Bound URL, AMD and gut proteome causal claims (batch52)

[realmarcin]

Scope

Closes #1501. Closes #1502. Closes #1503.
Related #1504 remains OPEN for the unresolved Hualgayoc extension; this PR does not resolve it.

• Bound URL genomic functions and remove two contextual arrows.
• Qualify MAG-specific carbon flow; retain unresolved remediation outcome extension.
• Separate measured proteomic overlap and qPCR yield from proposed mediation.

Adversarial Review

• Whole275-line URL,628-line Hualgayoc and353-line gut records reviewed, including every original node and arrow. Complete cached primary main texts, Methods and embedded captions read, with Hualgayoc Table1. No original figure images, supplementary files, raw data or code audited.
• URL site/lithology association is not an isolated causal driver. Genome-based functional potential remains positive SUPPORT/COMPUTATIONAL evidence, not measured pathway flux. The two overview-to-hydrogen arrows were context/inclusion, not established causal direction, and are removed without deleting the distinct findings.
• Both canonical URL habitat labels sharing NCBITaxon131567 remain distinct. Horonobe-only transfer/genotype claims use only its participant. Hydrogen transfer stays PARTIAL without implying simultaneous sulfate reduction and hydrogen export. Genotypic similarity and coverage-qualified iRep do not establish transport, absolute growth rates or mutation rates.
• Hualgayoc retains the already-present MAG003-only first participant under816, and both participants for proposed acetate coupling. Both genomes encode glycerol-to-acetate potential. Organism assignment, pH threshold, acetate-toxicity relief and mineral phase are hypotheses distinct from the positive bulk chemistry. Repeated inoculation is explicit; bulk16S rRNA transcripts were measured, not absent.
• Hualgayoc remains needs_research under1504: the removed positive remediation outcome requires new structure. A real one-community dry run succeeded; the14343-character query is hash-bound. No paid provider job, report or new outcome node/arrow. Existing minor-acidogen discussion is semantically unchanged; no unsupported enum is added to hide the rendering issue.
• Gut partner-associated protein changes remain positive controlled findings, with abundance-matched mixed-isolate controls. Carbon effects are not denied. Detection thresholds and combined human/rumen scope prevent assigning all pooled results to every human member or condition.
• Annotated KO overlap is a proteomic metric, not measured competition, coexistence or metabolite flux. The exact Methods productivity denominator is mean monoculture qPCR abundance, not a sum or best-monoculture benchmark. Yield is not direct viable biomass or every-member mutualism. Both proposed directions stay PARTIAL without selective mediation.
• Full record diffs and focused tests inspected. Nine nodes retained, two contextual arrows removed, three arrows PARTIAL. Only graph, discussion and curation-history fields changed.457 other records,920 caches and non-graph raw blocks preserved, not certified. Two participant registry entries added; measured connectivity census unchanged.
• Actual schema, strict, terms, references, snippets, rank and history gates passed. Network equals baseline with34 existing findings and no structural errors. Repeat renders deterministic; exact node/arrow descriptions across456 pages parser-checked, not browser screenshots. Post-commit docs-current remains a separate publication gate.
• Dedup checked809 all-state titles/bodies and14 ignored/hidden local files; prior merged PR814 inspected, not every historical comment/review.1501/1502/1503 are repaired findings open until protected-main merge.1504 remains unresolved; original815 rendering complaint was addressed by removal in PR814. Source-based self-adversarial review is not independent approval.

Verification And Output Records

495 passed in 198.66s (0:03:18); six new focused tests. Schema, strict, term, reference, snippet and history gates pass. 61 snippets match unchanged caches. Text matching is not independent provenance or scientific support. CLI Total checks counts reported issues, not executed checks. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091) and selected-cache provenance (#1362) remain limitations.

