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Repair Richmond Mine ecological claims and preserve the iron cycle #1762
Description
Richmond_Mine_AMD_Biofilm.yaml (CommunityMech:000059) assigns CROSS_FEEDING/MUTUALISM to mineral chemistry, SYNTROPHY to cell contacts with unsupported species/subgroup identities, and COMPETITION to higher-pH distribution. Nitrogen-fixing capacity is not measured nitrogen transfer; PMID:19429552 explicitly reports nitrogen-fixation proteins not detected. Preserve the three existing Fe/mineral directions supported by DOI:10.1186/1467-4866-5-13, with external oxygen/site context and no species-resolved flux. Remove the unsupported nitrogen-sharing node and duplicate Parvarchaeota contact assignment; retain generic observed ARMAN contact. Bound the higher-pH node to observed distribution. Drop ungrounded CBB, pH homeostasis, iron-transport and reciprocal-fitness claims. PMID:15066799 is isolate physiology, PMID:20421484 is abstract-bounded contact evidence. No new topology.
Dedup: fresh all-state issue titles/bodies and ignored/hidden-inclusive local search with .git/docs/site/references_cache excluded; relevant caches separately inspected. Matching issues read, not duplicates of these findings. Comments/PRs not exhaustive. Source-based self-adversarial review, not independent approval. Graph-repair issues close only after protected-main merge.
Activity
realmarcin commentedon Oct 7, 2026
Addressed in #1765 at 69727be; exact-head self-review: #1765 (review). 872 passed in 505.26s (0:08:25); postcommit docs-current passed.42 actual validation outputs/digests plus decisions and source provenance are committed. Three records changed,FSQN unchanged;12nodes6existingdirections retained. The copied-participant-narrative finding was fixed with an extra append-only history and complete validation rerun. Non-graph1764 and existing loader1703/Linux DOI-cache1091 remain unresolved. Not independent approval; close only after protected-main merge.