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Bound inferred electron transfer in Geobacter-Clostridium (batch45) - #1479
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Source-based self-adversarial review at exact head 038ac9c; not independent approval.
Issue #1478 addressed after primary-text, graph diff and validation-output review.
The Geobacter-Clostridium graph now distinguishes conditional measured glycerol product yields from an inferred electron-transfer mediator.
- qPCR estimates growth, not electron uptake/current. The <0.6% balance assumes acetate as donor, 10% biomass allocation and 90% transfer. The existing mechanism and its one retained arrow are HYPOTHESIZED/PARTIAL.
- The 72-h +37% PDO/+38% butyrate and -16% butanol/-20% ethanol comparisons describe two responsive cultures among four initial cocultures. Eight of twelve subsequent cultures responded; growth/product regressions use responders. Reduced Clostridium growth does not establish mutualism.
- Merge the duplicate outcome into the measured response and remove the restatement arrow. Remove unsupported mutualism/syntrophy and electron-chain assertions from these nodes. Preserve exact two canonical participants.
- Update controversy anchors, proposed versus measured nanowire heterogeneity, and the obsolete DIET-filename note. The 2022 abstract supports a putative cobamide model; its full-body cell-free assay remains unverified.
Three original nodes to two; two arrows to one. No new causal structure or paid research for this repair.
455 passed in 168.19s (0:02:48); four new focused tests. Schema, strict, term, reference, snippet and history checks pass. All22 excerpts match the preserved caches; text matches do not establish scientific support or independent provenance. CLI Total checks:0 means no reported issues, not no executed checks; SupportingReference coverage remains incomplete under #476.
Both-root pre-paper baseline retained. Zero structural errors; all34 existing network warnings unchanged. All459 other records, all920 source caches, canonical taxonomy, non-graph raw blocks and prior history preserved. Stronger non-graph claims are not certified. Participant registry193 to194; one two-member community-level-only addition, no census-bound or production-logic changes. Repeat renders deterministic; descriptions parser-checked across all456 pages, without a browser screenshot claim.
Actual post-commit just check-docs-current exited0 with clean tree, log SHA256 0311d1bcc6ebdbb8df24381fc0df9d9321b7d0afc814fe38b9f615ab2a2c1bb4.
Whole record and all original nodes/arrows reviewed. Complete2017 primary main text/Methods/Table1/captions; complete2022 abstract only. No figure images, separate supplements, raw data or analysis code audited. Decisions, actual validation output/digests and limitations committed under reports/causal_graph_review, batch45.
Source-based self-adversarial review, not independent approval.
Protected main merge and full-corpus completion remain 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 b77a23f7d839efa48f3ca0834a774708ec744839
after protected main merge of #1328. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 3c84057a0efa0f1ca56f874dd8a7c7fab3ba0b8a.
The batch-owned binary patch is byte-identical
(SHA-256 48bd9115135c4c40d5d15816c88fc41cdb12d53a75f76d12a8a7237ee05a3bc3); 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 review refreshed at exact head d871f559fca25a1a4e570fdc4331570e8152b000
after protected main merge of #1334. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 3c84057a0efa0f1ca56f874dd8a7c7fab3ba0b8a.
The batch-owned binary patch is byte-identical
(SHA-256 48bd9115135c4c40d5d15816c88fc41cdb12d53a75f76d12a8a7237ee05a3bc3); 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 review refreshed at exact head b69023efbc25f4689cd6a322e1b320e2ae2aa102
after protected main merge of #1339. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 3c84057a0efa0f1ca56f874dd8a7c7fab3ba0b8a.
The batch-owned binary patch is byte-identical
(SHA-256 48bd9115135c4c40d5d15816c88fc41cdb12d53a75f76d12a8a7237ee05a3bc3); 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 review refreshed at exact head 83042c7a46e77460bb7fc987c321b1c8d765e212
after protected main merge of #1346. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 3c84057a0efa0f1ca56f874dd8a7c7fab3ba0b8a.
