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Repair mineral roles and reactor causal claims (batch115) - #1900
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Source-based self-adversarial review at exact head 12eefd9; not independent approval.
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Retain intrinsic iron oxidation and its mineral-oxidation link; no recipient, CBB attribution or density-control proof.; Retain sulfur physiology and qualified dispersal interpretation, not demonstrated passivation-removal mutualism.; Retain dual substrate capacity with condition-specific results and the actual 2020 comparator; no universal cooperation.; Retain consortium dissolution and the physical iron-recycling feedback, not pairwise mutualism or isolated QS mediation.; Separate externally dosed consortium responses from directly measured biogenic DSF in the 2021 study and hypothetical natural niche defense.; Separate added DL-AHL/transcript responses from endogenous production, direct motility measurement and unsupported compound stereochemistry.
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Keep the Afipia pathway as computationally predicted intrinsic capacity, not measured flux or cross-feeding.; Retain observed selection and a qualified link to enriched genomic potential; remove shared-perturbation-as-mediation arrow.; Distinguish R4/R5 high-loading instability from stable R3 and keep biofilm/nitrogen/cofactor explanations hypothetical.
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Retain iron oxidation in the field-derived model without acid-generation stoichiometry errors or mutualism; qualify the retained direction as ferric acceptor supply.; Correct the existing Acidiphilium role to ferric reduction coupled to organic-carbon respiration, not ferrous oxidation or traced partner carbon.; Retain review-supported phototrophic production with primary-abstract corroboration; remove the untraced carbon-transfer arrow.; Retain complementary physiological capacities, not measured mutualism, passivation removal or uniform abundance.
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All 14 original nodes and seven directions have explicit dispositions: 13 nodes and four arrows retained, one unsupported fungal node and three arrows removed, four renames, no new topology. Targets and discussion anchors resolve.
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Pyrite overcorrection check: retain measured biogenic DSF in 2021 and the mineral iron-recycling loop. Nanomolar culture concentrations differ from micromolar additions; natural consortium signal transfer and density protection are not demonstrated. Fatty-acid stress and signaling were not selectively separated. Intrinsic physiological roles remain in prose without treating broad process annotations as causal evidence.
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AHL: 2025 methods specify an added DL mixture; remove incorrect exact-L/generic CURIE substitutions, not the compound names or doses. Flagellar transcripts support a motility interpretation, not direct motility-rate measurements or A. caldus AHL production. Non-graph compound identity remains follow-up #1896.
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Sulfobacillus: the 2020 simultaneous-inoculation improvement uses the Sulfobacillus-alone comparator, not all monocultures; precolonization can impair leaching. The 2025 DSF biofilm relative distribution was unchanged at 7/14 days in this mixed assay. No universal mutualism, partner-lysate feeding or species-optimum substitution.
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SCN: Afipia pathway evidence is COMPUTATIONAL/PARTIAL; selection enriches genomic potential, not pathway induction or assigned flux. Remove the common-cause-as-mediation arrow. Preserve R2/R3 fixed 250 mg/L versus other ramps; stable R3 performance must not be conflated with R4/R5 high-loading instability. Biofilm, nitrogen and cofactor mediation remain hypothetical.
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Tinto: 2003 Figure 6 and p4863 assign Acidiphilium ferric reduction with carbon respiration; the retained incoming link supplies ferric acceptor, not traced autotroph carbon. Eukaryotic/fungal presence and production do not establish specific carbon transfer. Hortaea ascomycete identity cannot justify Basidiomycota; primary fungal isolations support both phyla, so no absence claim.
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Source scope: four fresh primary XML main bodies, complete 2003 Tinto PDF text and Figure 6 visual read, 2013 review, and two eukaryote/fungal primary abstracts read. Other original figure pixels, supplements, raw data and detailed corrupted PDF table cells were not audited. All 25 quotations match fresh sources and caches: 23 primary, two review. No new publication bodies or caches.
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Three guarded records and histories preserve 457 other records, 923 caches, all non-graph raw blocks and prior history/decision artifacts. Three participant-list users added. Measured survey: 414 community-level, 136 mixed, 278 community-only, 1568 taxa and 1280 without pairwise nodes. That last survey count is not proof of actual coverage. Connectivity rules and share guard unchanged.
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Network: 56 prior warnings preserved; one intentional DISCONNECTED warning for Basidiomycota exposed by removing unsupported exchange. Do not silence it with unrelated participant credit or call the corpus warning-free. Identity/functional-coverage follow-up #1898 remains open. Zero structural defects.