All nine nodes retained, two contextual URL arrows removed and three proposed arrows explicitly PARTIAL. Hualgayoc remains needs_research; unresolved outcome extension1504 is not closed by this repair. Both-root baseline retained; zero structural errors and all34 prior network findings unchanged. All457 other records and920 caches preserved, not certified. Measured connectivity census unchanged. Two participant registry entries added; no census-bound or production matching change.

Repeat renders deterministic; exact descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 ee653074c3964dfdeedf7244e6fa4e2929c8ea95ba1a14e4de7511d7e80d36c6.

Source decisions, actual validation outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch52. Not independent approval. Corpus181 reviewed /264 pending /15 needs_research, not complete.

Dependency

Draft depends on #1500. Do not merge into the topic parent. Require eligible exact-head CI and the protected main queue after parent merges. Move dependents before deleting merged branches. Hualgayoc one-community Edison dry run only; no provider job or spend. New outcome structure remains pending specific authorization and source-checked report review.

[realmarcin]

Source-based self-adversarial review at exact head 683e765; not independent approval.

Repair issues #1501, #1502 and #1503 addressed; research issue #1504 remains unresolved; original815 rendering complaint was addressed by removal in PR814.

• Bound URL genomic functions and remove two contextual arrows.

• Qualify MAG-specific carbon flow; retain unresolved remediation outcome extension.

• Separate measured proteomic overlap and qPCR yield from proposed mediation.

• Whole275-line URL,628-line Hualgayoc and353-line gut records reviewed, including every original node and arrow. Complete cached primary main texts, Methods and embedded captions read, with Hualgayoc Table1. No original figure images, supplementary files, raw data or code audited.

• URL site/lithology association is not an isolated causal driver. Genome-based functional potential remains positive SUPPORT/COMPUTATIONAL evidence, not measured pathway flux. The two overview-to-hydrogen arrows were context/inclusion, not established causal direction, and are removed without deleting the distinct findings.

• Both canonical URL habitat labels sharing NCBITaxon131567 remain distinct. Horonobe-only transfer/genotype claims use only its participant. Hydrogen transfer stays PARTIAL without implying simultaneous sulfate reduction and hydrogen export. Genotypic similarity and coverage-qualified iRep do not establish transport, absolute growth rates or mutation rates.

• Hualgayoc retains the already-present MAG003-only first participant under816, and both participants for proposed acetate coupling. Both genomes encode glycerol-to-acetate potential. Organism assignment, pH threshold, acetate-toxicity relief and mineral phase are hypotheses distinct from the positive bulk chemistry. Repeated inoculation is explicit; bulk16S rRNA transcripts were measured, not absent.

• Hualgayoc remains needs_research under1504: the removed positive remediation outcome requires new structure. A real one-community dry run succeeded; the14343-character query is hash-bound. No paid provider job, report or new outcome node/arrow. Existing minor-acidogen discussion is semantically unchanged; no unsupported enum is added to hide the rendering issue.

• Gut partner-associated protein changes remain positive controlled findings, with abundance-matched mixed-isolate controls. Carbon effects are not denied. Detection thresholds and combined human/rumen scope prevent assigning all pooled results to every human member or condition.

• Annotated KO overlap is a proteomic metric, not measured competition, coexistence or metabolite flux. The exact Methods productivity denominator is mean monoculture qPCR abundance, not a sum or best-monoculture benchmark. Yield is not direct viable biomass or every-member mutualism. Both proposed directions stay PARTIAL without selective mediation.

• Full record diffs and focused tests inspected. Nine nodes retained, two contextual arrows removed, three arrows PARTIAL. Only graph, discussion and curation-history fields changed.457 other records,920 caches and non-graph raw blocks preserved, not certified. Two participant registry entries added; measured connectivity census unchanged.

• Actual schema, strict, terms, references, snippets, rank and history gates passed. Network equals baseline with34 existing findings and no structural errors. Repeat renders deterministic; exact node/arrow descriptions across456 pages parser-checked, not browser screenshots. Post-commit docs-current remains a separate publication gate.