The batch-owned binary patch is byte-identical
(SHA-256 48bd9115135c4c40d5d15816c88fc41cdb12d53a75f76d12a8a7237ee05a3bc3); 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 review refreshed at exact head 271946cddf80bfc72cdd9bf7ab50c226550f2ccb
after protected main merge of #1350. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 3c84057a0efa0f1ca56f874dd8a7c7fab3ba0b8a.
The batch-owned binary patch is byte-identical
(SHA-256 48bd9115135c4c40d5d15816c88fc41cdb12d53a75f76d12a8a7237ee05a3bc3); 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 review refreshed at exact head f9487ac8a83792865d70443150244bff4728f246
after protected main merge of #1355. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 3c84057a0efa0f1ca56f874dd8a7c7fab3ba0b8a.
The batch-owned binary patch is byte-identical
(SHA-256 48bd9115135c4c40d5d15816c88fc41cdb12d53a75f76d12a8a7237ee05a3bc3); 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 integration review at exact head b91c9097c45fd73a72dfdcd1070d99a4936d1f78. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head f9487ac8a83792865d70443150244bff4728f246, 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 48bd9115135c4c40d5d15816c88fc41cdb12d53a75f76d12a8a7237ee05a3bc3). 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 809986cd700d0216eba09ccaf406a812ca2f37ec
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 533bf2346f21d9c8ca2671da09cc69ed38078efe.
The batch-owned binary patch is byte-identical
(SHA-256 48bd9115135c4c40d5d15816c88fc41cdb12d53a75f76d12a8a7237ee05a3bc3); 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 6822aeeaf1319ad5c851325fd97cd5ea8f279923. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 809986cd700d0216eba09ccaf406a812ca2f37ec, 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 48bd9115135c4c40d5d15816c88fc41cdb12d53a75f76d12a8a7237ee05a3bc3). 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 4e3a2167ae2a0e6013920032b1a6c791d8a2b1fc.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 48bd9115135c4c40d5d15816c88fc41cdb12d53a75f76d12a8a7237ee05a3bc3.
Tree a6b1efca1ce76466bcd908a92d64d5ba80f6ac1b matches the independently computed clean merge.
Compared with historical tree 40017efa833e321d8871d8e31ec989106437cdc0, 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 #1478.
The Geobacter-Clostridium graph now distinguishes conditional measured glycerol product yields from an inferred electron-transfer mediator.
Three original nodes to two; two arrows to one. No new causal structure or paid research for this repair.
Verification And Output Records
455 passed in 168.19s (0:02:48); four new focused tests. Schema, strict, term, reference, snippet and history checks pass. All22 excerpts match the preserved caches; text matches do not establish scientific support or independent provenance. CLI Total checks:0 means no reported issues, not no executed checks; SupportingReference coverage remains incomplete under #476.
Both-root pre-paper baseline retained. Zero structural errors; all34 existing network warnings unchanged. All459 other records, all920 source caches, canonical taxonomy, non-graph raw blocks and prior history preserved. Stronger non-graph claims are not certified. Participant registry193 to194; one two-member community-level-only addition, no census-bound or production-logic changes. Repeat renders deterministic; descriptions parser-checked across all456 pages, without a browser screenshot claim.
Actual post-commit just check-docs-current exited0 with clean tree, log SHA256 0311d1bcc6ebdbb8df24381fc0df9d9321b7d0afc814fe38b9f615ab2a2c1bb4.
Whole record and all original nodes/arrows reviewed. Complete2017 primary main text/Methods/Table1/captions; complete2022 abstract only. No figure images, separate supplements, raw data or analysis code audited. Decisions, actual validation output/digests and limitations committed under reports/causal_graph_review, batch45.
Source-based self-adversarial review, not independent approval.
Corpus:168 reviewed /280 pending /12 needs_research across460 records. Methanosaeta and Methanosarcina source review is deferred, not counted as completed here. Full-corpus completion is not claimed.
Dependency
Draft depends on #1477. Do not merge into the topic parent. Require eligible exact-head checks and the protected main queue after parents merge; move dependents before deleting merged branches.