Review three cellulose-conversion causal graphs (batch 19) by realmarcin · Pull Request #1328 · CultureBotAI/CommunityMech

realmarcin · 2026-10-05T23:56:41Z

Summary

Source-review the cellulose-to-electricity, AECC-to-solvents and cellulose-to-methane cocultures.
Preserve nine nodes and three supported/qualified arrows; remove three unsupported arrows and perform four exact node renames. No new graph structure.
Bound residual-pool inference, competition, formate use, product-removal feedback and fitness claims while retaining measured outcomes and controls.
Add three knowledge gaps, three append-only histories, four focused regression tests, decision/adversarial/validation records and regenerated pages.

Closes #1324. Closes #1325. Closes #1326. Separate non-graph follow-up #1327 remains open.

Validation

All 30 local gates completed; 247 passed in 163.73s (0:02:43).
Workspace-rights tests: 3 passed in 1.48s.
79 MATCH snippets; all other classes zero.
Zero structural/network errors; 25 existing warnings unchanged.
53 unrelated top-level YAML blocks and all five reference caches byte-preserved.
Two identical full renders with complete published node/edge description coverage.
Stacked inventory: 106 reviewed, 351 pending, 3 needs research out of 460. Not corpus completion.

Review Limits

Source-based self-adversarial review, not independent approval. Both MFC papers remain abstract-bounded. AECC ABE and cellulose-methane main bodies, Methods, table and figure captions read; no visual image/supplement inspection. Primary XML remains outside git. No Edison submission or spend.

Stacked on batch 18 PR #1323. Do not merge into the topic parent. After the parent merges, verify tree identity, retarget to main, attach an exact-head review and use required checks and the protected merge queue. Delete branches only after dependents move.

realmarcin

Source-based self-adversarial review at exact head 3619c52dbd64fccba58dfcd1a3815d6d3685411c. Addressed graph issues #1324, #1325 and #1326; separate non-graph follow-up #1327 remains open. Read all three whole records, both MFC primary abstracts, and AECC ABE/cellulose-methane primary main bodies, Methods, table and captions. No visual image/supplement review claimed. Nine nodes retained, three arrows removed, three retained with appropriate certainty, four exact renames and no new structure. Checked the exact repository SYNTROPHY definition and corrected MFC supply to CROSS_FEEDING; separated nonsignificant cell growth from similar reported yields. All 30 local gates pass, including 247 regressions, 79 MATCH snippets with all other classes zero, three rights tests, identical renders, and actual post-commit docs-current with a clean tree. Decision ledger accounts for every node/arrow and binds file/cache hashes; 53 unrelated raw YAML blocks and five caches unchanged. This is self-adversarial review, not independent approval. Protected CI and main merge queue remain required; never merge into the topic parent.

github-actions · 2026-10-05T23:57:19Z

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, 25 warning across 10 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)

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

Source-based self-adversarial review refreshed at exact head b2ff78be7c72cf747e8eb5dba398ffd9aa0ca16f after protected merge of parent PR #1298. Rebase preserves reviewed tree 1f5d5fc93d658f94381c529fa42eab88fc2a8872 byte-for-byte; 1 batch-owned commit(s) retained. Existing committed decision, adversarial-review and validation artifacts remain applicable to this identical tree. Historical ledger base SHAs are provenance, not rewritten. This is not independent approval. No new source/graph changes were introduced by restacking. Required CI and protected main merge queue remain mandatory; do not merge into the topic parent.

realmarcin

Source-based self-adversarial review refreshed at exact head 12b61983c16cada2aa3375ee354bdc20b25a4f5b after protected merge of #1302. Not independent approval.

All 1 batch-owned commit(s) were retained. The batch's diff against its parent is byte-identical to its prior reviewed diff (SHA-256 85eb339ef2e0b6dce61141b83d59561773746a8fb036d77716384352a4ebc6a8). The only whole-tree change is the exact four-file #1329 history-base CI fix, already reviewed and merged through #1302. No additional scientific, grounding, history, generated-page or test-bound edits were made. New tree: d47c4f98e0e746b38205cd6337f8e61d2f6ff7f6.

Committed decision/adversarial/validation records remain the scientific review evidence; their base SHAs are historical provenance. Required CI must pass for this new head. Do not merge into a topic parent or bypass the protected main queue.

realmarcin

Source-based self-adversarial review refreshed at exact head d5a92adfc4ac51dc1b61dd84cbbed6f83fd84206 after integrating merged website PR #1303 (a937575f88ab11ff74683a8902fe13fd80c96165). Not independent approval.

