Qualify CPR lipid hypotheses and retain unresolved source gaps (batch 27)

[realmarcin]

Scope

Three complete records assessed: Crystal Geyser changed/reviewed, defined three-strain nitrifier unchanged/reviewed, DCPP unchanged/needs_research. Only two completed graph reviews are added. Corpus: 125 reviewed / 331 pending / 4 needs_research, across 460 records in both roots.

Closes #1365. Non-graph Crystal Geyser metadata #1366 and DCPP source follow-up #596 remain open.

Repair And Adversarial Review

Crystal Geyser retains three nodes and two arrows. Positive isotope/genomic carbon-source evidence is retained, but bacterial lipid acquisition and curvature benefit are explicitly hypothetical. Mixed-fraction lipidomics/FTIR and missing known biosynthetic pathways do not resolve transfer flux, exclude unknown ACP-independent synthesis, or demonstrate syntrophy/commensal fitness. All canonical participants are preserved; broad producer context does not assert archaeal-to-CPR donation. Three renames propagate to arrows and an anchored knowledge gap.

The nitrifier's directly abstract-supported aggregate conversion remains unchanged, including selected organic-nitrogen conditions and the endpoint-nitrite boundary. No extra arrows are inferred from relative-abundance associations.

DCPP's complete primary body was not accessible. Nineteen snippets remain absent from independently retrieved abstract text; two match. Selected excerpts are not promoted to primary evidence, and diagnostic exit zero is not represented as all snippets matching. The record is unchanged and not certified as reviewed. Exact strain comparisons, partner-specific detoxification and LC-MS details remain unresolved.

Verification

330 passed in 225.67s (0:03:45). Six new regression tests; focused schema, strict, term, reference, snippet and applicable history checks completed, with DCPP's source gap retained. Zero structural errors; the same 25 existing network warnings, with raw warning exits preserved.

The first regression run caught an omitted participant-user registry entry (one failed, 329 passed). Add exactly Crystal Geyser to the pinned set, 167 to 168 users; both connectivity surveys remain identical, including 124 mixed-scope records. No bound or production logic was loosened, and the complete validation rerun passed. The original failed run remains in the review output.

One guarded YAML edit, one llm-assisted curation event, one append-only history and one regenerated community page. The other 459 records, all non-graph blocks and all 920 caches are byte-preserved. Repeated renders are deterministic; exact node/edge descriptions are checked on all 456 community pages. Actual post-commit just check-docs-current passed cleanly. No browser screenshot review is claimed.

Review outputs are committed under reports/causal_graph_review/: decisions/20261006-three-records-batch27.yaml, validation-20261006-batch27.json, and adversarial-review-20261006-batch27.yaml. This is source-based self-adversarial review, not independent approval. One complete primary main body and two complete abstracts were read; no figure images or supplements inspected. Non-graph metadata is not certified. No full text/PDF, new graph structure or paid Edison job is introduced.

Stacking

Draft dependency on #1363. Do not merge into the topic parent. Require exact-head CI and the protected main queue after parents merge; move dependents before deleting branches. This batch does not complete the full-corpus goal.

[realmarcin]

Source-based self-adversarial review at exact head d82bf3ed87f5166e7ae41d763f90ff4d2bd8cccc, not independent approval.

Addressed graph issue #1365: retain the positive primary carbon-source evidence while bounding CPR lipid acquisition, both existing arrows and curvature adaptation. Alternative biosynthesis, mixed fractions, unresolved donors and absent fitness perturbations remain explicit. No new graph structure was introduced. The unchanged nitrifier retains its bounded abstract-level aggregate claim without inferred extra arrows.

Open findings are not hidden: #1366 tracks non-graph Crystal Geyser overstatements; #596 tracks DCPP primary-body access and 19 missing-from-retrieved-text snippets. DCPP is unchanged/needs_research, not certified as a completed review. Three records assessed adds only two completed reviews.

330 passed in 225.67s (0:03:45); focused validation, six new tests, 456-page description comparisons, deterministic renders and actual post-commit docs-current passed. Network findings remain the same 25 warnings and zero structural errors. One guarded edit/history; 459 other records and all 920 caches preserved. Complete decision and validation artifacts are committed, with source-access and non-graph scope limitations.

