Review wild-type fusion coculture causal graph (batch 17)

[realmarcin]

Summary

• Review all nine original nodes and three arrows of the wild-type fusion coculture against three primary main bodies/Methods/captions and the founding abstract.
• Remove the engineered-donor DNA endpoint and incoming arrow with full evidence preserved in the decision ledger. Qualify causal mechanisms without erasing measured gas, supplementation, glucose-consumption or product results.
• Retain eight nodes and two arrows; four exact node renames, two focused knowledge gaps, one append-only history, regression tests and regenerated page.

Closes #1316. Separate non-graph followup #1317 and broader model issues #749/#752 remain open.

Validation

• 16 local gates passed; 239 passed in 161.89s (0:02:41).
• 3 passed in 1.67s for workspace-rights tests.
• 41 MATCH snippets; all other audit classes zero.
• Zero structural/network errors; 25 existing warnings unchanged.
• 18 unrelated top-level YAML blocks byte-preserved; four reference caches unchanged.
• Two identical full renders and complete published node/edge-description coverage.
• Stacked inventory: 100 reviewed, 357 pending, 3 needs research out of 460. Not corpus completion.

Review Limits

Source-based self-adversarial review, not independent approval. Three primary main bodies, Methods and main figure captions were read; figure images and supplements were not visually inspected. The founding 2019 paper remains abstract-bounded. Source XML stays outside git. No new causal structure, Edison run or spend.

Stacked on batch 16 PR #1315. Do not merge into the topic parent. After parent merges, verify tree identity, retarget to main, attach an exact-head review, and use protected checks and the merge queue. Delete branches only after dependents have moved.

[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 of exact head f76f44c (tree 801470dce7328cad581e9438c69aa28644bbaf29), compared with immediate parent 487f121. All nine PR files checked against the intended scope.

#1316 is addressed: the engineered plasmid-donor DNA endpoint and incoming arrow are removed from the explicitly wild-type graph with their full original evidence preserved in the ledger. Wild-type fusion/protein labeling is distinguished from reporter RNA and engineered DNA. Measured gas, supplementation, glucose-consumption and condition-specific products remain; direct flux, hydrogenase mediation, reciprocal growth, competition and fusion-specific product causality are bounded appropriately. Four exact renames resolve every retained arrow and discussion anchor.

Verification: 16 local gates, 239 regressions, 3 rights tests, all 41 snippets MATCH, two identical full renders, zero structural/network errors and 25 unchanged warnings. Eighteen unrelated top-level blocks and four caches are byte-preserved. Actual post-commit docs-current passed. After inheriting the separately verified batch-14 census fix, an exact path/blob comparison proves graph/review data unchanged and 13 fusion/FT92W/census regressions passed again. New-head full protected CI is pending.

Three primary main bodies/Methods/captions were read; figure images and supplements were not visually inspected, and the founding study is abstract-bounded. No new causal structure or Edison spend for this repair. #1317 is an explicit non-graph followup, not silently closed. No remaining finding in the graph-only patch. Self-adversarial review, not independent approval or corpus completion. Keep draft until parent PR #1315 merges, then retarget/review main and use its protected queue.

[realmarcin]

Source-based self-adversarial review refreshed at exact head 8e2237ff7e028b9762357576b3916f35fe389b9b after protected merge of parent PR #1298. Rebase preserves reviewed tree 801470dce7328cad581e9438c69aa28644bbaf29 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 44dd34045fec52a0776345333d605bb2eba0209a 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 1d44c83422fde7164de5254e42524091e1768d17c31f473d67e375e3d8d9902a). 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: 973179342750d5e37ccbae788f564326b026d2cd.

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 89e2817cb0e21f484390e802507a67e89cd7c01a 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: fbdf2d9b101822a4493962eb2a367f0bca8e6ce9c961e00d860de2425108dc57. New whole-tree SHA: adc159627605e7b2beec704d4a78271f6aac259f. 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 e18db49a8bc87975d204069a388ac4539bf9e809
after protected main merge of #1307. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree adc159627605e7b2beec704d4a78271f6aac259f.
The batch-owned binary patch is byte-identical
(SHA-256 8d0d4e1f91176bc4a8669b81b9ad3c78338d8c0db349bf0f21c153281bd1cf10); 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 bc8c7df0ec11757dc15827e20ed687244838f11a
after protected main merge of #1312. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree adc159627605e7b2beec704d4a78271f6aac259f.
The batch-owned binary patch is byte-identical
(SHA-256 8d0d4e1f91176bc4a8669b81b9ad3c78338d8c0db349bf0f21c153281bd1cf10); 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 b7967696cc02bd953fe34df9423204c02815cbf4
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree adc159627605e7b2beec704d4a78271f6aac259f.
The batch-owned binary patch is byte-identical
(SHA-256 8d0d4e1f91176bc4a8669b81b9ad3c78338d8c0db349bf0f21c153281bd1cf10); 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]

Operational CI refresh only: no checks were created at exact reviewed head b796769 after ancestry-only restack and retargeting to main. Closing/reopening this same PR to trigger eligible pull_request checks. No code, source review, protection or approval changes; not a manual-dispatch substitute and not a bypass.

[realmarcin]

Protected merge verified at cb81d27 (2026-10-06T10:36:31Z). Required merge-group checks passed. Batches 18-40 were restacked with whole-tree and batch-owned binary-patch identity checks, atomically pushed with exact leases, and given refreshed exact-head self-adversarial COMMENT reviews (not independent approval). Batch 18 (#1323) is ready on main with protected auto-merge requested; later PRs remain dependent drafts. All dependents were moved before deleting the merged batch-17 local, remote and tracking branch. Main was fast-forwarded; ignored/untracked collision checks passed and all 46 nonignored untracked files retained their content hashes. Lifecycle receipt: /private/tmp/communitymech-batch25/finish-stack-17.json. No later merge or full-corpus completion is claimed.