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Correct X514 output and B12 graph direction and causal certainty #1337

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@realmarcin

Source-based self-adversarial finding in Clostridium_Thermoanaerobacter_Cellulosic_Bioethanol_Coculture (CommunityMech:000168).

Enhanced ethanol output is encoded as X514-to-LQRI CROSS_FEEDING, but community product formation does not establish ethanol donation. The B12-associated performance node is similarly encoded as directed COMMENSALISM without demonstrated donor/recipient fitness or vitamin transfer. Its arrow currently states association rather than a bounded causal hypothesis.

Acceptance: retain the cellulose-derived sugar-supply model and measured ethanol improvement. Represent output as a community endpoint; represent X514 B12 capacity without inventing vitamin donation. Preserve the 39E supplementation result while distinguishing it from selective perturbation of X514. Retain or remove the existing B12 arrow according to explicit certainty, not merely its correlation wording. Do not conflate batch comparisons with cyclic fed-batch process conditions.

Sources: 2011 mechanism paper, PMID:21868218 (abstract read; full body unavailable), and 2013 fed-batch paper, PMID:23275517 (publisher main text/Methods/tables/captions read). Images/supplements not inspected; no copyrighted full text added. Exact deduplication used 674 issue titles/bodies and ignored-inclusive local files. Broader #746/#749/#752 remain separate. Self-review, not independent approval.

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  1. realmarcin commented on Oct 6, 2026

    @realmarcin
    ContributorAuthor

    Addressed in #1339 at b4fd7d01144bf9815c3c5b5ce8c1c7b628a0a018. Exact-head source-based self-adversarial review: #1339 (review). All 30 local gates and actual post-commit docs-current passed; 262 passed in 220.78s (0:03:40); 83 MATCH snippets, zero other classes; 3 passed in 2.34s; 55 unrelated raw blocks and four caches byte-preserved. See committed batch21 decision/adversarial/validation records for assay bounds and full node/arrow accounting. This issue remains open until protected main merge; #1338 is separate non-graph work.

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