Review JN4-GD17, staged butanol and wetland causal graphs (batch 22) by realmarcin · Pull Request #1346 · CultureBotAI/CommunityMech

realmarcin · 2026-10-06T01:39:51Z

Summary

Source-review JN4-GD17, staged-butanol and seawater-ion wetland causal graphs.
Retain all ten nodes and six arrows, with six exact renames and assay-specific uncertainty. No new structure or Edison spend.
Preserve positive controls and measured outcomes while bounding exchange, viability, redox and gene-mediated causality.
Add three knowledge gaps, three append-only histories, eight focused regressions, complete review records and regenerated pages.
Verify precisely two new mixed-scope records, then adjust only the documented census bound from 120 to 122 (Account for two source-backed mixed-scope records in connectivity census #1344).

Closes #1340. Closes #1341. Closes #1342. Closes #1344. Nongraph #1343 and existing #746/#524 remain open.

Validation

All 30 local gates completed; 270 passed in 237.82s (0:03:57).
Rights checks: 3 passed in 2.14s.
87 MATCH snippets; all other classes zero.
Zero structural/network errors; 25 existing warnings unchanged.
55 unrelated YAML blocks and seven tracked cache artifacts byte-preserved.
Two identical full renders and exact parsed node/edge description coverage.
Two intentional participant-registry additions; exact-set equality preserved. Before/after census: mixed 120 -> 122, taxa credited solely by the rule unchanged at 1218. Other bounds unchanged.
Stacked coverage: 115 reviewed, 342 pending, 3 needs research out of 460. Not corpus completion.

Review Limits

Source-based self-adversarial review, not independent approval. Three primary main bodies with Methods, tables/captions and three additional abstracts were read. No visual images or supplementary files inspected. No copyrighted full body added; all seven caches unchanged. Unrelated metadata preserved, not certified.

Stacked on batch21 PR #1339. 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 merged parent branches only after dependents move. The batch13 history-base CI fix will be incorporated through the pending protected-parent restack.

realmarcin

Source-based self-adversarial review at exact head d71b3800c819fff8b4c5a32bb99d0f68e5ca85c3, not independent approval.

Addressed #1340, #1341, #1342 and #1344. All ten nodes and six arrows retained, with six exact renames and no new structure. Preserve supported conversion and perturbation results; qualify resource-competition signs, estimated biomass, substrate carryover, redox association, relative DNA abundance and treatment-specific gas comparisons.

All 30 local gates pass: 270 passed in 237.82s (0:03:57); 87 MATCH snippets, zero other classes; 3 passed in 2.14s; 55 unrelated raw blocks and seven caches byte-preserved. Two identical full renders and exact description coverage; actual post-commit just check-docs-current passed and left the tree clean. Only two intentional participant-registry additions. Both-root census verifies mixed records 120 -> 122, with taxa credited solely by the rule unchanged at 1218; only the corresponding census ceiling and comment change.

Committed decision, adversarial and validation records bind all nodes, arrows and record/cache hashes. Three primary main bodies and three additional abstracts reviewed. No visual image/supplement inspection or copyrighted full-body addition claimed. Nongraph #1343 and existing #746/#524 remain open. Coverage is 115/460 reviewed, not corpus completion.

Required CI and protected main queue remain mandatory. Do not merge into the topic parent. Batch13 has merged; its four-file history-base CI fix will be incorporated via the guarded restack.

github-actions · 2026-10-06T01:40:58Z

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 eabaa6b3bccc20c8eea91cce9849c6e64ea945da 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 fd9699bd017e8c9301fab0525bee9be8f2dccd088d53f50c4563bfc815d5c853). 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: cb6d9d6c562c27eb897fe8e033ab2ab953723d9b.

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 99167c705fc16c07379f4c9d0ae09d66f81a83c8 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: 5e3e77789631e1736472baaac6aeb2e9f4fa15c44e6bdd977e6aa43aa14b1380. New whole-tree SHA: 2eb0584e11e4c2da26b87e198016ac06377a4694. 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 e4c0ba1c63c6d0e90a62d2cdce454b2e41d22505
after protected main merge of #1307. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 2eb0584e11e4c2da26b87e198016ac06377a4694.
The batch-owned binary patch is byte-identical
(SHA-256 16d59ea428538db0f3c0d4bd9e8449d675a582b41b15b026a27b4450541a3304); 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 83849265255e54ca06c9d4f7f59d9ef58f5c5623
after protected main merge of #1312. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 2eb0584e11e4c2da26b87e198016ac06377a4694.
The batch-owned binary patch is byte-identical
(SHA-256 16d59ea428538db0f3c0d4bd9e8449d675a582b41b15b026a27b4450541a3304); 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 abc204b6b662ee6784041c63a893396f1dcaf861
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 2eb0584e11e4c2da26b87e198016ac06377a4694.
The batch-owned binary patch is byte-identical
(SHA-256 16d59ea428538db0f3c0d4bd9e8449d675a582b41b15b026a27b4450541a3304); 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 645421ce0b699c22da2c8b7230b0203c1cca2452
after protected main merge of #1318. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 2eb0584e11e4c2da26b87e198016ac06377a4694.
The batch-owned binary patch is byte-identical
(SHA-256 16d59ea428538db0f3c0d4bd9e8449d675a582b41b15b026a27b4450541a3304); 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 0872694a529a8122d0096dfb3f2ecdfa954c3676
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 2eb0584e11e4c2da26b87e198016ac06377a4694.
The batch-owned binary patch is byte-identical
(SHA-256 16d59ea428538db0f3c0d4bd9e8449d675a582b41b15b026a27b4450541a3304); 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 ffe9595d4d6427ecc61eb235c973baa670f96609
after protected main merge of #1328. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 2eb0584e11e4c2da26b87e198016ac06377a4694.
The batch-owned binary patch is byte-identical
(SHA-256 16d59ea428538db0f3c0d4bd9e8449d675a582b41b15b026a27b4450541a3304); 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.