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Separate strain variants and inferred causal networks (batch119) - #1930
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Source-based self-adversarial review at exact head 0c53674; not independent approval.
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Retain locus-dependent UW101 inhibition without asserting bilateral fitness harm.; Retain experimental transcriptional dependence with correct denominators and direct/indirect limits.; Retain UW101 protection with all three participants, while bounding the CI04 chemical mechanism.
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Separate TYQ1 inoculation from nematode-driven enrichment and avoid assigning mutualism from abundance.; Retain all seven positive biofilm pairings with the SX attraction exception and in-vitro provenance.; Retain measured spent-medium cross-feeding with AS, medium, direction and network-weight limits.; Retain biological omission and host-outcome evidence without overclaiming the specific mediator.
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Retain the field-treatment input with correct evidence source and unresolved timing boundary.; Retain reported agronomic outcomes without typing host benefit as microbial mutualism or measured nitrogen fixation.; Keep soil relative-abundance responses separate from inoculant establishment and absolute growth.; Represent Bacillus centrality as computational association, not validated ecological function or necessity.
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Retain the abiotic enrichment design and its two selection arrows without asserting niche partitioning.; Preserve carbon-associated ASV sorting with representative participants and no inferred substrate flux.; Define fast/slow as operational abundance classes rather than growth-rate measurements or hub membership.; Keep transfer-specific hubs computational and distinguish centrality from ecological necessity.; Keep recurring hubs as statistical observations without assigning validated PGP or stability function.; Retain reproducible revival only for the five selected stocks and separate it from initial enrichment stability.
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All20original nodes/10arrows accounted for:17nodes/10arrows retained,three nodes removed,nine renames,no new topology. Targets and discussion anchors resolve; no shortcut edge invented.
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THOR2022Methods explicitly identify UW101,not founding CI04. Keep UW101 inhibition,locus-dependent expression and three-member protection. One-sided inhibition is not bilateral competition. Expression percentages describe greater-than-twofold pairwise DEGs,not whole genomes. CI04 biofilm stays positive contextual evidence,not a UW101 node; chemical mediation remains PARTIAL.
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TYQ1 retains all seven positive biofilm pairings with the SX attraction exception. Cross-feeding is medium- and direction-specific,with the AS reverse-use exception and rich-medium negative result. Carrying-capacity weights are not flux. Real strain omission remains positive experimental evidence,distinct from Gephi node removal; specific biofilm/exchange mediation remains PARTIAL.
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Teosinte formulation/preparation nodes removed while non-graph protocol remains. Reported field-treatment effects and both treatment arrows retained; no field-statistics reproduction claimed. Soil relative abundance does not track inoculant strains. Bacillus centrality is computational correlation,not microbial mutualism,measured nitrogen fixation or necessary function.
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mCAFEs is multiple enrichment communities. Carbon and transfer-interval interventions retain two selection arrows. Fast/slow is an operational abundance comparison,not measured isolate growth rates. Hub membership is not growth-class membership. Statistical hubs are not experimental keystones or validated PGP functions. Positive revival is bounded to five selected stocks,not all initial enrichments.
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Thirty-eight graph and five discussion quotes match five fresh primary texts and caches. Five complete main-body XML texts read,including methods,tables and captions; no original pixels,supplements,raw data or analysis-code audit. Matching is not entailment certification. One CC-BY4.0 cache receives four missing selected excerpts append-only,not a full-body import.
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Four guarded writes and append-only histories preserve456otherrecords,922caches,unrelated raw blocks and previous histories/decisions. Canonical taxon identities/ranks unchanged; source-identity limitations remain separate issues1926-1929. Shared evidence aliases detached before edits.
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Fifteen focused tests and twelve control/mutation/restored-control probes pass. Mutations reject bilateral competition,unbounded molecular mediation,CI04-to-UW101 transfer,erasure of positive biofilm/cross-feeding/omission evidence,unmeasured nitrogen fixation,experimental hub necessity,loss of observed selection and universal stock revival. No canonical writes during probes.
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All four records pass schema,strict,terms,full-record references,snippets,rank and history.1116selected tests including palette pass; not full Linux CI certification. Network57unchanged warnings,zero structural defects.456pages/1361nodes/523arrows exactly match descriptions with deterministic rendering,not screenshot QA.
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Participant-list users rise298to299 for THOR protection. Record-scope census remains414community-level,136mixed,278community-only,1568taxa; sole credit rises1280to1281 because Bacillus leaves the incorrect pairwise node and is named in three-member protection. Initial verifier expectation corrected after inspecting this delta; no graph or threshold changed to pass. Scope credit is not actual participant coverage. Connectivity logic and all thresholds unchanged.
