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Bound inferred mechanisms while preserving measured outcomes (batch120) - #1938
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Source-based self-adversarial review at exact head 5afca28; not independent approval.
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Retain experimentally supported carbon cross-feeding and tracer direction without inventing a compound or nitrogen flux.; Retain reciprocal-growth mutualism with direct growth evidence, bounding supplemented-culture comparisons and genomic route inference.
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Retain measured external-gas methane production without coding abiotic supply as microbial cross-feeding or qPCR as activity.; Retain VFA measurements and source interpretations while removing an unsupported demonstrated-syntrophy type.
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Retain reported maturation without coding aggregate improvement as mutualism; bound the remaining environmental-mediation arrow.; Retain positive later attenuation and the early rebound without claiming universal viable-pathogen elimination or bilateral competition.; Represent KEGG and network findings as HGT potential, not measured transfer, expression or motility.
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Retain positive compound responses with isolate-specific limits and the Y878 null result.; Keep antagonism and compatibility distinct from cheA-based potential and unmeasured colonization.; Preserve the positive field co-treatment outcome while bounding qPCR, Tax4Fun and mechanistic attribution.
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All 10 original nodes and 4 arrows accounted for: 10 nodes and 3 arrows retained, one unsupported common-treatment arrow removed, six renames, no new topology. Targets and discussion anchors resolve. No direction invented.
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Arsenic carbon transfer and reciprocal growth remain positive evidence, retaining CROSS_FEEDING and MUTUALISM. Genomic complementarity is not direct nitrogen/oxygen tracing. Oxygen-supplemented pure culture is not a demonstrated oxygen requirement. Exact strains and canonical identities unchanged.
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Biomethane 86% by day 69 remains observed; above 90% remains proposed. External cylinder gas is not microbial cross-feeding. qPCR/16S profiles are not viability or taxon-specific flux; positive plate recovery is separate. VFA pools and inferred routes do not establish thermodynamic syntrophy. Prewashout sampling quotation explicitly belongs to phase 1, not demonstrated phase 4 timing.
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Compost retains maturation, transient ARG rebound, later attenuation and reported pathogen elimination. Aggregate treatment benefit is not mutualism or bilateral competition. KEGG and potential host-gene network signals are not expression, motility or actual transfer events. 26.6% refers to potential associations. One environmental-mediation arrow stays PARTIAL; common-treatment maturation-to-HGT arrow removed.
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Tobacco retains isolate-specific positive resource responses, Y878 null enhancement, compatible antagonist isolates and positive combined field treatment. cheA PCR is not measured migration/colonization; cheA-negative isolates also antagonize. The resource library cites tomato exudates. Missing non-chemotactic controls are explicit future work. qPCR and Tax4Fun are not viability/activity. Results/Discussion counts and tomato-caption inconsistencies are not silently reconciled.
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Twenty-seven graph and six discussion quotes match fresh primary texts and all existing caches. Full main bodies, methods, results, discussion, table text and captions read for biomethane and tobacco; arsenic and compost review bounded to fresh primary abstracts. No original figure pixels, supplements, raw data or analysis-code audit. No cache edits or full-body imports. Tobacco license is CC BY-NC-ND 4.0, not unrestricted CC BY. Matching is not entailment certification.
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Four guarded writes and append-only histories preserve 456 other records, all 923 caches, unrelated raw blocks and previous histories/decisions. Canonical taxon identities/ranks unchanged. Metadata/composition/scope findings remain separate issues #1935-#1937. Shared evidence aliases detached before edits.
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Fifteen focused tests and twelve control/mutation/restored-control probes pass. Mutations reject loss of positive carbon/field evidence, syntrophy overclaims, oxygen inference promotion, external-gas cross-feeding, compost mutualism, HGT proof promotion, loss of ARG rebound, restored common-treatment arrow, loss of Y878 null and unmeasured chemotaxis. No canonical writes during probes.
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The initial mutation harness removed a required dictionary key and stopped with KeyError before producing a report. It was changed to a wrong interaction-type value so the intended scientific assertion is exercised. All 12 cases then completed with restored controls; no test or canonical-record weakening.
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All four records pass schema, strict, terms, full-record references, snippets, rank and history. 1131 selected tests including palette pass; not full Linux CI certification. Network: 57 unchanged warnings, zero structural defects. Descriptions on 456 pages, 1361 nodes and 522 arrows exactly match descriptions with deterministic rendering, not screenshot QA.
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All participant lists and scopes unchanged; 299 participant-list users. Census: 414 community-level, 136 mixed, 278 community-only, 1568 taxa, 1281 solely credited unchanged. Scope credit is not actual participant coverage. Connectivity logic and thresholds unchanged.
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Issues #1931-#1934 addressed pending protected-main merge; #1935-#1937 remain open. No Edison extension or credits. Prior Ruegeria #1883 still needs configured authentication and was not retried unchanged. Self-adversarial review is not independent approval; root #1836 and actual exact-head protected checks remain required.
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Corpus: 388 reviewed, 18 pending, 54 needs_research across 460 records. Overall goal, protected merge and branch deletion incomplete. Postcommit docs-current and exact-head publication are separate gates, not preasserted here.
1131 passed in 305.98s (0:05:05); fifteen focused tests and twelve real in-memory mutation probes. All four edited records pass schema, strict, terms, full-record references, snippets, rank and history. 41 gate outputs retain commands, output tails and digests. All 456 other records, all 923 caches and unrelated raw fields are unchanged.
