Bound field selection, yeast rescue and hydrolysis causal claims (batch79)

[realmarcin]

Scope

Closes #1652.
Closes #1653.
Closes #1654.
Closes #1655.
Research #1656/#1657 and non-graph #1658 stay OPEN after graph-repair merge.

• Retain controlled isolate tolerance, correct uranyl grounding and keep bounded selection arrow; remove unsupported redox coupling.; Retain genus-level field enrichment without species/denitrification or nitrate-selective-toxicity overclaims.; Keep abstract-bounded redox potential without cross-feeding, measured flux or unmeasured ionic speciation.
• Preserve observed complementation with two-pair OD range, carbon-source and labeled-strain limits.; Retain directed sulfur-exchange model as hypothesized while preserving measured supplement rescue.; Preserve controlled ratio effects without universal growth, increasing-fraction or identical-endpoint claims.
• Preserve quantified DB1/DB2 cellulase and DB1 beta-glucosidase activities at isolate-assay scope.; Preserve positive DB2/DB13 xylan-hydrolase results and qualify their proposed contribution.; Retain assembled-consortium potential and both hypothesis arrows without promoting prospective benefits to measured synergy.
• Preserve significant optimized laboratory NDFD with null endpoints, formulation and inoculum-concentration limits.; Preserve predicted enzyme complement and Fig7 evidence without promoting annotation to demonstrated expression or synergy.; Preserve time-dependent cattle fermentation outcomes and nonsignificant fiber trends with animal-level replication limits.

Adversarial Review

• Fresh baseline across kb/communities and data/isolates preceded papers. Whole records and every12existing node/4arrow were read. One cross-study arrow removed and three bounded arrows retained. Sparse graphs remain in scope; topology is not invented to satisfy density.
• Oak Ridge has real isolate perturbation evidence for field selection, not merely a correlation. Preserve eight resistant contaminated-well Rhodanobacter isolates and186uncontaminated-well comparator isolates, recognizing provenance confounding. Neutral-pH resistance of some Pseudomonas strains prevents a universal genus-susceptibility claim.
• Low pH plus seven metal ions is eight selective ions including protons. Nitrate is correlated/toxic but not selectively inhibitory in the assayed pair; it may be an electron acceptor. Organic carbon and speciation alter thresholds, and no direct in situ perturbation was done. Preserve the selection arrow with these limits.
• Correct uranyl to official ChEBI43515, not free uranium6+. Remove the unproved species-specific source annotation from genus enrichment while preserving canonical taxonomy. Field clone-library redox potential is not flux or cross-feeding; remove tolerance-to-redox-guild coupling between different studies. Do not transfer isolate R2A culture conditions to the field community.
• Ogataea growth complementation is a positive result on glucose and methanol. The27.3-28.5range covers two pairs and does not establish significant superiority over FY00; methanol remains below FY00. Distinguish fluorescent tracking derivatives FY31/FY34 from all screening strains, preserving canonical labels and OD600medium evidence.
• Retain the directed sulfur-exchange model as hypothesized. Single-strain supplement rescue proves differential use of the tested compounds, not secretion or transfer. No rescue by sodium sulfide is not proof of a particular toxicity mechanism. Figure1/5schematics do not override the explicit isotope/metabolomics research gap.
• Controlled initial ratios affect growth: low initial met10fraction gives higher biomass, high met10ratios grow weakly while remaining biased. Endpoint met10bias is not necessarily increasing fraction in every culture, identical final ratio, equal establishment or long-term stability. Keep ratio biology without an unisolated mutualism annotation.
• Okeke isolate filter-paper cellulase, beta-glucosidase, xylanase and beta-xylosidase are positive measured results, and five-isolate consortium construction is retained. Accessible abstract proposes broad processing benefit rather than quantifying synergy. Keep both contribution arrows as hypotheses; no obligate syntrophy, lignin degradation or demonstrated product-inhibition relief inferred.
• Okeke normal publisher subscription preview and field publisher403 are respected. Inaccessible full text does not prove experiments absent. Three full primary main bodies, captions and three further abstracts read; no separate supplements, original figure pixels or raw datasets inspected. Whitespace-only primary/cache matching verifies21quotations but does not replace entailment review.
• Rumen Group41 preserves significant66.84%48hNDFD and20.56%reported relative improvement. Null DMD/gas in optimized five-member group must not inherit initial seven-member gas improvement. Concentrations are added-suspension descriptors, not final-bottle doses. Filtration-sterilized rumen fluid is not silently recast as a native living microbiota inoculum.
• Rumen CAZy/COG/KEGG annotations,47GH/19CBMfamily breadth and existing Fig7evidence survive. These predict function without measuring expression, metabolic exchange or pathway mediation. The in vitro-to-cattle workflow arrow stays removed.
• Cattle DM/NDF/ADF72htrends are nonsignificant despite broader source conclusions. Preserve early negative and later positive VFA effects, null propionate and lower NH3-N. Six cattle means three animals per treatment, not nine independent animals from three bags each. No durable engraftment or gene-to-outcome causality asserted.
• All456other records,920caches, canonical membership and raw non-graph blocks preserved; four new append-only histories. Prior258/650/981/1149/1150/1151repairs maintained. Metadata1658 remains open, including documented provenance-vocabulary inconsistency despite passing baseline gates; no nonexistent validation failure claimed.
• Ogataea missing topology remains1656with one11815character Edison LITERATURE dry run, zero provider submissions/credits and unanswered scoped approval. Okeke authorized full-text review remains1657. Repair1652-1655issues stay OPEN until protected-main merge; research/metadata remain afterward. Self-review is COMMENT, not independent approval or corpus completion.
• All focused gates, both-root inventory/network/rank, related regressions and deterministic rendering have actual logs/digests. Exact descriptions parsed across456pages are not browser screenshots. Postcommit docs-current and remote exact-head COMMENT are separate publication gates; protected lifecycle must preserve dependent branches.