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Seven real in-memory control/mutation/restored-control probes reject biogenic DSF erasure, AHL support inflation, the wrong dual-culture comparator, Afipia support inflation, the common-cause arrow, Acidiphilium redox reversal and untraced algal transfer. Mutations and rejecting assertions are recorded; canonical hashes unchanged; not additional pytest tests.
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Eleven focused tests and 1044 combined regressions pass. All three records pass schema, strict, terms, full references, snippets, history and rank. Deterministic rendering and exact HTML-description coverage: 456 pages, 1365 nodes, 528 arrows, not UI screenshots. Local macOS reference passes do not certify Linux; the full-corpus snippet audit is informational.
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Graph issues #1893-#1895 await protected-main merge; metadata #1896-#1898 remain open. No Edison invocation or new topology. Prior Ruegeria extension #1883 and other needs_research records remain incomplete. Self-review is not independent approval; postcommit docs-current and exact-head publication are separate gates. Root CI blocker #1836 is not bypassed; dependent branches are not deleted.
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Corpus: 369 reviewed, 37 pending, 54 needs_research across 460 records. The overall goal remains incomplete.
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CI exposed stale Synechococcus smoke expectations from batch109: names and single-evidence count. Issue #1899 records the real failed batch114 run and local reproduction. The corrected test checks exact reviewed names, target resolution, pairwise taxa, qualified mediation, and SUPPORT/PARTIAL evidence. Dedicated pytest and seven additional counterfactual probes pass without changing the canonical record. Propagation through older affected PRs is still required; 1044 regressions plus the focused smoke run are not a new full-suite pass. #1703 loader work remains separate.
1044 passed in 338.70s (0:05:38); eleven focused tests and seven real in-memory mutation probes. All three records pass schema, strict, terms, full-record references, snippets and history. 34 validation outputs retain commands, tails and log digests. All 457 other records, 923 caches and non-graph raw blocks are unchanged.
Of fourteen original nodes and seven directions, thirteen nodes and four directions remain; one node and three arrows are removed, with four renames and no new topology. Retain measured DSF production without conflating natural concentrations with added compounds. Distinguish Afipia genomic potential from strain flux and shared environmental causes from mediation. Correct Acidiphilium to ferric reduction; do not infer specific carbon delivery from phototrophic or fungal presence.
Four fresh primary XML main bodies, the institutional 2003 Tinto PDF and its Figure6, the 2013 eukaryote review and two primary eukaryote/fungal abstracts were read. All25 graph/discussion quotes match fresh sources and existing caches:23 primary and2 REVIEW. Other original figure pixels, supplements, raw data and detailed corrupted PDF-table cells were not audited. No publication bodies or caches committed.
Corpus:369 reviewed,37 pending,54 needs_research. All56 prior network warnings remain, with one intentional new Basidiomycota DISCONNECTED warning after the unsupported fungal exchange was removed; zero structural defects. Do not suppress that gap with unrelated participant credit. Three new participant-list users; connectivity logic and share guard unchanged. Rendering is deterministic with exact description coverage, not screenshots. Postcommit docs-current passed clean; SHA256 eef731f349daf4245eda4ee9aa75282ce52f44ee5936a4ef25bd6ea3a324f7fb. Local macOS reference passes do not certify Linux; full-corpus snippet audit is informational.
Decision ledger, provenance, validation, three append-only histories and self-adversarial review are committed. Metadata #1896-#1898 remain open, including Tinto fungal identity/coverage and the reactor-ramp error left by #513. No Edison invocation or new topology; prior Ruegeria extension #1883 remains incomplete. This COMMENT is self-review, not independent approval. Root blocker #1836 remains subject to real protected checks; no artificial CI, protection bypass or premature branch deletion.
CI follow-up #1899: batch114 strict CI failed on the old Synechococcus smoke-test names/evidence count introduced by the batch109 graph review. This PR fixes the exact smoke contract, with a separate focused test run and seven rejecting counterfactual probes. This is not a new full-suite pass. Propagation through batches109-114 and fresh exact-head checks remain required; do not close #1899 yet.
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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Self-adversarial review refreshed at exact head 3d04751 after propagating the real CI correction #1899. Not independent approval.
Original head: 12eefd9. Current parent: ce4adc5. Only tests/test_datamodel.py changes in the tree for batches109-114; batch115's whole tree is unchanged. Scientific records, prior histories/decisions, caches, renderings and all other files are byte-identical to the respective reviewed trees. Each batch-owned patch excluding this test is byte-identical (SHA256 4fe7c86da3bc8db207dae3b10e8aa07c03b031885444603ee34db7fd6ee2db2d).