The first candidate's participant registry omission was caught by the full suite. Adding exactly Crystal Geyser to the pinned set corrects it; unchanged before/after connectivity surveys and the complete rerun show no loosened bounds or algorithm changes. The one-failed/329-passed run is retained as historical evidence, not reported as the final result.

No figure-image, supplement, independent approval, new Edison job, protected CI success or full-corpus completion is claimed. Protected main merge remains required; do not merge into the topic parent or delete branches with dependents.

[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]

Self-adversarial review refreshed at exact head fcb7a1959ae515d03b7bb6a124a217308ecba22e
after protected main merge of #1307. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d8866edf7be233097d0a555495d24b04fce71827.
The batch-owned binary patch is byte-identical
(SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7); 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 397328d8cf9ececac0e2be8daaf11894993c3fb6
after protected main merge of #1312. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d8866edf7be233097d0a555495d24b04fce71827.
The batch-owned binary patch is byte-identical
(SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7); 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 c48d69621d4c635f9d6819c1aa8c82bfae9f1063
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d8866edf7be233097d0a555495d24b04fce71827.
The batch-owned binary patch is byte-identical
(SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7); 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 0294216a1d442f3e8ad031c4d92fd1c4c40b8c96
after protected main merge of #1318. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d8866edf7be233097d0a555495d24b04fce71827.
The batch-owned binary patch is byte-identical
(SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7); 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 3971cffde104d3c3207ee07e4f69fdae5e530925
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d8866edf7be233097d0a555495d24b04fce71827.
The batch-owned binary patch is byte-identical
(SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7); 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 887df7c30855cc954c0b1b43c302ea561ea4affd
after protected main merge of #1328. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d8866edf7be233097d0a555495d24b04fce71827.
The batch-owned binary patch is byte-identical
(SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7); 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 e29eb558e5fa0983abb15e1619560baef6e47651
after protected main merge of #1334. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d8866edf7be233097d0a555495d24b04fce71827.
The batch-owned binary patch is byte-identical
(SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7); 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 1f805749c7b19e6213ae6e9f059066e22bc1b842
after protected main merge of #1339. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d8866edf7be233097d0a555495d24b04fce71827.
The batch-owned binary patch is byte-identical
(SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7); 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 9046fe545b613fe82508167c158dc24f8bc4323e
after protected main merge of #1346. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d8866edf7be233097d0a555495d24b04fce71827.
The batch-owned binary patch is byte-identical
(SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7); 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 c5d8a65b6b43ee39959705daf15b05cba1b528c1
after protected main merge of #1350. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d8866edf7be233097d0a555495d24b04fce71827.
The batch-owned binary patch is byte-identical
(SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7); 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 020eb151fe98d6646fbb0a45f4a3302bcd8f4d4d
after protected main merge of #1355. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree d8866edf7be233097d0a555495d24b04fce71827.
The batch-owned binary patch is byte-identical
(SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7); 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 integration review at exact head 39afb25d3ff2d404a2f6b1467c36453a8be82635. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 020eb151fe98d6646fbb0a45f4a3302bcd8f4d4d, the only changes are the canonical schema pin, shared schema and generated datamodel from that main commit. Every other tracked file is identical; the batch-owned binary patch remains byte-identical (SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7). All 60 published batch patches were checked this way. No scientific assertion, reference cache, history, decision ledger or generated page was edited by this integration.

Adversarial checks: no inherited schema-file edits lost; generated CrossCorpusLink remains standalone and does not add a causal claim; normal strict validation passed all 460 records; required CrossCorpusLink fields enforced. Fresh broad regression runs on both ends of the stack: 302 passed in 172.77s (0:02:52); 756 passed in 255.55s (0:04:15). Docs-current passed clean at batches25/84, and vendored-sync passed. The 58 intermediate combinations were not independently retested. Existing primary-source review limitations and unresolved research issues remain applicable; historic validation receipts are not rewritten as new scientific reviews.