Verification And Output Records

706 passed in 206.85s (0:03:26); ten new focused tests. All four schema, strict, term, full-record reference, snippet and history gates passed. All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. All21 graph quotations independently match fresh primary text and unchanged cache. Literal matching is not entailment. Three main bodies and three further primary abstracts were read; no recertification of every cache or non-graph field.

All12 original nodes and4arrows reviewed;12nodes3arrows remain. Four records repaired. Retain experimentally supported field selection, yeast complementation and ratio effects, measured isolate hydrolases, predicted rumen enzyme complement and positive laboratory/cattle outcomes with explicit assay limits. Yeast topology and authorized Okeke full-text review remain #1656/#1657; metadata #1658 stays OPEN.

All456 other records,920 caches and raw non-graph blocks verified unchanged. Canonical taxa and auditor rules unchanged. Zero structural defects;44 baseline warnings and connectivity census unchanged. Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots.

Postcommit just check-docs-current passed with clean tree; log SHA256 a88bd3cb387a52a96ab768d222638689e3246e55ebbc89531a8d1b04082aad26. Every-node/every-arrow decisions,40 actual check outputs/digests and source-based self-adversarial review committed under reports/causal_graph_review, batch79. Final focused rerun:19 passed. Corpus:252 reviewed,176 pending,32 needs_research. One Ogataea Edison dry run; zero paid submissions/credits, scoped question unanswered. Not independent approval or corpus completion.

