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Remove common-cause arrows from wetland oxygen-sulfate graph #1918

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Description

@realmarcin

Finding

CommunityMech:000255: gas-shift and methane-suppression endpoints do not themselves cause the modeled lactate-sulfate subnetwork; both existing arrows restate shared experimental exposure. Remove them. Preserve measured treatment responses, qualify competition as guild-level mechanistic inference, and distinguish fitted fluxes from measured metabolite accumulation. Oxygen response is not evidence of niche partitioning, and a biochemical subnetwork alone does not establish a donor-recipient cross-feeding interaction. Keep sulfate reduction under oxic treatment contextual and do not equate residual CH4 with zero.

Evidence And Limits

https://pmc.ncbi.nlm.nih.gov/articles/PMC11222425/

Whole canonical records and all graph snippets read after a complete two-root baseline. Fresh primary abstracts and Crossref identities checked. Watermelon/wetland main-body XML, methods, results, discussion and captions read; no figure-pixel, supplementary-file, model-code or raw-data audit. Viili/sludge changes are abstract-bounded; bounded DOI/publisher searches did not yield an inspected open full text. No access bypass or cache imports.

Fresh all-state issue titles/bodies searched; matching1014/1015/1452/644 read and distinct. Hidden/ignored-inclusive local searches exclude.git,docs,site,reference caches,.env; not an exhaustive historical PR-comment search.

Lifecycle

Address in batch118; close only after protected-main merge. Self-adversarial review is not independent approval.

Activity

  1. realmarcin commented on Oct 8, 2026

    @realmarcin
    ContributorAuthor

    Graph repair addressed; close only after protected-main merge. #1921 at 97c4851; self-review #1921 (review). 1101 passed in 379.68s (0:06:19); postcommit docs-current passed. Four append-only histories, 41 validation outputs and ten mutation probes recorded. No new topology or Edison invocation in this batch; prior research extensions remain incomplete. Self-review is not independent approval.

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