Rhodopseudomonas-Geobacter magnetite redox: curate causal graph#246
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Add directed `downstream` causal edges to the four existing ecological_interactions of CommunityMech:000268, from the Edison causal-graph run (PaperQA3; PMID:25814583 Byrne et al. 2015 Science, + doi:10.1126/science.aaa4834). Wiring — the reversible magnetite "battery" loop: - Phototrophic Magnetite Fe(II) Oxidation -> Anaerobic Magnetite Fe(III) Reduction (TIE-1 photo-oxidation of Fe(II) supplies the Fe(III) acceptor G. sulfurreducens reduces). - Anaerobic Magnetite Fe(III) Reduction -> Phototrophic Magnetite Fe(II) Oxidation (Geobacter regenerates the Fe(II) donor for TIE-1; reversible in co-cultures) — closing the 2<->3 redox loop. - Phototrophic ... Oxidation, Anaerobic ... Reduction, and Magnetite-Mediated Electron Sharing all -> Biogeochemical Battery Function (the two half-reactions + electron sharing constitute the emergent, reusable mineral electron store). InteractionDownstream carries target + causal description only; evidence stays on the parent nodes (existing PMID:25814583 snippets). Schema validates; no new snippets or terms. Record HTML page regenerated. First causal record curated via a normal `just research-community-causal` run after the .env-precedence fix (#245) — no `env -u` workaround. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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The new downstream entries follow the existing schema and reference interaction names that exist in the same record, and the docs update matches the curated edges.
Note: this review does not count toward required approvals for merging.
Pull request overview
This PR curates a directed causal “downstream” wiring among the existing ecological interactions in CommunityMech:000268 (Rhodopseudomonas–Geobacter magnetite redox coculture), encoding the reversible magnetite redox loop and its emergent “biogeochemical battery” function without adding new evidence items.
Changes:
- Adds
downstreamcausal edges to the relevantecological_interactionsinRhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml, referencing existing interaction names as targets. - Regenerates the corresponding community HTML page so the new downstream edges render in the docs.
File summaries
| File | Description |
|---|---|
| kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml | Adds downstream causal edges linking the magnetite oxidation/reduction/electron-sharing interactions to each other and to the emergent battery function. |
| docs/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.html | Updates rendered documentation to display the new downstream effects for the affected interactions. |
Review details
- Files reviewed: 2/2 changed files
- Comments generated: 0
- Review effort level: Low
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realmarcin
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Jul 22, 2026
#245) (#248) Add CommunityMech:000268 (Rhodopseudomonas-Geobacter magnetite battery) to the causal "done" list (~60/304), point Next at ORNL trophic model 000176, and replace the Edison env-shadowing workaround note with the runner fix (#245): load_api_key() now treats the repo .env FILE as source of truth, so a plain `just research-community-causal <id>` works with no `env -u`. Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Adds directed
downstreamcausal edges to the fourecological_interactionsof CommunityMech:000268 from an Edison causal-graph run (PaperQA3; PMID:25814583 Byrne et al. 2015 Science + doi:10.1126/science.aaa4834).Wiring — reversible magnetite "battery" loop:
InteractionDownstreamcarries target + causal description only; evidence stays on the parent nodes (existing PMID:25814583 snippets). No new snippets or terms; canonical NCBITaxon ids.Verification:
just validateclean; HTML page regenerated (5 edges render). First causal record curated via a normaljust research-community-causalrun after the.env-precedence fix (#245) — noenv -u.Continues the causal thread (#226/#229/#230/#243).
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