Review three syngas and minimal-medium coculture causal graphs

[realmarcin]

Summary

• Review three coculture records: autoethanogenum/kluyveri, thermophilic minimal medium, and carboxidivorans/kluyveri.
• Preserve nine nodes and four supported/qualified arrows; remove one medium-context-only arrow and perform three exact node renames. No new causal structure.
• Resolve product attribution, distinguish inferred ethanol flux, qualify feedback, preserve measured molecular responses, bound reactor-stage mechanisms and correct hexanoate grounding.
• Three knowledge gaps, three append-only histories, four focused regression tests, full decision ledger and adversarial/validation records, regenerated pages.

Closes #1319. Closes #1320. Closes #1321. Separate non-graph issue #1322 remains open.

Validation

• 30 local gates completed; 243 passed in 170.92s (0:02:50).
• 3 passed in 1.56s for workspace-rights tests.
• 91 MATCH snippets; all other snippet classes zero.
• Zero structural/network errors; 25 existing warnings unchanged.
• 50 unrelated top-level YAML blocks byte-preserved; seven reference caches unchanged.
• Two identical full renders with complete published node/edge description coverage.
• Stacked inventory: 103 reviewed, 354 pending, 3 needs research out of 460. Not corpus completion.

Review Limits

Source-based self-adversarial review, not independent approval. Four primary main bodies/Methods/tables/captions read; C. bescii primary Results selectively reviewed; exact-system minimal-medium paper remains abstract-bounded; computational model abstract/Introduction only. No visual inspection of images or supplements. Source XML stays outside git. No Edison run or spend.

Stacked on batch 17 PR #1318. Do not merge into the topic parent. After parent merges, verify tree identity, retarget to main, attach an exact-head review and use required checks and protected merge queue. Delete branches only after dependents move.

[realmarcin]

Source-based self-adversarial review of exact head db05129, tree 4105e96e29592a5e137815dc317b8ce3bc18761c. This is not independent approval.

Reviewed the full three-record diff against the source scopes and artifact hashes in reports/causal_graph_review/decisions/20261005-three-records-batch18.yaml. Findings #1319, #1320 and #1321 are addressed: preserve observed conversion and molecular results, distinguish inferred flux and hypothesized feedback, remove the medium-context-only edge, bound reactor effects and correct the C6 anion grounding. Separate metadata followup #1322 remains open.

Nine nodes retained, three exact renames, five original arrows fully accounted for as four retained plus one removed. No new nodes/arrows or Edison spend. All 50 unrelated raw YAML blocks and seven reference caches remain unchanged. Three append-only histories and focused regression coverage included.

All 30 local gates completed: 243 regression tests passed, three rights tests passed, 91 MATCH snippets with all other classes zero; zero network/structural errors and 25 unchanged warnings. Two identical full renders verified all 456 published pages and their 1460 node / 708 edge descriptions. Detailed adversarial findings and validation output are committed alongside the ledger.

Limits: four primary main bodies/Methods/tables/captions read; C. bescii Results selectively read; the exact minimal-medium paper is abstract-bounded and the computational model abstract/Introduction only. No image or supplement visual inspection claimed. Stacked inventory 103 reviewed / 354 pending / 3 needs research, not corpus completion.

Do not merge into the topic parent. After parent #1318 merges, restack with tree-identity verification, retarget to main, attach an updated exact-head review, require protected checks and merge queue, and delete the branch only after all dependents move.

[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, 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 31c24c80f100ad91ec1d0838055adb754ee1730a after protected merge of parent PR #1298. Rebase preserves reviewed tree 4105e96e29592a5e137815dc317b8ce3bc18761c 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 252bbbc7ed04f00f860aaff9e1633393f46d89a1 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 640fe2317556078933485b4a0619a36bc9b68d7032fbded6773545ce4d369d28). 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: ea4ac5f97794f14f9cfe1aba18cdc27cb4a5469f.

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 deb2de1136310cd86257968cf3905a3201ccee8b 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: 3241112c1f0fb7ba39a9c909041c8cef158741337ace79df6a32d3d7db3c9cdb. New whole-tree SHA: 9a865686204e62a8a409c82dff6c27aedb181de0. 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 ff17980a0facdc5f3270174aaf9a4eab52403b2e
after protected main merge of #1307. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 9a865686204e62a8a409c82dff6c27aedb181de0.
The batch-owned binary patch is byte-identical
(SHA-256 5acc115edce8ffe260d4883ad1f7f2cf4be4d4dab05925ad54f740f96ab77d61); 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 cd5b26ba972b7a4034cca2b5b4966ac8cdcca27d
after protected main merge of #1312. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 9a865686204e62a8a409c82dff6c27aedb181de0.
The batch-owned binary patch is byte-identical
(SHA-256 5acc115edce8ffe260d4883ad1f7f2cf4be4d4dab05925ad54f740f96ab77d61); 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 491a5c058e03bbfc99636703f449379a5ac36017
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 9a865686204e62a8a409c82dff6c27aedb181de0.
The batch-owned binary patch is byte-identical
(SHA-256 5acc115edce8ffe260d4883ad1f7f2cf4be4d4dab05925ad54f740f96ab77d61); 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 e25d8750c360c9738558ea671af3ad689dfb372e
after protected main merge of #1318. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 9a865686204e62a8a409c82dff6c27aedb181de0.
The batch-owned binary patch is byte-identical
(SHA-256 5acc115edce8ffe260d4883ad1f7f2cf4be4d4dab05925ad54f740f96ab77d61); 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]

Protected main merge confirmed at 40a56b9 (2026-10-06T11:46:07Z), after all required pull-request and merge-group checks passed. Issues #1319, #1320 and #1321 are closed. All 25 dependent batches 19-43 were moved with identical whole trees and byte-identical batch-owned patches, atomically pushed with exact leases, and given refreshed exact-head self-adversarial COMMENT reviews. This ancestry-only update is not independent approval or a new source/test rerun. PR #1328 is now ready on main with protected auto-merge requested; its new-head required checks remain pending. The merged batch-18 branch was deleted locally, remotely and from remote tracking only after dependents moved. Main was fast-forwarded; ignored/untracked collision checks passed and all 46 nonignored untracked user files were hash-preserved. Detailed lifecycle receipt: finish-stack-18.json. Latest new review outputs and addressed findings #1471/#1472 are published in draft #1473; full-corpus review and that PR main merge remain incomplete.