Bound predictions and DIET proposals; remove noncausal plasmid arrows (batch 28)

[realmarcin]

Scope

Four complete records assessed: cultivated-meat contaminant SynCom unchanged/reviewed; Fahmy T4, Cyprus bioleaching and DIETsimp changed/reviewed. Corpus: 129 reviewed / 327 pending / 4 needs_research across 460 records in both roots.

Closes #1368. Closes #1369. Closes #1370. Non-graph metadata follow-ups #1371, #1372 and #1373 remain open.

Repairs And Adversarial Review

Fahmy T4 retains predicted five-class enzyme coverage and the positive HPLC parent-removal result, including the recovered-start denominator and native-microbiota context. Remove unsupported mutualism labels, identify all six canonical participants, and distinguish annotation from expression, member flux, mineralization and reciprocal benefit. No prediction-to-assay workflow arrow is restored.

Cyprus retains measured mineral/fraction composition patterns and predicted plasmid functions. Remove two arrows representing recovery context and a general-repertoire example, not causal dependencies. Mineral differences do not isolate Fe. Plasmid hosts/functions remain qualified; Alphaproteobacteria-associated resistance is not assigned to a specific Rhodospirillales or archaeal member. CRISPR matches support a proposed host-associated capability, not observed taxon competition, cleavage, plasmid exclusion or confirmed co-residence.

DIETsimp retains two parallel donor-to-methanogen arrows explicitly as hypotheses. Positive pH-dependent conductivity and cytochrome-associated signals remain in scope, without proving donor-specific flux or excluding hydrogen/formate mediation. The intrinsic methanogen step becomes source-only using the existing PAIRWISE convention; exact names/anchors and contradictory no-downstream gap wording are repaired.

The cultivated-meat record remains unchanged: predicted complementarity is not experimentally resolved exchange, exogenous antimicrobial suppression is not intermember antagonism, and MIC is not the unspecified long-term effective dose. No invented edit event or history.

Verification

336 passed in 306.36s (0:05:06); six new focused tests. Schema, strict, terms, references, independent snippet audit and applicable history checks passed. Raw outputs distinguish diagnostic reference results from snippet counts. Zero structural errors and the same 25 network warnings, with warning exits preserved.

Ten existing nodes retained, two Cyprus arrows removed and two DIETsimp arrows qualified; six renames propagate exactly. Three guarded writes, three llm-assisted events, three append-only histories and three regenerated pages. All non-graph blocks, the other 457 records and all 920 caches are byte-preserved. Repeated rendering is deterministic; exact node/arrow descriptions were compared on all 456 community pages. Actual post-commit just check-docs-current passed cleanly. No browser screenshot review is claimed.

The pinned participant registry adds only Fahmy T4 and Cyprus, 168 to 170 users. Both connectivity surveys are recorded; mixed-scope count remains 124. No numeric bounds or production algorithms are changed.

Review records are committed under reports/causal_graph_review/: decisions/20261006-four-records-batch28.yaml, validation-20261006-batch28.json, and adversarial-review-20261006-batch28.yaml. This is source-based self-adversarial review, not independent approval. Two complete primary main bodies and two complete abstracts were reviewed; no figure images or supplements. No primary full text/PDF, new graph structure or paid Edison job is introduced.

Stacking

Draft dependency on #1367. Do not merge into the topic parent. Require exact-head CI and 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 8e46f69f9498a03915cdc0ab33c2f8f2c8e19e91, not independent approval.

Addressed #1368, #1369 and #1370. Preserve positive HPLC/composition/conductivity observations while distinguishing predicted enzymes and proposed electron-transfer mechanisms from measured activity, member flux and fitness. Remove the two noncausal Cyprus arrows and qualify the two existing parallel DIETsimp arrows. Keep CRISPR inference host-associated without claims of co-residence, exclusion or taxon competition. No new structure is introduced.

All ten original nodes and four arrows have explicit decisions; six exact renames and their anchors/targets are checked. Cultivated-meat is unchanged/reviewed, not an invented edit. Non-graph #1371, #1372 and #1373 remain open; non-graph blocks are preserved, not certified.

