Qualify tomato host mediation and syntrophy mechanisms (batch 32) by realmarcin · Pull Request #1401 · CultureBotAI/CommunityMech

realmarcin · 2026-10-06T06:50:23Z

Scope

Three graph-only corrections: tomato SynCom C, DvH/M. maripaludis and D. desulfuricans/M. barkeri. Two reviews completed; Methanosarcina remains needs_research for a candidate negative arrow. Corpus: 139 reviewed / 315 pending / 6 needs_research across 460 records in both roots.

Closes #1394. Closes #1395. Closes #1396. Non-graph #1397/#1398/#1399 and graph research #1400 remain open.

Changes And Review

Ten nodes and seven arrows retained; no new structure. Remove unsupported tomato MUTUALISM, add canonical five-member participants, distinguish sterile-sand validation from nonsterile screening, classify whole-host graph evidence IN_VIVO and qualify two mediation arrows. Preserve the earlier workflow-edge removal and shared non-graph evidence anchor.

Represent DvH electron-transfer machinery as an intrinsic process. Preserve the physiological feedback cycle and explicit partner directions; distinguish conditional mutant effects, respiratory Hmc effects, proposed electron routing and substep thermodynamics. General abstract snippets are PARTIAL for exact-pair physiology.

Represent M. barkeri acetate use as intrinsic recipient metabolism, not community-level cross-feeding. Hydrogen-associated delay is not resource competition or universal methanogenic toxicity. Qualify partner attribution using coculture versus pure-culture evidence. Keep strain and YE/RV context distinct. Candidate negative structure remains pending under #1400; one-community Edison dry run only, no job/charge.

Verification

360 passed in 247.76s (0:04:07); six new tests. Schema, strict, ontology, independent snippet and history gates passed. All three reference-validator commands exit 0 but perform zero checks: no-op, not evidence validation. Textual MATCH is not scientific support.

Zero structural errors and all 31 baseline warnings unchanged. Participant registry 175 to 176 adds only tomato. Intrinsic recipient correction removes one mixed community-level record and two CL-counted taxa; no survey algorithms or numeric bounds changed.

Three guarded writes, append-only histories, llm-assisted events and regenerated pages. All non-graph raw blocks, 457 other records and 920 caches preserved. Repeat rendering deterministic and exact descriptions checked across 456 pages. Actual post-commit docs-current passed with a clean tree. No browser screenshots claimed.

Decision ledger, validation report and self-adversarial findings are committed under reports/causal_graph_review, dated 20261006, batch32. Complete primary-body/table/caption access is recorded; no figures visually inspected or supplement files read. No article body/PDF committed. This is self-adversarial review, not independent approval.

Dependency

Draft depends on #1393; do not merge into the topic parent. Require protected exact-head main checks and queue after parents merge. Move dependents before deleting branches. Full-corpus completion is not claimed.

realmarcin

Source-based self-adversarial review at exact head ccc4b87; not independent approval.

Addressed existing graph defects #1394/#1395/#1396 after primary-source review and actual diff inspection. Ten nodes and seven arrows retained. Tomato mediation remains PARTIAL, benefits are not mutualism, and assay context is explicit. Intrinsic DvH machinery differs from exchange, conditional mutant effects differ from universal necessity, and product-removal feedback is not reverse donation. M. barkeri acetate use is intrinsic; conditional hydrogen inhibition is not competition or general toxicity. The new negative arrow remains pending.

360 passed in 247.76s (0:04:07); six new tests. Focused schema/strict/terms/snippet/history checks, deterministic rendering, exact descriptions across 456 pages and actual post-commit docs-current passed. Reference validator performed zero checks despite exit 0; no-op is not evidence validation. Zero structural errors and 31 unchanged warnings. Registry and measured survey changes follow curated scope, no algorithms or numeric bounds changed. All non-graph raw blocks, 457 other records and 920 caches preserved.

Metadata #1397-1399 and research #1400 remain OPEN. Methanosarcina is needs_research, not a completed graph review. Edison dry run only, no job/charge. No article body/PDF committed; no visual figure or supplement inspection claimed. Protected main merge and full-corpus completion are not asserted. Committed decisions/validation/self-review records retain source limitations.

github-actions · 2026-10-06T06:50:59Z

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, 31 warning across 12 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)

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 040704d091626bb8a508a1cab8811309ad934381
after protected main merge of #1312. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree fc50a90d2857aed359133d5c1e2a1188f1446818.
The batch-owned binary patch is byte-identical
(SHA-256 f5b2bfb653081996ee17262f1bcd8ec32444dea2df95e56099d33540ad9f8db0); 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 81d41fa684ab70ad3b9552e4b549fdd28a086c44
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree fc50a90d2857aed359133d5c1e2a1188f1446818.
The batch-owned binary patch is byte-identical
(SHA-256 f5b2bfb653081996ee17262f1bcd8ec32444dea2df95e56099d33540ad9f8db0); 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 fb0ae63bdff039ef029c8531dc6dcd073d850053
after protected main merge of #1318. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree fc50a90d2857aed359133d5c1e2a1188f1446818.
The batch-owned binary patch is byte-identical
(SHA-256 f5b2bfb653081996ee17262f1bcd8ec32444dea2df95e56099d33540ad9f8db0); 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 · 2026-10-06T11:24:57Z

Reference-counter correction (#1469)

The earlier statement that linkml-reference-validator 0.1.7's Total checks: 0 means zero executed checks or a no-op is incorrect and withdrawn. The installed CLI prints the number of validation issues, not checks performed. Existing positive/negative and field-discovery canaries pass; EvidenceItem snippets are genuinely checked. SupportingReference coverage remains incomplete under #476. Text matching is not scientific support or independent source provenance.