Source Limits

• Fresh pre-paper baseline covers460 records and920 caches across both roots, including ignored/hidden files. Every12 existing node and4arrow was reviewed;12nodes3arrows remain. Four guarded repairs/history events;456 other records and all920 caches unchanged.
• Three complete primary main bodies read from fresh Europe PMC XML: metal-tolerance, Ogataea and rumen papers. Captions read; no embedded main-text tables in these XML files. Field clone-library, Rhodanobacter taxonomy and Okeke sources read at primary-abstract scope. No separate supplements, raw datasets or original figure pixels audited.
• Normal Okeke publisher access confirms subscription preview; field publisher403 and Microbiology Society full-text delivery failure respected. No access restriction bypass. Existing Okeke cache is abstract-only; inaccessible full text does not establish absence of experiments.
• All21 graph quotations independently match primary text and unchanged cache with whitespace-only comparison. Literal matching is not entailment. Early oversized combined/cache reads were truncated; fresh main texts were read in bounded chunks, and no absence finding relies on truncated output.
• Oak Ridge retains experimentally supported selection, not mere unqualified correlation. Isolate provenance, pH, mixture effects, organic matter and ion speciation bound transfer to field conditions. Nitrate toxicity was not selective in the strain comparison; genus enrichment is not species identity or redox flux. Official ChEBI confirms uranyl is43515, not free uranium6+.
• Ogataea retains cooperative growth, actual nutrient rescue and controlled ratio effects. Directed metabolite exchange is hypothesized, not measured. Two-pair OD range, methanol shortfall, distinct labeled tracking strains and weak-growth high-met10 ratios are explicit; endpoint bias is not identical convergence or long-term stability.
• Okeke positive isolate hydrolases and five-member construction remain. Both proposed hydrolytic-contribution arrows are retained as hypotheses; accessible abstract does not quantify synergy, product-inhibition relief or lignin degradation. Full-text acquisition remains needs_research, not a declaration of no experiments.
• Rumen significant optimized in vitro NDFD, predicted gene complement and time-dependent cattle fermentation are preserved. Initial seven-member gas effects differ from final five-member null gas result. Inoculum is not final bottle concentration; bags are subsamples of three cattle per group. Nonsignificant72h fiber trends are not proven improvement. No genome-to-outcome or workflow arrow added.
• One Ogataea Edison LITERATURE dry run used zero provider submissions/credits. Scoped paid question unanswered. Missing input/outcome and exchange-to-rescue structure stays1656; Okeke full-text follow-up1657 requires its own workflow if new topology becomes justified. Earlier denied/pending scopes unchanged.
• Dedup searched933 all-state issue titles/bodies and25 ignored/hidden-inclusive local matched files, excluding git/docs/site/cache. Matching258/650/981/1149/1150/1151 read; no exhaustive PR-comment audit. Prior field-community, medium, canonical-strain, Figure7 evidence and dangling/workflow-arrow fixes preserved.
• Repair issues1652-1655 remain OPEN until protected-main merge; research1656/1657 and metadata1658 remain OPEN afterward. Canonical membership and raw non-graph blocks are preserved, not certified. Rumen documented vocabulary inconsistency is not a claimed gate failure: baseline schema and strict checks passed. Self-adversarial review is not independent approval or corpus completion.

Dependency

Draft depends on #1651. Do not merge into the topic parent. Require eligible exact-head CI and protected main queue after the parent merges. Move dependents before deleting parent branches.

[realmarcin]

Source-based self-adversarial review at exact head 5099a66; not independent approval.

Repairs #1652-#1655 addressed; non-graph #1658 unresolved.

• Retain controlled isolate tolerance, correct uranyl grounding and keep bounded selection arrow; remove unsupported redox coupling.; Retain genus-level field enrichment without species/denitrification or nitrate-selective-toxicity overclaims.; Keep abstract-bounded redox potential without cross-feeding, measured flux or unmeasured ionic speciation.

• Preserve observed complementation with two-pair OD range, carbon-source and labeled-strain limits.; Retain directed sulfur-exchange model as hypothesized while preserving measured supplement rescue.; Preserve controlled ratio effects without universal growth, increasing-fraction or identical-endpoint claims.

