-mediated electron storage without direct donor-recipient nutrient CROSS_FEEDING.; Retain light-driven oxidation and both existing directions, correcting discharge terminology.; Retain reduction and both existing directions, correcting charge terminology and removing transport misannotation.; Retain the observed reusable reservoir without SYNTROPHY or perpetual-cycle claims; remove secondary editorial evidence.
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Retain measured host-carbon-supported proliferation; qualify its existing mitigation arrow as a hypothesis.; Retain reported extracellular protonation/Al mitigation, with downstream mediation explicitly uncertain.; Retain the proposed legacy-P pathway as HYPOTHESIZED/PARTIAL, not quantified uptake.; Retain the primary 26.36% field-yield result, removing commentary from graph evidence.
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Retain complementary growth-associated contributions as PARTIAL without MUTUALISM or unverified stereochemistry.; Retain observed biocontrol and positive disease-index result without COMPETITION or compound-specific causal certainty.; Retain the concurrent greenhouse phenotype without COLONIZATION_FACILITATION or field/duckweed-intervention generalization.
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Fresh both-root baseline preceded papers. All four whole records,15originalnodes and14arrows accounted for;14nodes13existingdirections retained, one assembly node/arrow removed. No new topology.
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E.coli-R.palustris reciprocal CROSS_FEEDING remains positive, with donor/recipient scope. Consumed organic acids are distinguished from formate and ethanol excretion. Initial dry-run quote proof encountered a PDF page/figure boundary; the replacement quote directly supports acid use and exclusion of formate, and passes independent primary/cache matching. No genetic design or feedback extension.
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Magnetite reduction charges and oxidation discharges. Preserve the real reversible coculture cycle, not just an acyclic simplification. External light/electron-donor conditions bound the cycle. Mineral redox is not direct nutrient transfer, iron-ion transport, a resource-competition experiment or demonstrated syntrophic metabolic/fitness feedback. Current SYNTROPHY does not require obligacy. Both recorded taxa remain explicit; primary PMID evidence replaces the secondary editorial quote.
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Acid-soil assembly is experimental design and remains in that section, not an interaction node. Root-carbon use, extracellular protonation/Al mitigation and26.36%field yield remain positive. The primary abstract describes legacyP as promising; keep phosphorus PARTIAL and four mediation directions explicitly uncertain. Complete main text was not read and commentary does not substitute for it.
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Rice-duckweed full-text limitations constrain the graph: positive greenhouse growth/disease endpoints remain, metabolite-to-phenotype mediation is PARTIAL. Dropout contributions are not bacterial abundance, reciprocal fitness, competition or colonization facilitation. Unqualified2,3-butanediol does not establish the existing specific stereoisomer, so that graph grounding is removed rather than replaced by a guessed CURIE. Source conflicts about auxin roles and duckweed-comparison outcomes remain unresolved; no field efficacy or general safety claim.
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Two complete primary main texts and one fresh PMC main body read, plus primary acid-soil abstract/limited preview. Only E.coli page2/Figure1 visually inspected; no general supplement, raw-data or figure-pixel certification.21graph/new-discussion quotations freshly matched to independent source text and unchanged caches; lexical agreement is not entailment. Failed empty eScholarship/EuropePMC XML/pypdf attempts are not successful full-text access. No challenge bypass.
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All923baselinecaches,456otherrecords, prior histories/decisions and all non-graph raw blocks preserved. Four append-only histories record the changes. Explicit-participant fixture adds magnetite; legacy census changes are measured, not evidence for ecology. Existing source-cache licensing and provenance are not rewritten.
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Eight new tests and864combined regressions pass, plus focused schema/strict/term/reference/snippet/history gates. All56network warnings unchanged, zero structural defects. Exact HTML-description coverage and deterministic rendering are not browser screenshots. Reference checks ran on macOS, not Linux; issue1091 remains. Loader1703 remains outside certification.