The source-backed correction and historical candidate inventory are committed in #1470 at 22b5b12c2386a949d1ec4ddb1f79ee288085bd1c, under reports/causal_graph_review/README.md and reference-validator-correction-20261006-batch42.json. Earlier raw command output, source review, biological decisions and tested bytes are preserved; this notice does not claim a rerun of this PR's validation or change its biological findings. The older CLI counter is not a coverage metric.

The new Fucoidan batch separately retains 14 baseline reference-CLI failures and 15 baseline snippet-audit mismatches for supplement-sidecar excerpts. Those are not failures attributed to this older PR. This correction is self-review, not independent approval or merge authorization beyond the existing protected workflow.

realmarcin

Self-adversarial review refreshed at exact head be3bed87db0aec8913906de78c4e9b0c670c1195
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree fc50a90d2857aed359133d5c1e2a1188f1446818.
The batch-owned binary patch is byte-identical
(SHA-256 f5b2bfb653081996ee17262f1bcd8ec32444dea2df95e56099d33540ad9f8db0); 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 e5e9aa5df40c29c4f092daea978678356c70a800
after protected main merge of #1328. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree fc50a90d2857aed359133d5c1e2a1188f1446818.
The batch-owned binary patch is byte-identical
(SHA-256 f5b2bfb653081996ee17262f1bcd8ec32444dea2df95e56099d33540ad9f8db0); 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 95363378b2e96bac779dbc16e7101d0e4009e847
after protected main merge of #1334. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree fc50a90d2857aed359133d5c1e2a1188f1446818.
The batch-owned binary patch is byte-identical
(SHA-256 f5b2bfb653081996ee17262f1bcd8ec32444dea2df95e56099d33540ad9f8db0); 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 3ab2d5fc4e94b82b1ec10c2e0d271bdcb10d22ec
after protected main merge of #1339. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree fc50a90d2857aed359133d5c1e2a1188f1446818.
The batch-owned binary patch is byte-identical
(SHA-256 f5b2bfb653081996ee17262f1bcd8ec32444dea2df95e56099d33540ad9f8db0); 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 66e7843eebd0537adc2230929573b9c2f4202358
after protected main merge of #1346. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree fc50a90d2857aed359133d5c1e2a1188f1446818.
The batch-owned binary patch is byte-identical
(SHA-256 f5b2bfb653081996ee17262f1bcd8ec32444dea2df95e56099d33540ad9f8db0); 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 03b23e6bad9a740bde72832c1f5c7262be1aa4bb
after protected main merge of #1350. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree fc50a90d2857aed359133d5c1e2a1188f1446818.
The batch-owned binary patch is byte-identical
(SHA-256 f5b2bfb653081996ee17262f1bcd8ec32444dea2df95e56099d33540ad9f8db0); 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 af77c8039c4b4692d66b8b6559cd9de0161ecb59
after protected main merge of #1355. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree fc50a90d2857aed359133d5c1e2a1188f1446818.
The batch-owned binary patch is byte-identical
(SHA-256 f5b2bfb653081996ee17262f1bcd8ec32444dea2df95e56099d33540ad9f8db0); 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 f959ccd33b02fce91b50fa52231790fa56decc05. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head af77c8039c4b4692d66b8b6559cd9de0161ecb59, 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 f5b2bfb653081996ee17262f1bcd8ec32444dea2df95e56099d33540ad9f8db0). 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 5042f2e1923d47bc089f5e3361db839fb47f6785
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree a5503a3c0eb96a2b83306996f07f643b8cd05baf.
The batch-owned binary patch is byte-identical
(SHA-256 f5b2bfb653081996ee17262f1bcd8ec32444dea2df95e56099d33540ad9f8db0); 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 afc3c5997d0717ca8cd57c905237cb5853d22068. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 5042f2e1923d47bc089f5e3361db839fb47f6785, 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 f5b2bfb653081996ee17262f1bcd8ec32444dea2df95e56099d33540ad9f8db0). 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 a7ec3d47db6b313aa97d8e0bb0c2ac253dc7fca2.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 f5b2bfb653081996ee17262f1bcd8ec32444dea2df95e56099d33540ad9f8db0.
Tree ab0a614a3000bd8333d2aec68b0d64c3e05d6276 matches the independently computed clean merge.
Compared with historical tree 6ca126a32fef639717811be949cebc700a921f98, 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.