• Preserve quantified DB1/DB2 cellulase and DB1 beta-glucosidase activities at isolate-assay scope.; Preserve positive DB2/DB13 xylan-hydrolase results and qualify their proposed contribution.; Retain assembled-consortium potential and both hypothesis arrows without promoting prospective benefits to measured synergy.

• Preserve significant optimized laboratory NDFD with null endpoints, formulation and inoculum-concentration limits.; Preserve predicted enzyme complement and Fig7 evidence without promoting annotation to demonstrated expression or synergy.; Preserve time-dependent cattle fermentation outcomes and nonsignificant fiber trends with animal-level replication limits.

• Fresh baseline across kb/communities and data/isolates preceded papers. Whole records and every12existing node/4arrow were read. One cross-study arrow removed and three bounded arrows retained. Sparse graphs remain in scope; topology is not invented to satisfy density.

• Oak Ridge has real isolate perturbation evidence for field selection, not merely a correlation. Preserve eight resistant contaminated-well Rhodanobacter isolates and186uncontaminated-well comparator isolates, recognizing provenance confounding. Neutral-pH resistance of some Pseudomonas strains prevents a universal genus-susceptibility claim.

• Low pH plus seven metal ions is eight selective ions including protons. Nitrate is correlated/toxic but not selectively inhibitory in the assayed pair; it may be an electron acceptor. Organic carbon and speciation alter thresholds, and no direct in situ perturbation was done. Preserve the selection arrow with these limits.

• Correct uranyl to official ChEBI43515, not free uranium6+. Remove the unproved species-specific source annotation from genus enrichment while preserving canonical taxonomy. Field clone-library redox potential is not flux or cross-feeding; remove tolerance-to-redox-guild coupling between different studies. Do not transfer isolate R2A culture conditions to the field community.

• Ogataea growth complementation is a positive result on glucose and methanol. The27.3-28.5range covers two pairs and does not establish significant superiority over FY00; methanol remains below FY00. Distinguish fluorescent tracking derivatives FY31/FY34 from all screening strains, preserving canonical labels and OD600medium evidence.

• Retain the directed sulfur-exchange model as hypothesized. Single-strain supplement rescue proves differential use of the tested compounds, not secretion or transfer. No rescue by sodium sulfide is not proof of a particular toxicity mechanism. Figure1/5schematics do not override the explicit isotope/metabolomics research gap.

• Controlled initial ratios affect growth: low initial met10fraction gives higher biomass, high met10ratios grow weakly while remaining biased. Endpoint met10bias is not necessarily increasing fraction in every culture, identical final ratio, equal establishment or long-term stability. Keep ratio biology without an unisolated mutualism annotation.

• Okeke isolate filter-paper cellulase, beta-glucosidase, xylanase and beta-xylosidase are positive measured results, and five-isolate consortium construction is retained. Accessible abstract proposes broad processing benefit rather than quantifying synergy. Keep both contribution arrows as hypotheses; no obligate syntrophy, lignin degradation or demonstrated product-inhibition relief inferred.

• Okeke normal publisher subscription preview and field publisher403 are respected. Inaccessible full text does not prove experiments absent. Three full primary main bodies, captions and three further abstracts read; no separate supplements, original figure pixels or raw datasets inspected. Whitespace-only primary/cache matching verifies21quotations but does not replace entailment review.

• Rumen Group41 preserves significant66.84%48hNDFD and20.56%reported relative improvement. Null DMD/gas in optimized five-member group must not inherit initial seven-member gas improvement. Concentrations are added-suspension descriptors, not final-bottle doses. Filtration-sterilized rumen fluid is not silently recast as a native living microbiota inoculum.

• Rumen CAZy/COG/KEGG annotations,47GH/19CBMfamily breadth and existing Fig7evidence survive. These predict function without measuring expression, metabolic exchange or pathway mediation. The in vitro-to-cattle workflow arrow stays removed.