All 10 original nodes and 4 arrows reviewed. Ten nodes and three arrows remain; one unsupported common-treatment arrow removed; six renames; no new topology. Arsenic retains measured carbon transfer and reciprocal growth without conflating genomic predictions with nitrogen/oxygen tracing. Biomethane retains external-gas methane production and VFA measurements without demonstrated syntrophy or qPCR-based activity. Compost retains reported maturation and attenuation while KEGG and network findings remain potential, not measured HGT. Tobacco retains isolate-specific positive results, Y878 null enhancement and the positive combined field treatment without cheA-mediated colonization proof.
Four fresh primary abstracts and identities checked. Complete main-body XML texts, methods, results, discussion, table text and captions read for biomethane and tobacco; arsenic and compost changes are abstract-bounded. No original figure pixels, supplements, raw data or analysis-code audit. All 33 graph/discussion quotes match fresh sources and caches; this is not entailment certification. No cache edits or publication-body imports; tobacco license is CC BY-NC-ND 4.0.
Corpus: 388 reviewed, 18 pending, 54 needs_research; 57 unchanged network warnings, zero structural defects. Participant lists and scopes unchanged: 299 list users, 414 community-level, 136 mixed, 278 community-only, 1568 taxa, 1281 solely credited. No connectivity logic or threshold edits. Descriptions on 456 pages, 1361 nodes and 522 arrows exactly match the source, with deterministic rendering, not screenshot certification. Postcommit docs-current passed clean; log SHA256 7038e3f86c2c9db82118ba3812613499bfbfd5f57c5281aec45eeb3552517fdd. Selected local passes are not full Linux CI certification; corpus snippet audit remains informational.
Decision ledger, provenance, validation, four append-only histories and self-adversarial review are committed. Metadata/composition/design #1935-#1937 remain open. No Edison invocation or new topology; prior Ruegeria #1883 still needs configured authentication. This COMMENT is self-review, not independent approval. Root blocker #1836 requires actual protected checks. No artificial CI, protection bypass, merge or premature branch deletion.
Network integrity findingsWarnings 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. The full report is attached to the workflow run as an artifact. |
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Exact-head self-adversarial restack review at b68fe05f370a17152ab59ca2a05c6569113e95ea.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 2149e15fc53d47c3a7dfdd9d3d0c366a8f6d5fa49fef3e49bf807cc921599038.
Tree 7048a48feea0c45ec46b34f2832883cd65b56383 matches the independently computed clean merge.
Compared with historical tree d78af7c5ca32b724f1a57b22ac40391989f72c89, 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.
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Superseded by the protected cumulative merge #1975 at 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. |
1 participant
Scope
Closes #1931.
Closes #1932.
Closes #1933.
Closes #1934.
Non-graph metadata/composition/design #1935-#1937 remain open; this batch does not resolve prior research extensions.
The genuine palette correction #1913 is inherited from the verified parent; required current-head CI remains a separate gate.
Adversarial Review
Verification And Output Records
1131 passed in 305.98s (0:05:05); fifteen focused tests and twelve real in-memory mutation probes. All four edited records pass schema, strict, terms, full-record references, snippets, rank and history. 41 gate outputs retain commands, output tails and digests. All 456 other records, all 923 caches and unrelated raw fields are unchanged.
All 10 original nodes and 4 arrows reviewed. Ten nodes and three arrows remain; one unsupported common-treatment arrow removed; six renames; no new topology. Arsenic retains measured carbon transfer and reciprocal growth without conflating genomic predictions with nitrogen/oxygen tracing. Biomethane retains external-gas methane production and VFA measurements without demonstrated syntrophy or qPCR-based activity. Compost retains reported maturation and attenuation while KEGG and network findings remain potential, not measured HGT. Tobacco retains isolate-specific positive results, Y878 null enhancement and the positive combined field treatment without cheA-mediated colonization proof.
Four fresh primary abstracts and identities checked. Complete main-body XML texts, methods, results, discussion, table text and captions read for biomethane and tobacco; arsenic and compost changes are abstract-bounded. No original figure pixels, supplements, raw data or analysis-code audit. All 33 graph/discussion quotes match fresh sources and caches; this is not entailment certification. No cache edits or publication-body imports; tobacco license is CC BY-NC-ND 4.0.
Corpus: 388 reviewed, 18 pending, 54 needs_research; 57 unchanged network warnings, zero structural defects. Participant lists and scopes unchanged: 299 list users, 414 community-level, 136 mixed, 278 community-only, 1568 taxa, 1281 solely credited. No connectivity logic or threshold edits. Descriptions on 456 pages, 1361 nodes and 522 arrows exactly match the source, with deterministic rendering, not screenshot certification. Postcommit docs-current passed clean; log SHA256 7038e3f86c2c9db82118ba3812613499bfbfd5f57c5281aec45eeb3552517fdd. Selected local passes are not full Linux CI certification; corpus snippet audit remains informational.
Decision ledger, provenance, validation, four append-only histories and self-adversarial review are committed. Metadata/composition/design #1935-#1937 remain open. No Edison invocation or new topology; prior Ruegeria #1883 still needs configured authentication. This COMMENT is self-review, not independent approval. Root blocker #1836 requires actual protected checks. No artificial CI, protection bypass, merge or premature branch deletion.
Dependency
Draft depends on #1930. Do not merge into the topic parent. Require actual exact-head checks through protected main. Move dependents before deleting parent branches.