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Separate observed outcomes from causal inference (batch88) - #1731
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Source-based self-adversarial review at exact head 8c3f238; not independent approval. Repairs1724-1727addressed;765/1728/1729remain unfinished.
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Preserve TCE removal and Rhodococcus dominance without assigning active enzymes.; Preserve cDCE removal and genus dominance without invented exchange.; Preserve substrate selection and qualify its mediation of function.; Preserve restricted DCE removal and qualify toxicity and selection.
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Preserve community benefit without outcome-to-transcription causality.; Preserve biosynthesis transcription with source-attribution discrepancy.; Preserve transporter response without proven transfer or competition.; Preserve proposed carbon reciprocity as a hypothesis.
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Preserve enhanced aniline removal without certifying mineralization or exchange.
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Preserve the statistical phenotype with illustrative-ranking and absorbance limits.
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Fresh both-root baseline preceded papers; all11originalnodes6arrows have dispositions:10nodes4arrows retained, one assembly node and two outcome-to-expression directions removed. No new topology or reverse arrows.
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Propanotroph positive removal and genus-selection findings survive. Expression was not examined; gene content and abundance do not identify active enzymes or cross-feeding. Three existing directions remain with explicit partial/hypothesized mediation, not blanket deletion of selection findings.
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Prymnesium observed whole-community outcomes and expression responses remain. Correlation-like arrows do not establish outcome-to-transcription causality. Carbon reciprocity remains the authors hypothesis. No directly measured extracellular flux or competitive fitness cost is claimed.
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Prymnesium producer attribution is inconsistent across source sections. The disputed participant is omitted without substituting a new strain. Existing roles and proposed experiments remain outside certification; no new experimental procedures, genetic designs or growth-optimization details are added.
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Aniline retains the positive monoculture comparisons and previously corrected evidence. Analytical removal is not proof of complete mineralization or a named pathway; conclusions and main results differ in evidentiary scope. Supplements were not inspected, so source-exhaustive absence is not claimed.
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Factorial assembly is removed as a workflow. The existing statistical phenotype is preserved with illustrative-ranking and nonlinear-absorbance limits. The discussion no longer presupposes secreted or contact mechanisms. No biological mechanism or optimization procedure is invented.
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Five factorial panel members lose artificial connectivity supplied by the method node. Those warnings remain visible and exact-strain bounded, with metadata1729open. No taxonomy or auditor-rule change and no all-member credit assigned to a subset outcome.
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Two fresh main texts and two other fresh abstracts read. Factorial relevant cached results/discussion/method passages read after failed fresh retrieval, not a complete or independent full-text review. Three graph and one discussion matches are explicitly cache-only. No separate supplements, raw data or figure pixels audited.
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All921caches456otherrecords and raw non-graph blocks preserved; four append-only histories and ten focused tests. Legacy community-level census unchanged; all51oldwarnings retained with only five expected additions; zero structural defects.
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Executed local gates and deterministic HTML-description checks are not browser screenshots or generated-model loader certification. Loader1703remains open. Repairs1724-1727await protected-main merge;765/1728/1729remain open. No paid Edison job or inferred authorization. Self-review is not independent approval or corpus completion.
796 passed in 321.32s (0:05:21); ten new focused tests. Four schema/strict/term/reference/snippet/history gates passed. Four full-record reference-validator runs passed. CLI Total checks counts issues, not executed checks. Eighteen graph and seven discussion quotations match available primary/cache text;21are independent fresh-primary matches and4factorial quotes are existing-cache-only. Literal matching is not entailment or full-text certification.
All11originalnodes6arrows reviewed;10nodes4arrows retained. One experimental-method node and two correlation-like directions removed; no new topology. Positive community outcomes remain distinct from gene/transcript associations, mineralization inference and statistical interaction.
456otherrecords, all921caches and raw non-graph blocks unchanged. All51existing network findings preserved; five exact panel-member disconnections exposed, zero structural defects. Deterministic rendering and exact HTML-description parsing, not browser screenshots. Informational full-corpus snippet audit is not clean-corpus certification. Loader #1703 and follow-ups #765/#1728/#1729 remain unresolved.
Postcommit check-docs-current passed clean, SHA256 6235db47ea4c237894b53ca732cca7748dddd9f6f4716cd30b4199b62c702a25. Decision ledger,42actual output records/digests and self-adversarial review committed under reports/causal_graph_review for batch88. Corpus272reviewed/140pending/48needs_research. No Edison dry run or paid submission; no new biological mechanism or experimental design. Not independent approval or corpus completion.
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 review refreshed at exact head da9a0a84fbe53408a281b14dac37a86af73cb5d4
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 858317fa4a4fd442bd33cbe81483f1a0f30f9012.
The batch-owned binary patch is byte-identical
(SHA-256 12404504b060549fe66a9a3e951ce41a2f9ff216acc344c55602d555296e001d); 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 1480b15357b8c0ef9a4693503cfdfb5f5db5386b. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head da9a0a84fbe53408a281b14dac37a86af73cb5d4, 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 12404504b060549fe66a9a3e951ce41a2f9ff216acc344c55602d555296e001d). 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 3d20756860994c1fca1aebe0fad081aa17e49f3a.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 12404504b060549fe66a9a3e951ce41a2f9ff216acc344c55602d555296e001d.
Tree c7efa741c3081c745578fee1b0a0c819b89d5c71 matches the independently computed clean merge.
Compared with historical tree 7f352301fc33b792b662a81d258e91ccf8af5459, 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 #1724.
Closes #1725.
Closes #1726.
Closes #1727.
Follow-ups #765/#1728/#1729 remain OPEN after graph-repair merge.
Adversarial Review
Verification And Output Records
796 passed in 321.32s (0:05:21); ten new focused tests. Four schema/strict/term/reference/snippet/history gates passed. Four full-record reference-validator runs passed. CLI Total checks counts issues, not executed checks. Eighteen graph and seven discussion quotations match available primary/cache text;21are independent fresh-primary matches and4factorial quotes are existing-cache-only. Literal matching is not entailment or full-text certification.
All11originalnodes6arrows reviewed;10nodes4arrows retained. One experimental-method node and two correlation-like directions removed; no new topology. Positive community outcomes remain distinct from gene/transcript associations, mineralization inference and statistical interaction.
456otherrecords, all921caches and raw non-graph blocks unchanged. All51existing network findings preserved; five exact panel-member disconnections exposed, zero structural defects. Deterministic rendering and exact HTML-description parsing, not browser screenshots. Informational full-corpus snippet audit is not clean-corpus certification. Loader #1703 and follow-ups #765/#1728/#1729 remain unresolved.
Postcommit check-docs-current passed clean, SHA256 6235db47ea4c237894b53ca732cca7748dddd9f6f4716cd30b4199b62c702a25. Decision ledger,42actual output records/digests and self-adversarial review committed under reports/causal_graph_review for batch88. Corpus272reviewed/140pending/48needs_research. No Edison dry run or paid submission; no new biological mechanism or experimental design. Not independent approval or corpus completion.
Source Limits
Dependency
Draft depends on #1723. Do not merge into the topic parent. Require exact-head CI and protected-main queue after parent merge. Move dependents before deleting parent branches.