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Issues1922-1925 addressed pending protected-main merge;1926-1929 remain open. No Edison extension or credits. Prior Ruegeria1883 still needs configured authentication and was not retried unchanged. Self-adversarial review is not independent approval; root1836 and real exact-head protected checks remain required.
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Corpus384reviewed,22pending,54needs_research across460records. Overall goal,protected merge and branch deletion incomplete. Postcommit docs-current and exact-head publication are separate gates,not preasserted here.
1116 passed in 319.85s (0:05:19); 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. All456otherrecords,922caches and unrelated raw fields are unchanged.
All20original nodes/10arrows reviewed. Seventeen nodes and ten arrows remain,three nodes removed,nine renames,no new topology. THOR separates founding CI04 biofilm from UW101 inhibition,expression and protection. TYQ1 retains biofilm,cross-feeding and real biological omission while specific mediation remains partial. Teosinte retains reported field-treatment effects without formulation-workflow nodes or mutualistic soil-network claims. mCAFEs retains selection and five-stock revival while abundance classes and statistical hubs stay distinct from measured growth and ecological necessity.
Five fresh primary abstracts/identities and complete main-body XML texts,methods,results,discussion,table text and captions read; not original figure pixels,supplements,raw data or analysis code. All43graph/discussion quotes match fresh sources and caches,not entailment certification. Four missing CC-BY4.0 excerpts appended to one THOR cache,preserving its prefix; no full-body import.
Corpus384reviewed,22pending,54needs_research;57unchanged network warnings,zero structural defects. One participant-list user added (299total). Sole community-level credit rises1280to1281 because Bacillus moves from an incorrect pairwise node into explicit three-member protection; record-scope counts stay unchanged. Initial verifier expectation corrected after inspecting that delta; no connectivity logic or threshold edits.456pages/1361nodes/523arrows exactly match source descriptions,with deterministic rendering,not screenshot certification. Postcommit docs-current passed clean; log SHA256 21509d03c81b306f3c753e58b89cb182872f663188414450b8701659ff0a9347. 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 #1926-#1929 remain open. No Edison invocation or new topology; prior Ruegeria1883 still needs configured authentication. This COMMENT is self-review,not independent approval. Root blocker1836 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 43a916f8543b8274323713a58ae1906010322b88.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 54340a1a97848163b466ec4cd1f9253ab37c7dab8419e61951bc2d85c26148c5.
Tree 86f66a1959274200cb2aaf22238ed57df4655a30 matches the independently computed clean merge.
Compared with historical tree 000b678a6237ea7c28c562d153fa8f66cbcda2b2, 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 #1922.
Closes #1923.
Closes #1924.
Closes #1925.
Non-graph metadata/composition/design #1926-#1929 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
1116 passed in 319.85s (0:05:19); 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. All456otherrecords,922caches and unrelated raw fields are unchanged.
All20original nodes/10arrows reviewed. Seventeen nodes and ten arrows remain,three nodes removed,nine renames,no new topology. THOR separates founding CI04 biofilm from UW101 inhibition,expression and protection. TYQ1 retains biofilm,cross-feeding and real biological omission while specific mediation remains partial. Teosinte retains reported field-treatment effects without formulation-workflow nodes or mutualistic soil-network claims. mCAFEs retains selection and five-stock revival while abundance classes and statistical hubs stay distinct from measured growth and ecological necessity.
Five fresh primary abstracts/identities and complete main-body XML texts,methods,results,discussion,table text and captions read; not original figure pixels,supplements,raw data or analysis code. All43graph/discussion quotes match fresh sources and caches,not entailment certification. Four missing CC-BY4.0 excerpts appended to one THOR cache,preserving its prefix; no full-body import.
Corpus384reviewed,22pending,54needs_research;57unchanged network warnings,zero structural defects. One participant-list user added (299total). Sole community-level credit rises1280to1281 because Bacillus moves from an incorrect pairwise node into explicit three-member protection; record-scope counts stay unchanged. Initial verifier expectation corrected after inspecting that delta; no connectivity logic or threshold edits.456pages/1361nodes/523arrows exactly match source descriptions,with deterministic rendering,not screenshot certification. Postcommit docs-current passed clean; log SHA256 21509d03c81b306f3c753e58b89cb182872f663188414450b8701659ff0a9347. 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 #1926-#1929 remain open. No Edison invocation or new topology; prior Ruegeria1883 still needs configured authentication. This COMMENT is self-review,not independent approval. Root blocker1836 requires actual protected checks. No artificial CI,protection bypass,merge or premature branch deletion.
Dependency
Draft depends on #1921. Do not merge into the topic parent. Require actual exact-head checks through protected main. Move dependents before deleting parent branches.