• Cattle DM/NDF/ADF72htrends are nonsignificant despite broader source conclusions. Preserve early negative and later positive VFA effects, null propionate and lower NH3-N. Six cattle means three animals per treatment, not nine independent animals from three bags each. No durable engraftment or gene-to-outcome causality asserted.

• All456other records,920caches, canonical membership and raw non-graph blocks preserved; four new append-only histories. Prior258/650/981/1149/1150/1151repairs maintained. Metadata1658 remains open, including documented provenance-vocabulary inconsistency despite passing baseline gates; no nonexistent validation failure claimed.

• Ogataea missing topology remains1656with one11815character Edison LITERATURE dry run, zero provider submissions/credits and unanswered scoped approval. Okeke authorized full-text review remains1657. Repair1652-1655issues stay OPEN until protected-main merge; research/metadata remain afterward. Self-review is COMMENT, not independent approval or corpus completion.

• All focused gates, both-root inventory/network/rank, related regressions and deterministic rendering have actual logs/digests. Exact descriptions parsed across456pages are not browser screenshots. Postcommit docs-current and remote exact-head COMMENT are separate publication gates; protected lifecycle must preserve dependent branches.

706 passed in 206.85s (0:03:26); ten new focused tests. All four schema, strict, term, full-record reference, snippet and history gates passed. All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. All21 graph quotations independently match fresh primary text and unchanged cache. Literal matching is not entailment. Three main bodies and three further primary abstracts were read; no recertification of every cache or non-graph field.

All12 original nodes and4arrows reviewed;12nodes3arrows remain. Four records repaired. Retain experimentally supported field selection, yeast complementation and ratio effects, measured isolate hydrolases, predicted rumen enzyme complement and positive laboratory/cattle outcomes with explicit assay limits. Yeast topology and authorized Okeke full-text review remain #1656/#1657; metadata #1658 stays OPEN.

All456 other records,920 caches and raw non-graph blocks verified unchanged. Canonical taxa and auditor rules unchanged. Zero structural defects;44 baseline warnings and connectivity census unchanged. Repeat renders deterministic; exact descriptions parsed across456 pages, not browser screenshots.

Postcommit just check-docs-current passed with clean tree; log SHA256 a88bd3cb387a52a96ab768d222638689e3246e55ebbc89531a8d1b04082aad26. Every-node/every-arrow decisions,40 actual check outputs/digests and source-based self-adversarial review committed under reports/causal_graph_review, batch79. Final focused rerun:19 passed. Corpus:252 reviewed,176 pending,32 needs_research. One Ogataea Edison dry run; zero paid submissions/credits, scoped question unanswered. Not independent approval or corpus completion.

Protected-main merge pending.

[github-actions]

Network integrity findings

Warnings 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.

Network Integrity Audit Report
================================================================================

0 error, 44 warning across 16 records with findings
Only error-severity findings fail the build.

Algal_Methanotroph_Biogas_Valorization_Coculture
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Leptolyngbya' has no interactions

Total: 1 issues (0 error, 1 warning)

At_RSPHERE_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Flavobacterium sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhodococcus sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptomyces sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Variovorax sp.' has no interactions

Total: 5 issues (0 error, 5 warning)

Australian_Lead_Zinc_Polymetallic
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acidithiobacillus ferrooxidans' has no interactions
  [warning] DISCONNECTED: Taxon 'Leptospirillum ferriphilum' has no interactions

Total: 2 issues (0 error, 2 warning)

Bacillus_G12_Y4_X25_Tobacco_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Bacillus_siamensis_vallismortis_HT_Masson_Pine_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Fusarium oxysporum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)

Total: 3 issues (0 error, 3 warning)

Brocadia_Low_Nitrogen_Anammox_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Ca. Kuenenia early-acclimation lineage' has no interactions

Total: 1 issues (0 error, 1 warning)

Dangl_SynComm_35
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Escherichia coli DH5α' has no interactions
  [warning] DISCONNECTED: Taxon 'Flavobacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Microbacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Stenotrophomonas species' has no interactions
  [warning] DISCONNECTED: Taxon 'Xanthomonadales members' has no interactions

