Review cellobiose biofilm, yeast-cellulose and X514 causal graphs (batch 21) by realmarcin · Pull Request #1339 · CultureBotAI/CommunityMech

realmarcin · 2026-10-06T01:11:45Z

Summary

Source-review the cellobiose biofilm, yeast-cellulose and X514 ethanol graphs.
Retain all ten nodes and seven arrows, with five exact node renames and assay-specific uncertainty. No new structure or Edison spend.
Preserve glucose, necromass, oxygen and supplementation controls; distinguish measured outcomes from inferred flux and causal contributions.
Correct community versus directed-interaction scope using existing canonical participants.
Add three knowledge gaps, three append-only histories, eight focused regressions, review records and regenerated pages.

Closes #1335. Closes #1336. Closes #1337. Non-graph #1338 and existing #746 remain open.

Validation

All 30 local gates completed; 262 passed in 220.78s (0:03:40).
Workspace-rights checks: 3 passed in 2.34s.
83 MATCH snippets; all other classes zero.
Zero structural/network errors; 25 existing warnings unchanged.
55 unrelated YAML blocks and four reference caches byte-preserved.
Repeated identical full renders and exact parsed node/edge description coverage.
Participant registry adds only two intentional users; exact-set and connectivity/GTDB census bounds unchanged.
Stacked inventory: 112 reviewed, 345 pending, 3 needs research out of 460. This is not corpus completion.

Review Limits

Source-based self-adversarial review, not independent approval. Three primary main bodies, Methods and tables/captions were read. The 2011 X514 mechanism paper was available only as a complete abstract. No visual image or supplementary-file inspection. No copyrighted full body added; four caches unchanged. Unrelated metadata is preserved, not certified.

Stacked on batch20 PR #1334. Do not merge into the topic parent or bypass checks. After protected parent merges, restack the owned commit, retarget to main, refresh exact-head review and use the protected queue. Delete parent branches only after dependents move. The pending batch13 CI-fix commit is not yet in this branch; incorporate it through the protected parent restack.

realmarcin

Source-based self-adversarial review at exact head b4fd7d01144bf9815c3c5b5ce8c1c7b628a0a018, not independent approval.

Addressed #1335, #1336 and #1337. Retained all ten nodes and seven arrows, with five exact renames and no new graph structure. Preserved glucose/necromass controls, respiratory protection and conditional mutualism, measured products and viable populations, and the positive 39E supplementation control. Distinguished assay regimes, polymer versus cellobiose conversion, genomic qPCR versus viability, biofilm biomass versus unmeasured products, and proposed flux/B12 contributions versus selective causal demonstrations.

All 30 local gates pass: 262 passed in 220.78s (0:03:40); 83 MATCH snippets, zero other classes; 3 passed in 2.34s; 55 unrelated raw blocks and four caches byte-preserved. Two identical full renders with exact node/edge-description coverage; actual post-commit just check-docs-current passed and left the tree clean. Only the two intentional participant-registry users were added; exact-set and connectivity/GTDB census bounds remain unchanged.

The decision/adversarial/validation records under reports/causal_graph_review/ bind every node/arrow and record/cache hashes. Three primary main bodies with Methods and tables/captions were read; the 2011 mechanism paper was abstract-only. No visual image/supplement review or copyrighted full-body addition is claimed.

Non-graph #1338 and existing #746 remain open. Stacked coverage is 112/460 reviewed, not corpus completion. Required CI and protected main merge queue remain mandatory; do not merge into the topic parent. The separate batch13 CI fix will be incorporated through the protected parent restack.

github-actions · 2026-10-06T01:12:20Z

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 189de5cb28b628390a7cda118c5ffa8911a4434b 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 ac269d653c71522b6dc9f53fdaf952a846cf4f10a49a43a9511ef3dbd9485a40). 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: 733239bcfd1eaf6e0e7b7bcf60f6a130891a9d96.

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 86df6a9a7a4ff8782d865522ea6f4b283099f4ef 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: b89789441e2a789869eff70ef00bcf29c8bc48825b31937ad82c70e7b6111c96. New whole-tree SHA: 07a40b9dc0dba3503aceb6c85dc17f143d251062. 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 1053b8ae600ff75dfa87e26bb1a2895cf087828f
after protected main merge of #1307. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 07a40b9dc0dba3503aceb6c85dc17f143d251062.
The batch-owned binary patch is byte-identical
(SHA-256 e47240c7236dcba54864354407fa1e41366d618cace9faba3b13b6d4d610d0a3); 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 cb1ebefa6fd7bc6c6c2e237d3f604f0531e9af7e
after protected main merge of #1312. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 07a40b9dc0dba3503aceb6c85dc17f143d251062.
The batch-owned binary patch is byte-identical
(SHA-256 e47240c7236dcba54864354407fa1e41366d618cace9faba3b13b6d4d610d0a3); 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 6519f8f209e1b196212864bf33c644b3ffc4227c
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 07a40b9dc0dba3503aceb6c85dc17f143d251062.
The batch-owned binary patch is byte-identical
(SHA-256 e47240c7236dcba54864354407fa1e41366d618cace9faba3b13b6d4d610d0a3); 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 b586c468ddc183548c6f7dcb49236674168024fd
after protected main merge of #1318. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 07a40b9dc0dba3503aceb6c85dc17f143d251062.
The batch-owned binary patch is byte-identical
(SHA-256 e47240c7236dcba54864354407fa1e41366d618cace9faba3b13b6d4d610d0a3); 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 b7eef67787f2eec618b976b21f318e488e97486d
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 07a40b9dc0dba3503aceb6c85dc17f143d251062.
The batch-owned binary patch is byte-identical
(SHA-256 e47240c7236dcba54864354407fa1e41366d618cace9faba3b13b6d4d610d0a3); 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 b3ca1ff77e66e0e7cd9661a7795ebf3be154a53c
after protected main merge of #1328. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 07a40b9dc0dba3503aceb6c85dc17f143d251062.
The batch-owned binary patch is byte-identical
(SHA-256 e47240c7236dcba54864354407fa1e41366d618cace9faba3b13b6d4d610d0a3); 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.