Repository navigation
Bound treatment sequences, metabolic inference and vitamin mutualism (batch117) - #1914
realmarcin wants to merge 1 commit into
Conversation
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Source-based self-adversarial review at exact head e3ad14c; not independent approval.
-
Retain hydrogen cross-feeding with enriched-culture identity and purity limits.; Retain sequential phenol delivery as cross-feeding, not demonstrated reciprocal syntrophy.; Represent DS degradation as a recipient outcome and distinguish the phenol tracer from labeled TBP.; Preserve experimental mineralization with explicit functional participants and sequential assembly.
-
Keep proposed sulfate-reducer hydrogen transfer explicitly hypothetical in name, evidence and arrow.; Preserve expressed methanogenesis evidence without treating it as measured hydrogen flux.; Preserve experimentally observed magnetotaxis while leaving unmeasured mutual fitness untyped.; Make the inferred joint hydrogen-sink benefit explicit without upgrading pathway expression to energetics.
-
Retain guild ureolysis without claiming equal member contributions or measured individual necessity.; Separate nitrifier function from the distinct ammonium-fed salt-challenge benchmark.; Preserve reactor and batch nitrate outcomes with all five participants, not space-fertilizer validation.
-
Scope thiamine cross-feeding to the tested yeast and separate production assay from network inference.; Preserve reciprocal vitamin evidence with spent-medium and exclusive-mediation limits.; Retain experimental mutual benefit while documenting inconsistent reported fold changes.
-
Every original node and arrow accounted for:14nodes and9arrows retained,5renames,no new topology. All targets and discussion anchors resolve; no node minted to repair an edge.
-
Tribromophenol overclaim check: hydrogen supply and phenol delivery remain experimental functional cross-feeding. FTH1 is enriched,not a proven pure isolate; DS introduction is sequential. Phenol radiotracer evidence is not mislabeled as TBP tracing or reciprocal DS-to-FTH1 benefit.
-
Tropidoatractus overcorrection check: active field-reversal responses and internal magnetite chains remain positive evidence. Gene expression supports proposed H2 transfer,not measured gas flux or host fitness. FailedFISH limits genome-to-cell identity; native polarity after six-month Munich storage is unknown. Capability provision remains untyped,consistent with existing749.
-
Urine assay check: R1 ammonium-fed pair salt adaptation,R2 five-member urine-fed nitrate production and separate batch activity rates are not collapsed. Heterotroph individual necessity is not claimed; organic-removal optimization and application motivation prevent spaceflight/fertilizer readiness claims.
-
Vitamin overcorrection check: experimental bilateral growth benefit remains MUTUALISM. Thiamine recipient is the tested yeast,not every network-correlated auxotroph. Yeast was absent from the correlation network. Production quantification uses a separate supplemented assay. Supplementation and extracellular vitamins support exchange without exclusive mediation or demonstrated native pairing.
-
Primary-source discrepancy check: retain qualitative vitamin benefit without correcting inconsistent abstract/discussion,Fig6caption and Results-density fold changes. Results and Methods differ on spent-medium source; no uniquely resolved source invented. Raw-data and supplementary-file review was not performed.
-
All24graph and4discussion quotations match fresh primary artifacts and existing caches,not entailment certification. Tropidoatractus/Variovorax main-body XML including methods/captions read; no original figure pixels or SI. Tribromophenol/urine final-abstract-bounded; earlier urine thesis identified but unread. No cache changes or full publication imports.
-
Preservation:4guarded writes,4append-only histories,456otherrecords,923caches,all non-graph raw blocks and prior history/decisions unchanged. Alias detachment prevents accidental evidence propagation. Canonical labels/ranks retained. Participant-list users296; census414community-level,136mixed,278community-only,1568taxa,1280solelycredited. Sole-credit is not actual participant-coverage certification; logic/shareguard unchanged.
-
Ten real control/mutation/restored-control probes reject pure-isolate substitution,wrong tracer,overstated H2 flux/fitness,forced MUTUALISM,reactor conflation,spaceflight overclaim,network-wide recipients,loss of bilateral benefit and silent numerical reconciliation. Initial probe harness KeyError is separately retained and not counted; valid incorrect-enum mutation exercises the intended assertion. No canonical/test edits were needed for that harness correction.
-
Twelve focused and1068combinedtests including datamodel pass. All4records pass schema,strict,terms,full-record references,snippets,rank,history. 57unchangednetworkwarnings,zero structural defects. All456renderedpages,1365nodes,527arrows exactly match source descriptions with deterministic rendering,not UI screenshot certification. Local reference passes are macOS,not Linux certification; corpus snippet audit remains informational.