Total: 5 issues (0 error, 5 warning)

Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Methylophaga' has no interactions

Total: 1 issues (0 error, 1 warning)

East_River_Floodplain_Core_Microbiome
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acidobacteriota floodplain representatives' has no interactions
  [warning] DISCONNECTED: Taxon 'Nitrospirae core floodplain members' has no interactions

Total: 2 issues (0 error, 2 warning)

GLBRC_UFMP_Fermentation_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'RUG023 sp. (MAG SPH2)' has no interactions

Total: 1 issues (0 error, 1 warning)

KBase_Models_for_Zahmeeth_Original_PLOS
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Klebsiella' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas fluorescens' has no interactions

Total: 2 issues (0 error, 2 warning)

Lake_Washington_Methane_Oxygen_Methylotroph_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Methylosarcina' has no interactions

Total: 1 issues (0 error, 1 warning)

Lotus_LjSC3
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Burkholderiaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule210' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule215' has no interactions
  [warning] DISCONNECTED: Taxon 'Mesorhizobium sp. LjNodule218' has no interactions
  [warning] DISCONNECTED: Taxon 'Microbacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Oxalobacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Phyllobacteriaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonadaceae bacterium' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhizobiaceae bacterium' has no interactions

Total: 9 issues (0 error, 9 warning)

Nitrifying_Wastewater_Ammonia_Oxidizing_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Legionella MAGs' has no interactions

Total: 1 issues (0 error, 1 warning)

Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Space_Habitat_SevenMember_Stress_Tolerance_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acinetobacter radioresistens 50V1' has no interactions
  [warning] DISCONNECTED: Taxon 'Micrococcus luteus W4-Al-K1' has no interactions
  [warning] DISCONNECTED: Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas antarctica CMS 35T' has no interactions
  [warning] DISCONNECTED: Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptococcus halotolerans HTS9T' has no interactions

Total: 6 issues (0 error, 6 warning)

The full report is attached to the workflow run as an artifact.

[realmarcin]

Self-adversarial integration review at exact head 21f46bb10aee5f7c7d50573413cdadd05aaeeeda. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 5099a6687c72197d247aa549b1707d4047f9c0eb, 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 12156d5a425c0d62157e15f5b2974693e0f229f09e48034e11acf3a2f955c5c7). 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.

[realmarcin]

Self-adversarial review refreshed at exact head 8ea4e9e079606e37b17f0339439ba27a927a17f2
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d253f21164c70d5c4c76bc466923a251dd4945b7.
The batch-owned binary patch is byte-identical
(SHA-256 12156d5a425c0d62157e15f5b2974693e0f229f09e48034e11acf3a2f955c5c7); 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.

[realmarcin]

Self-adversarial governance integration review at exact head 1948b60dc67bebff654e5a80f182db491ef49c4f. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 8ea4e9e079606e37b17f0339439ba27a927a17f2, 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 12156d5a425c0d62157e15f5b2974693e0f229f09e48034e11acf3a2f955c5c7). 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.

[realmarcin]

Exact-head self-adversarial restack review at 392767f110b2dcac119a8ad051cc0b688361e82d.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 12156d5a425c0d62157e15f5b2974693e0f229f09e48034e11acf3a2f955c5c7.
Tree 54582e0271464a53198e37fe54b00b667bc92cd1 matches the independently computed clean merge.
Compared with historical tree 5737799ab311ce78f69c5faeb0cc039bf2c05693, 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.

[realmarcin]

Superseded by the protected cumulative merge #1975 at 42959bef2549f9a42c3e3303a0e10fd5be99f30e. This PR's reviewed source head 913296cf68f560203c08ebde42909fc4777ccab6 was included in the cumulative branch; the final squash tree matches the reviewed integration tree exactly, and all seven required merge-group checks passed.

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.