336 passed in 306.36s (0:05:06); six new tests, focused validation, 456-page description comparisons, deterministic renders and actual post-commit docs-current passed. Zero structural errors; the same 25 network warnings. Three guarded edits/history entries; 457 other records and all 920 caches preserved. Exact participant census 168 to 170 with measured before/after connectivity and no relaxed bounds.

Committed decisions, validation and adversarial output preserve source-access limits. Two complete main bodies and two complete abstracts reviewed; no figure images or supplements. No 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 17b5c3da1722987a42a9d0c26d2f6ec4b3a834f2
after protected main merge of #1307. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree c99b34388ade0b2e176fa442c6fb8122fc5ff942.
The batch-owned binary patch is byte-identical
(SHA-256 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9); 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 287faa64bf34bb0bce9e87c94d121b77090f5891
after protected main merge of #1312. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree c99b34388ade0b2e176fa442c6fb8122fc5ff942.
The batch-owned binary patch is byte-identical
(SHA-256 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9); 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 45898b9a895944784f1b617a4bd83c78781901c9
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree c99b34388ade0b2e176fa442c6fb8122fc5ff942.
The batch-owned binary patch is byte-identical
(SHA-256 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9); 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 b64120c816ccf38731fe70c16dc55298dab4cb41
after protected main merge of #1318. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree c99b34388ade0b2e176fa442c6fb8122fc5ff942.
The batch-owned binary patch is byte-identical
(SHA-256 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9); 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 1784affa69b1df7a5852c13f0ec30fddd47862a5
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree c99b34388ade0b2e176fa442c6fb8122fc5ff942.
The batch-owned binary patch is byte-identical
(SHA-256 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9); 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 d277141df96e20baaea7885bd641d15eefddb053
after protected main merge of #1328. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree c99b34388ade0b2e176fa442c6fb8122fc5ff942.
The batch-owned binary patch is byte-identical
(SHA-256 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9); 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 c03a1eae1bd7fbeb7d254dc2e25cb435ea0d88e3
after protected main merge of #1334. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree c99b34388ade0b2e176fa442c6fb8122fc5ff942.
The batch-owned binary patch is byte-identical
(SHA-256 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9); 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 6cc7be39500165f6fbadb3383a83dea08fc23c7c
after protected main merge of #1339. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree c99b34388ade0b2e176fa442c6fb8122fc5ff942.
The batch-owned binary patch is byte-identical
(SHA-256 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9); 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 769527e37d4f1393e75c1f0b663432ac01cee5af
after protected main merge of #1346. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree c99b34388ade0b2e176fa442c6fb8122fc5ff942.
The batch-owned binary patch is byte-identical
(SHA-256 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9); 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 c2fd68c06e214be59898ef2370e2dd1adbfe9b4d
after protected main merge of #1350. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree c99b34388ade0b2e176fa442c6fb8122fc5ff942.
The batch-owned binary patch is byte-identical
(SHA-256 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9); 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 414bdf4b8067567479df99be1cdf9e69aeab8d72
after protected main merge of #1355. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree c99b34388ade0b2e176fa442c6fb8122fc5ff942.
The batch-owned binary patch is byte-identical
(SHA-256 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9); 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 286b70e32439e7481e9a6fbb12d1cda20c3e9806. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 414bdf4b8067567479df99be1cdf9e69aeab8d72, 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 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9). 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 e9411239d21db2e532488bd7fa3da9a34206c7c5
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 31596a5cc5bb11e5efdeb32ce723f26b0cd8c943.
The batch-owned binary patch is byte-identical
(SHA-256 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9); 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 133f4a7c689a761ec88f3f6121621d2b613b1ba9. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head e9411239d21db2e532488bd7fa3da9a34206c7c5, 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 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9). 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 9517b72c725c5624ea520ce2c9436fd24162d012.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 7a5af73807b297ece8ff76deab02560424825f005783bbdeea58ed30b590e8b9.
Tree 2d8125d4daf3ce5a43a915799d667c9cecb2b0c5 matches the independently computed clean merge.
Compared with historical tree 12d7689b8f0a5a44c53d28397f313c08677fe885, 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 44593064c0e3615bd5e0f45ef5854fd0aba41725 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.