An additional generated-datamodel loading check FAILED and is retained in the integration receipt. Differential testing found exactly the same failures on all 460 paths before and after this integration:417 unhashable TaxonDescriptor and43 unhashable CultureCollectionEnum exceptions, with linkml-runtime1.11.1. Existing tests explicitly use plain YAML instead of this loader. Pre-existing defect #1703 remains OPEN; no datamodel-loader success is claimed. Normal strict schema validation is a separate passing path, not a relabeling of that failure.

Required CI must pass on this exact head and the protected merge-queue candidate. No manual workflow dispatch, artificial status, administrative merge or protection bypass. Dependents stay draft until their parent is confirmed merged; move dependents before branch deletion.

[realmarcin]

Self-adversarial review refreshed at exact head 7125ba523e7d037a252d455617f4071bb0e2c16c
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 0873dfff275c95d2b1168bc2d184a1a921b01e6e.
The batch-owned binary patch is byte-identical
(SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7); 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 governance integration review at exact head 9d1c77c256ded7d121fcf45445e8570c351ad68c. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 7125ba523e7d037a252d455617f4071bb0e2c16c, exactly two files changed: scripts/.vendored_canon_ref and tests/test_id_label_empty_adapter.py. Each resulting tree differs from its old tree by the exact binary patch from main, and each batch-owned binary patch remains byte-identical (SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7). These invariants passed on all 74 published branches. Original heads are retained in local archive refs/archive/communitymech-pre-governance-20261007. No scientific record, source cache, history, decision ledger, schema, runtime code or generated page changed in this integration.

Adversarial inspection: the adapter regression still checks the empty sentinel and case-insensitive caching, now with an isolated fake oaklib module and a one-call selector assertion. No validation threshold or runtime behavior was relaxed. Fresh regressions at both stack ends: 337 passed in 214.19s (0:03:34); 917 passed in 402.58s (0:06:42). Docs-current and pinned vendored-sync passed at batches26/99. The 72 intermediate combinations were checked by tree/patch hashes, not independently retested. Historical source-review limitations and unresolved issues, including loader #1703 and cache #1091, remain applicable. This is not new paper review, independent approval, or a claim that those outstanding issues are fixed.

Digest-bound integration receipt/logs: /private/tmp/communitymech-governance-integration-20261007/receipt.json. Prior output/review records in reports/causal_graph_review/ remain unchanged. The prior lifecycle receipt is archived and will be updated only after all exact-head comments are verified.

Required CI and independent review must pass for the exact head and protected merge-queue candidate. No CI rerun, manual dispatch, fabricated status, admin merge or protection bypass. Dependents remain draft; move them before deleting a merged parent branch.

[realmarcin]

Exact-head self-adversarial restack review at b617e5daf0aee7d2888855cdf9ff99580a40bd7f.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 fb0e833e8f7feaf9bbe3c4c10721741ad712abb8ceff2749234b60cb8a8cdeb7.
Tree 6924311a18bea4d3132265afb2cedbaeb05abbea matches the independently computed clean merge.
Compared with historical tree 879ec62923f072b420ff3919ff92cb45f00954bd, only scripts/.vendored_canon_ref
changes, incorporating main PR #1834's pin 849f336e025510316a5f235eb0af8547b8bd50cc.
All curated records, source caches, review outputs, histories, regression tests, and rendered
pages remain unchanged. No new primary-source review or local scientific-test rerun is claimed.

This PR is now part of native stack #1973, rooted at #1363 on main. No protected merge
has occurred. Fresh eligible PR/merge-group CI remains mandatory. No rule bypass, fabricated
status, merge into a topic parent, or premature branch deletion.

[realmarcin]

Superseded by the protected cumulative merge #1975 at 42959bef2549f9a42c3e3303a0e10fd5be99f30e. This PR's reviewed source head f89ced919014bf0ab6ca9df10e5ccbcdee6741ea was included in the cumulative branch; the final squash tree matches the reviewed integration tree exactly, and all seven required merge-group checks passed.

Patch-inclusion receipt. Existing issue-closing links were transferred to #1975; unresolved research and non-graph gaps are not closed by this action. This PR is being closed as superseded, not represented as individually merged. Archival provenance tags retain source commits; cleanup removes branch refs only and preserves worktree files.