-
Graphissues1907-1910 addressed awaiting protected-main merge;metadata1911/1912 remainopen. Existing749 remains a separate broader issue. No Edison extension/spend; prior Ruegeria1883 still needs configured authentication. Self-adversarial review is not independent approval. Postcommit docs-current and exact-head publication are separate gates; no artificial CI or protection bypass.
-
Corpus376reviewed,30pending,54needs_research across460records. The overallgoal and protected merge remain incomplete.
-
Parent116 real strict CI failed the palette rarity test after commensalism became as rare as folded predation. Issue1913 records the exact run/log and is not resolved by this graph-only publication or its1068selected tests. A genuine template/legend correction and parent propagation remain required; no test threshold is relaxed.
1068 passed in 440.71s (0:07:20); twelve focused tests and ten real in-memory mutation probes. All four edited records pass schema, strict, term, full-record reference, snippet, rank and history checks. 41 gate outputs retain commands, output tails and digests. All 456 other records, 923 caches and non-graph raw blocks are unchanged.
Fourteen nodes and nine original arrows remain, with five renames and no new topology. Tribromophenol retains enrichment identity, sequential DS introduction and phenol radiotracing. Tropidoatractus retains observed magnetotaxis while H2 transfer and energetic benefit remain proposed. Urine graph separates R1, R2 and batch benchmarks. Vitamin mutualism remains experimentally supported for the tested pair, without network-wide recipients or exclusive vitamin mediation.
Fresh primary abstracts and identities checked. Complete Tropidoatractus/Variovorax main-body XML including methods and captions read, not original pixels, SI or raw data. Tribromophenol/urine are final-abstract-bounded; an earlier urine thesis was identified but unread. Inconsistent vitamin fold changes and spent-medium descriptions remain explicit, not silently corrected. All 28 graph/discussion quotations match fresh sources and caches, not entailment certification. No cache changes or publication-body imports.
Corpus: 376 reviewed, 30 pending, 54 needs_research; 57 unchanged network warnings, zero structural defects. One participant-list user added; narrowed vitamin claim lowers the community-level census by one with no sole-credit increase. Connectivity logic/share guard unchanged. Rendering is deterministic and all 456 pages' descriptions match YAML, not screenshot certification. Postcommit docs-current passed clean; log SHA256 697e0d54f8dcc5e4ca1cde4090e31a69ac0abf8770805dfb94e2117a4cfd8e8f. Local reference passes are macOS, not Linux certification; corpus snippets remain informational.
Decision ledger, provenance, validation, four append-only histories and self-adversarial review are committed. Initial probe harness error is retained separately and not counted as a pass; corrected valid mutation exercises the bilateral-benefit assertion without editing canonical data/tests. Metadata #1911/#1912 remain open and existing enum issue #749 is not duplicated. No Edison invocation; prior Ruegeria extension #1883 still needs a configured provider. This COMMENT is self-review, not independent approval. Root blocker #1836 requires actual protected checks; no artificial CI, protection bypass 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. |
44d2638 to
aa10cc1
Compare
e3ad14c to
fc5c4d1
Compare
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Self-adversarial review at exact head fc5c4d1 after real palette correction #1913. Not independent approval.
The prior116 strict run failed only the palette frequency guard: commensalism and predation had two occurrences each. Source-backed scientific labels were not reverted. The actual template now folds rare commensalism into Other, preserving exact type text. FOLD_HEADROOM=2 and MIN_SEPARATION=15 remain unchanged; six common colours are unchanged. Enum overlap and rare/untyped/common legend fixtures are tested. Parent correction passed1077selected tests,21palette tests and four inspected desktop/mobile light/dark browser views.
All canonical records,caches,prior histories/decisions and non-palette source files are byte-identical to the previously reviewed tree. Only template,palette tests,generated HTML and the new CI report/review/infrastructure history change. Each branch's patch excluding those palette paths remains byte-identical (SHA256 a83abc96489aea93ac7fb0818eda0614e96fcd32ddb1f310041caa7e720cb5da). Original heads are preserved by archive refs and earlier publication receipts. Generated conflicts,if any,were resolved only by rendering from unchanged canonical YAML.
Fresh head-specific tests: ........................................................................ [ 6%]
........................................................................ [ 13%]
........................................................................ [ 19%]
........................................................................ [ 26%]
........................................................................ [ 33%]
........................................................................ [ 39%]
........................................................................ [ 46%]
........................................................................ [ 52%]
........................................................................ [ 59%]
........................................................................ [ 66%]
........................................................................ [ 72%]
........................................................................ [ 79%]
........................................................................ [ 85%]
........................................................................ [ 92%]
........................................................................ [ 99%]
......... [100%]
1089 passed in 350.03s (0:05:50)
Test log SHA256 e163b11830899f244b7bf280b8c1a6a6bf2e55b87c3ba5122aa3e35f3280bf30. Fresh docs-current passed clean; log SHA256 697e0d54f8dcc5e4ca1cde4090e31a69ac0abf8770805dfb94e2117a4cfd8e8f.