The website merge conflicted only in the parent generated browser page; it was regenerated from the merged renderer and preserved KB. Each dependent owned commit was then rebased, generated pages refreshed, and actual post-commit just check-docs-current run successfully in every worktree. All branches were pushed atomically with exact leases.

Every non-document blob is verified identical to its previously reviewed version except the nine exact upstream website files. This includes unchanged scientific records, taxa, caches, histories, review ledgers and batch-owned regression code. Non-document manifest SHA-256: 9a81ad340b056a335dc3b80790f117a3a670905409cf9e5e934612304e7819d8. New whole-tree SHA: 4869403cc63b442eb5d25318325575f9a6216326. Whole-tree equality to the previous head is NOT claimed because upstream rendering changed.

The parent integration-focused tests passed. The final combined stack suite, including all batch regressions, site/link tests, corpus/network checks, reference-validator canaries and publication-rights tests, reports: 302 passed in 223.43s (0:03:43). All twelve worktrees passed actual docs-current. Batch-specific scientific/access limitations remain as recorded; batch25 still explicitly retains three primary-verified Results quotes absent from its abstract-only cache, not a passed reference gate.

The decision, adversarial-review and validation files remain historical source-review provenance. Required CI must pass at this new head and the protected main queue remains mandatory. Do not merge a child into a topic parent; delete merged branches only after their dependents move.

realmarcin

Self-adversarial review refreshed at exact head 3b6f35e6b22b667eee281cc02bb32136b038a239
after protected main merge of #1307. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4869403cc63b442eb5d25318325575f9a6216326.
The batch-owned binary patch is byte-identical
(SHA-256 ed0a730ac8b0c81e84e01c25b3c82873cc9eb58f37cd386b3431e719acc67a52); 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 76cfef7f1b1f8182fe51f66e147391a6bdf48830
after protected main merge of #1312. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4869403cc63b442eb5d25318325575f9a6216326.
The batch-owned binary patch is byte-identical
(SHA-256 ed0a730ac8b0c81e84e01c25b3c82873cc9eb58f37cd386b3431e719acc67a52); 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 fda250bf6c7645ba98583b700150ec7b4fd5a416
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4869403cc63b442eb5d25318325575f9a6216326.
The batch-owned binary patch is byte-identical
(SHA-256 ed0a730ac8b0c81e84e01c25b3c82873cc9eb58f37cd386b3431e719acc67a52); 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 8f83d38f7fed810641b436a00e51b45be744bac2
after protected main merge of #1318. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4869403cc63b442eb5d25318325575f9a6216326.
The batch-owned binary patch is byte-identical
(SHA-256 ed0a730ac8b0c81e84e01c25b3c82873cc9eb58f37cd386b3431e719acc67a52); 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 142074768a5592e2e96e2965f050e8c6aa2eab61
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 4869403cc63b442eb5d25318325575f9a6216326.
The batch-owned binary patch is byte-identical
(SHA-256 ed0a730ac8b0c81e84e01c25b3c82873cc9eb58f37cd386b3431e719acc67a52); 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 commented Oct 5, 2026

View reviewed changes

This was referenced Oct 5, 2026

Qualify cellulose-MFC metabolite transfer and remove localization causality #1324

Closed

Remove unsupported AECC coculture arrows and qualify competition evidence #1325

Closed

Bound cellulose-methane formate use and product-removal feedback #1326

Closed

realmarcin force-pushed the causal-graph-review-20261005-batch19 branch from 3619c52 to b2ff78b Compare October 5, 2026 23:57

realmarcin force-pushed the causal-graph-review-20261005-batch18 branch from db05129 to 31c24c8 Compare October 5, 2026 23:57

realmarcin commented Oct 5, 2026

View reviewed changes

realmarcin mentioned this pull request Oct 6, 2026

Review biohydrogen, minority-mediator and syngas causal graphs (batch 20) #1334

Merged

realmarcin force-pushed the causal-graph-review-20261005-batch18 branch from 31c24c8 to 252bbbc Compare October 6, 2026 01:42

realmarcin force-pushed the causal-graph-review-20261005-batch19 branch from b2ff78b to 12b6198 Compare October 6, 2026 01:42