The stale smoke test now requires the reviewed source and target names, resolving target, canonical pairwise taxa, qualified sucrose mediation and both SUPPORT/PARTIAL evidence. No graph was reverted or test skipped. The batch115 CI artifact records the original failed strict run, reproduction, 24 related test passes and seven rejecting counterfactual probes.
Fresh tests at this head: ............. [100%]
13 passed in 19.21s
Test log SHA256: 6adeb7dd8001a6bf904c507769689c33b7546c1955a69a28d9987e00ca551cbf. Fresh docs-current passed with a clean worktree; log SHA256 eef731f349daf4245eda4ee9aa75282ce52f44ee5936a4ef25bd6ea3a324f7fb.
The propagation-pending entries in batch115's immutable publication report describe the earlier publication state; this exact-head review records the subsequent propagation. Focused tests are not a new full-suite pass. Real exact-head protected CI remains required; #1836 independently blocks the upstream root PR. #1899 remains open until protected-main integration. No artificial CI, protection bypass, merge or branch deletion was performed.
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Exact-head self-adversarial restack review at 1ea62d4f2220b0e2659f96acd52d1a38accee932.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 4fe7c86da3bc8db207dae3b10e8aa07c03b031885444603ee34db7fd6ee2db2d.
Tree ff5ee2620a9421bb7ae853f9723980f4e2a0f0a3 matches the independently computed clean merge.
Compared with historical tree bba534e5fa47471840d82809c0310d8fde62af0f, 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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Scope
Closes #1893.
Closes #1894.
Closes #1895.
Metadata #1896-#1898 remain open; this batch does not resolve prior research extensions.
Adversarial Review
Verification And Output Records
1044 passed in 338.70s (0:05:38); eleven focused tests and seven real in-memory mutation probes. All three records pass schema, strict, terms, full-record references, snippets and history. 34 validation outputs retain commands, tails and log digests. All 457 other records, 923 caches and non-graph raw blocks are unchanged.
Of fourteen original nodes and seven directions, thirteen nodes and four directions remain; one node and three arrows are removed, with four renames and no new topology. Retain measured DSF production without conflating natural concentrations with added compounds. Distinguish Afipia genomic potential from strain flux and shared environmental causes from mediation. Correct Acidiphilium to ferric reduction; do not infer specific carbon delivery from phototrophic or fungal presence.
Four fresh primary XML main bodies, the institutional 2003 Tinto PDF and its Figure6, the 2013 eukaryote review and two primary eukaryote/fungal abstracts were read. All25 graph/discussion quotes match fresh sources and existing caches:23 primary and2 REVIEW. Other original figure pixels, supplements, raw data and detailed corrupted PDF-table cells were not audited. No publication bodies or caches committed.
Corpus:369 reviewed,37 pending,54 needs_research. All56 prior network warnings remain, with one intentional new Basidiomycota DISCONNECTED warning after the unsupported fungal exchange was removed; zero structural defects. Do not suppress that gap with unrelated participant credit. Three new participant-list users; connectivity logic and share guard unchanged. Rendering is deterministic with exact description coverage, not screenshots. Postcommit docs-current passed clean; SHA256 eef731f349daf4245eda4ee9aa75282ce52f44ee5936a4ef25bd6ea3a324f7fb. Local macOS reference passes do not certify Linux; full-corpus snippet audit is informational.
Decision ledger, provenance, validation, three append-only histories and self-adversarial review are committed. Metadata #1896-#1898 remain open, including Tinto fungal identity/coverage and the reactor-ramp error left by #513. No Edison invocation or new topology; prior Ruegeria extension #1883 remains incomplete. This COMMENT is self-review, not independent approval. Root blocker #1836 remains subject to real protected checks; no artificial CI, protection bypass or premature branch deletion.
CI follow-up #1899: batch114 strict CI failed on the old Synechococcus smoke-test names/evidence count introduced by the batch109 graph review. This PR fixes the exact smoke contract, with a separate focused test run and seven rejecting counterfactual probes. This is not a new full-suite pass. Propagation through batches109-114 and fresh exact-head checks remain required; do not close #1899 yet.
Dependency
Draft depends on #1892. Do not merge into the topic parent. Require actual exact-head checks through protected main. Move dependents before deleting parent branches.