• Dedup checked809 all-state titles/bodies and14 ignored/hidden local files; prior merged PR814 inspected, not every historical comment/review.1501/1502/1503 are repaired findings open until protected-main merge.1504 remains unresolved; original815 rendering complaint was addressed by removal in PR814. Source-based self-adversarial review is not independent approval.

495 passed in 198.66s (0:03:18); six new focused tests. Schema, strict, term, reference, snippet and history gates pass. 61 snippets match unchanged caches. Text matching is not independent provenance or scientific support. CLI Total checks counts reported issues, not executed checks. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091) and selected-cache provenance (#1362) remain limitations.

All nine nodes retained, two contextual URL arrows removed and three proposed arrows explicitly PARTIAL. Hualgayoc remains needs_research; unresolved outcome extension1504 is not closed by this repair. Both-root baseline retained; zero structural errors and all34 prior network findings unchanged. All457 other records and920 caches preserved, not certified. Measured connectivity census unchanged. Two participant registry entries added; no census-bound or production matching change.

Repeat renders deterministic; exact descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 ee653074c3964dfdeedf7244e6fa4e2929c8ea95ba1a14e4de7511d7e80d36c6.

Source decisions, actual validation outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch52. Not independent approval. Corpus181 reviewed /264 pending /15 needs_research, not complete.

Protected main merge remains 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, 34 warning across 14 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)

Mangrove_Benzene_MFC_Bioanode_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Pelobacter' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas' has no interactions

Total: 2 issues (0 error, 2 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 review refreshed at exact head 9aa62068f98118b8067b8fb438d183586e4056ed
after protected main merge of #1346. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 694f89b4f37bc4919a40e7b9b059cc49cfda9d02.
The batch-owned binary patch is byte-identical
(SHA-256 9b5026c033383e48e349e5a6fbbec3b48f15074ba324585ec74be8c35e3df4c3); 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 review refreshed at exact head 6ccdc34808baf544a5268898f2cc64c67a8c9555
after protected main merge of #1350. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 694f89b4f37bc4919a40e7b9b059cc49cfda9d02.
The batch-owned binary patch is byte-identical
(SHA-256 9b5026c033383e48e349e5a6fbbec3b48f15074ba324585ec74be8c35e3df4c3); 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 review refreshed at exact head 672fc6b41db32038d9ee7f74b840e4e74d3942d9
after protected main merge of #1355. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 694f89b4f37bc4919a40e7b9b059cc49cfda9d02.
The batch-owned binary patch is byte-identical
(SHA-256 9b5026c033383e48e349e5a6fbbec3b48f15074ba324585ec74be8c35e3df4c3); 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 integration review at exact head dbe6c6d4a247aa8d568ee19c67f6b7f11b30e36a. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 672fc6b41db32038d9ee7f74b840e4e74d3942d9, 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 9b5026c033383e48e349e5a6fbbec3b48f15074ba324585ec74be8c35e3df4c3). 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 66536fc060a265142a49bb86f0014729ba9efbdd
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 339d3347c8088bf0418aa76fee6427011bbeaa3a.
The batch-owned binary patch is byte-identical
(SHA-256 9b5026c033383e48e349e5a6fbbec3b48f15074ba324585ec74be8c35e3df4c3); 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 c154bd7fec285d4b752f2eb65378dc10766db08b. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 66536fc060a265142a49bb86f0014729ba9efbdd, 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 9b5026c033383e48e349e5a6fbbec3b48f15074ba324585ec74be8c35e3df4c3). 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 d3f10128e117386358c6e042bb5e4a3e2f952841.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 9b5026c033383e48e349e5a6fbbec3b48f15074ba324585ec74be8c35e3df4c3.
Tree 4a2c3e096e50791eec087aab17754a4e06a0efc8 matches the independently computed clean merge.
Compared with historical tree 93b691689227a77476de0880875ff14e4a434a5d, 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 7f498543797c88ae337d934ba2a1e13edd70db80 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.