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Separate treatment identity and model-based causal claims (batch118) - #1921
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Source-based self-adversarial review at exact head 97c4851; not independent approval.
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Retain experimental nitrogen cross-feeding while bounding the signaling bridge.; Keep AI-2 perturbation support without typing regulation as nutrient transfer.; Retain the three-member EPS maximum only among tested combinations with explicit participants.
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Retain observed spatial differentiation without exhaustive five-genus membership.; Limit biofilm roles to its three representative genera and omit unsupported within-fraction partitioning.; Limit suspension roles to its two representative genera without assigning each all pathways.; Qualify both EET arrows as computational inference and leave unspecified dependency untyped.
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Preserve seven positive spent-medium responses and three bilateral pairs with only potential cross-feeding.; Restrict the SSC8 outcome to measured growth without added pathogen.
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Retain measured sulfate effect with guild-level, pathway-inferred competition.; Keep the measured oxygen response untyped and do not convert residual methane to zero.; Qualify the fitted subnetwork without assigning directly measured cross-feeding or universal oxygen stimulation.
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All13original nodes/eight arrows accounted for:12nodes/four arrows retained,one misassigned node/four arrows removed,four renames,no new topology. Targets and discussion anchors resolve; no shortcut edge invented.
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Viili positive evidence retained: nutrient depletion/supplementation and AI-2 perturbations support their respective outcomes. The nitrogen-signaling bridge is partial,not growth-independent valine mediation. AI-2 regulation is untyped rather than nutrient transfer. Prior1014/1015 fixes preserved.
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Sludge division of labor and reactor outcomes retained. Biofilm participants are three representative genera; suspension participants are two. EET support is partial least squares inference,not an interruption/rescue experiment,genus-resolved flux or obligatory thermodynamic syntrophy.
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Watermelon SSC8 outcome is growth without added pathogen. Parent16-member SBC disease challenge and biofilm-pathway enrichment are not transferred. Seven partners have positive spent-medium effects; only three pairs are bilateral. Potential exchange is not compound-specific rescue or resolved stereochemistry. Exact SSC8 roster and non-graph fields remain1919.
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Wetland treatment responses remain experimental while pathway fluxes and competition are inferred. Shared exposure does not establish response-to-model arrows. Model subnetwork is not direct donor-recipient transfer; residual methane is not zero. Some source results/discussion statements differ and are not silently reconciled. Vessel and ingredient issues remain1920.
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Twenty-five graph and four discussion quotes match fresh primary texts and caches,not entailment certification. Two complete main-body XML texts read including methods/tables/captions; no original pixels,supplements,raw data or model-code audit. Viili/sludge are abstract-bounded; no claim of exhaustive full-text absence.
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Four guarded writes and append-only histories preserve456otherrecords,923caches,unrelated raw blocks and previous histories/decisions. Shared evidence aliases detached. Canonical taxon IDs/labels/ranks unchanged. No cache import.
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Twelve focused tests plus ten control/mutation/restored-control probes pass. Mutations reject erasing nutrient benefit,misclassifying signaling,overstating EET,wrong fraction credit,seven mutualisms,compound certainty,parent-to-SSC8 assay transfer,common-cause arrows and direct model cross-feeding. No canonical files changed during probes.
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All four records pass schema,strict,terms,full-record references,snippets,rank and history.1101selected tests including palette pass; not full Linux CI certification. Network has57unchanged warnings and zero structural defects.456pages/1364nodes/523arrows exactly match descriptions with deterministic rendering,not screenshot QA.
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Participant-list users rise296to298; scope census remains414community-level,136mixed,278community-only,1568taxa,1280solelycredited. This census is not actual participant coverage. Connectivity logic and all thresholds unchanged.
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Issues1915-1918 are addressed pending protected-main merge;1919/1920 remain open. No Edison extension or credits. Prior Ruegeria1883 still needs configured authentication. Self-adversarial review is not independent approval; root1836 and real exact-head protected checks remain required.
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Corpus380reviewed,26pending,54needs_research across460records. Overall goal,protected merge and branch deletion remain incomplete. Postcommit docs-current and exact-head publication are separate gates,not preasserted here.
1101 passed in 379.68s (0:06:19); twelve focused tests and ten 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,923caches and unrelated raw fields are unchanged.
All13original nodes/eight arrows reviewed. Twelve nodes and four arrows remain,one misassigned node/four unsupported arrows removed,four renames,no new topology. Viili retains nitrogen provision and positive AI-2 regulation while signaling mediation remains partial. Sludge EET arrows are PLS-model inference with fraction-specific participants. SSC8 growth without added pathogen is separated from the parent16-member disease/biofilm experiment. Wetland gas effects are retained without common-cause arrows to fitted metabolism.
Fresh primary abstracts/identities checked. Watermelon/wetland full main-body XML,methods,results,discussion,table text and captions read; not original pixels,supplements,raw data or model code. Viili/sludge are abstract-bounded. All29graph/discussion quotes match fresh sources and caches,not entailment certification. No cache changes or publication-body imports.
Corpus380reviewed,26pending,54needs_research;57unchanged network warnings,zero structural defects. Two participant-list users added (298total),scope census unchanged; no connectivity logic or threshold edits.456pages/1364nodes/523arrows exactly match source descriptions,with deterministic rendering,not screenshot certification. Postcommit docs-current passed clean; log SHA256 fadf27e9a7e2175cd9904844cad6d4c6753c926b821557cb0f207f09d35dc1d5. 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 #1919/#1920 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 4090932e6e3121a3b353f3ae29e14ee4d0a44ab8.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 5cc70feab38bdc46689aad98535af2638669dc2c095b8a9b6e7eac8d87a7057e.
Tree fcf385f23c9b505db51edfc6e571343ef0a470f1 matches the independently computed clean merge.
Compared with historical tree 1055d3cbe986e3fb1ada11583113930aac4adf2c, 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 #1915.
Closes #1916.
Closes #1917.
Closes #1918.
Metadata/composition #1919/#1920 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
1101 passed in 379.68s (0:06:19); twelve focused tests and ten 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,923caches and unrelated raw fields are unchanged.
All13original nodes/eight arrows reviewed. Twelve nodes and four arrows remain,one misassigned node/four unsupported arrows removed,four renames,no new topology. Viili retains nitrogen provision and positive AI-2 regulation while signaling mediation remains partial. Sludge EET arrows are PLS-model inference with fraction-specific participants. SSC8 growth without added pathogen is separated from the parent16-member disease/biofilm experiment. Wetland gas effects are retained without common-cause arrows to fitted metabolism.
Fresh primary abstracts/identities checked. Watermelon/wetland full main-body XML,methods,results,discussion,table text and captions read; not original pixels,supplements,raw data or model code. Viili/sludge are abstract-bounded. All29graph/discussion quotes match fresh sources and caches,not entailment certification. No cache changes or publication-body imports.
Corpus380reviewed,26pending,54needs_research;57unchanged network warnings,zero structural defects. Two participant-list users added (298total),scope census unchanged; no connectivity logic or threshold edits.456pages/1364nodes/523arrows exactly match source descriptions,with deterministic rendering,not screenshot certification. Postcommit docs-current passed clean; log SHA256 fadf27e9a7e2175cd9904844cad6d4c6753c926b821557cb0f207f09d35dc1d5. 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 #1919/#1920 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 #1914. Do not merge into the topic parent. Require actual exact-head checks through protected main. Move dependents before deleting parent branches.