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Ignored/hidden-inclusive local dedup and fresh all-state issue bodies recorded with exclusions; comments/PRs not exhaustive. Graph repairs1755-1758 remain open until protected-main merge;1759 remains a separate non-graph issue. Self-adversarial COMMENT is not independent approval. No Edison spend, new wet-lab protocol, branch-protection bypass or corpus-completion claim.
864 passed in 277.19s (0:04:37); eight new regressions. All four records passed schema, strict, term, reference, snippet and history checks.42 actual gate output records/digests are committed, alongside decisions, source provenance and self-adversarial findings under reports/causal_graph_review for batch94. Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; acid-soil primary is abstract bounded. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
All15originalnodes and14arrows reviewed;14nodes and13existingdirections retained. Experimental assembly node/arrow removed. Four records changed,456otherrecords and923baselinecaches preserved. No non-graph raw-block changes. Coverage292reviewed/120pending/48needs_research across460records. All56network warnings unchanged,zero structural defects. Measured participant census is not evidence of ecological mechanisms.
Deterministic page rendering and exact description parsing, not browser screenshots. Postcommit check-docs-current passed clean, SHA256 95c304578402d6726d19c7e898277198353bbb5a10b7c41ce782817cdb6562a2. Two complete primary main texts and one fresh PMC main body read; acid-soil source remains abstract/limited-preview bounded.21graph/new-discussion quotations freshly matched. Only E.coli page2/Figure1 inspected visually, not all figures or supplements. Full-corpus snippet audit is informational, not clean-corpus certification.
No new topology or paid Edison submission. Non-graph1759 remains open. Self-adversarial review is not independent approval. Protected-main merge 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 governance integration review at exact head 54b6e71c528717d166589263a14b7aba3a8aad8d. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 1b174298d4f58dc3222bbb020db2fc3ac123b865, 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 055446d6053c1ae68ace9d9f5a7572897773023ce0491d2f4365ddf2e055386c). 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 250d74907ec1d4ce9e1a56da3542e5200093cca8.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 055446d6053c1ae68ace9d9f5a7572897773023ce0491d2f4365ddf2e055386c.
Tree 4a6f185f7b435e4a9c996bf5b6bdfbafae5ef5a8 matches the independently computed clean merge.
Compared with historical tree 08fb75a9e22ab8124f64fc8290d5972dc2ba50c0, 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 #1755.
Closes #1756.
Closes #1757.
Closes #1758.
Non-graph #1759 remains open after this graph repair merges.
Adversarial Review
Verification And Output Records
864 passed in 277.19s (0:04:37); eight new regressions. All four records passed schema, strict, term, reference, snippet and history checks.42 actual gate output records/digests are committed, alongside decisions, source provenance and self-adversarial findings under reports/causal_graph_review for batch94. Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; acid-soil primary is abstract bounded. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
All15originalnodes and14arrows reviewed;14nodes and13existingdirections retained. Experimental assembly node/arrow removed. Four records changed,456otherrecords and923baselinecaches preserved. No non-graph raw-block changes. Coverage292reviewed/120pending/48needs_research across460records. All56network warnings unchanged,zero structural defects. Measured participant census is not evidence of ecological mechanisms.
Deterministic page rendering and exact description parsing, not browser screenshots. Postcommit check-docs-current passed clean, SHA256 95c304578402d6726d19c7e898277198353bbb5a10b7c41ce782817cdb6562a2. Two complete primary main texts and one fresh PMC main body read; acid-soil source remains abstract/limited-preview bounded.21graph/new-discussion quotations freshly matched. Only E.coli page2/Figure1 inspected visually, not all figures or supplements. Full-corpus snippet audit is informational, not clean-corpus certification.
No new topology or paid Edison submission. Non-graph1759 remains open. Self-adversarial review is not independent approval. Protected-main merge pending.
Source Limits
Dependency
Draft depends on #1754. Do not merge into the topic parent. Require exact-head CI and protected-main queue after parent merge. Move dependents before deleting parent branches.