The initial rebased tree 17a59ddb7b9d9dc2adfad8ecd75345ed1b3af6b4 passed1089selected tests but failed docs-current because an automatic HTML merge omitted one accessibility-description sentence. Fresh rendering corrected only docs/communities/Urine_Nitrification_SynCom.html. The intermediate commit, failed log (SHA256 da6fb69fc8ccd4ca0f3b3a75f34e1b0a823ee31dce81d72a0c8453e7856fdc52), and receipt are retained. All1089selected tests and docs-current were rerun successfully at this corrected exact head.
Reports: reports/causal_graph_review/ci-regression-1913-20261008.json and ci-review-1913-20261008.yaml. Their propagation-pending state and batch117's original CI-pending record are historical; this review documents subsequent verified propagation. Selected local tests are not full-suite/Linux CI certification. Actual protected checks remain required; #1836 independently blocks the root. Keep #1913 and scientific repair issues open until protected-main merge. No dispatch,rerun,artificial CI,protection bypass,merge or branch deletion.
aa10cc1 to
d1d05f0
Compare
fc5c4d1 to
afda283
Compare
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Exact-head self-adversarial restack review at afda28391dd8005cf2d99320086025ea87012e49.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 f8c62dd651b03ca65bf51d969bab24b0409784d9b8456e0cdcfa06659473c78c.
Tree d8590a888211c23dcf084cc44250ee16e4b65c93 matches the independently computed clean merge.
Compared with historical tree 497842ab64399d377c2737def4e0d93516085f99, 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.
afda283 to
7c76eac
Compare
|
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 #1907.
Closes #1908.
Closes #1909.
Closes #1910.
Metadata #1911/#1912 remain open; this batch does not resolve prior research extensions.
Parent strict-CI palette regression #1913 remains open at this graph-only publication. The selected local suite does not certify full CI; a real palette correction and verified propagation follow separately.
Adversarial Review
Verification And Output Records
1068 passed in 440.71s (0:07:20); twelve focused tests and ten real in-memory mutation probes. All four edited records pass schema, strict, term, full-record reference, snippet, rank and history checks. 41 gate outputs retain commands, output tails and digests. All 456 other records, 923 caches and non-graph raw blocks are unchanged.
Fourteen nodes and nine original arrows remain, with five renames and no new topology. Tribromophenol retains enrichment identity, sequential DS introduction and phenol radiotracing. Tropidoatractus retains observed magnetotaxis while H2 transfer and energetic benefit remain proposed. Urine graph separates R1, R2 and batch benchmarks. Vitamin mutualism remains experimentally supported for the tested pair, without network-wide recipients or exclusive vitamin mediation.
Fresh primary abstracts and identities checked. Complete Tropidoatractus/Variovorax main-body XML including methods and captions read, not original pixels, SI or raw data. Tribromophenol/urine are final-abstract-bounded; an earlier urine thesis was identified but unread. Inconsistent vitamin fold changes and spent-medium descriptions remain explicit, not silently corrected. All 28 graph/discussion quotations match fresh sources and caches, not entailment certification. No cache changes or publication-body imports.
Corpus: 376 reviewed, 30 pending, 54 needs_research; 57 unchanged network warnings, zero structural defects. One participant-list user added; narrowed vitamin claim lowers the community-level census by one with no sole-credit increase. Connectivity logic/share guard unchanged. Rendering is deterministic and all 456 pages' descriptions match YAML, not screenshot certification. Postcommit docs-current passed clean; log SHA256 697e0d54f8dcc5e4ca1cde4090e31a69ac0abf8770805dfb94e2117a4cfd8e8f. Local reference passes are macOS, not Linux certification; corpus snippets remain informational.
Decision ledger, provenance, validation, four append-only histories and self-adversarial review are committed. Initial probe harness error is retained separately and not counted as a pass; corrected valid mutation exercises the bilateral-benefit assertion without editing canonical data/tests. Metadata #1911/#1912 remain open and existing enum issue #749 is not duplicated. No Edison invocation; prior Ruegeria extension #1883 still needs a configured provider. This COMMENT is self-review, not independent approval. Root blocker #1836 requires actual protected checks; no artificial CI, protection bypass or premature branch deletion.
Dependency
Draft depends on #1906. Do not merge into the topic parent. Require actual exact-head checks through protected main. Move dependents before deleting parent branches.
Verified Palette Correction #1913
Real palette fix propagated at fc5c4d1. Exact-head self-review supersedes the earlier propagation-pending state, not source-history records. Required protected CI and root #1836 remain outstanding; no merge or deletion.