Bound Thermotoga proximity and aggregation causal claims to tested contrasts #1889

Finding

CommunityMech:000186: dialysis separation and size-fraction association suggest spatial proximity, not a directional colonization-facilitation phenotype or proof of direct contact. Aggregation/transcriptome observations are community context, not a second demonstrated pairwise metabolic exchange. Keep supported hydrogen syntrophy and qualify the existing arrows. The 292 vs 24 gene counts compare mid-log to early stationary phase within each culture; they are not 292 genes differing between coculture and monoculture. Growth response estimates and temperatures differ between the 1997 and 2006 assays. Higher density, hydrogen removal and coculture context should not become selective mediation of every EPS/transcript response.

Sources And Limits

https://pubmed.ncbi.nlm.nih.gov/18636642/
https://pubmed.ncbi.nlm.nih.gov/16391122/

Both whole records and all existing graph snippets read. Fresh primary abstracts and Crossref identities retrieved for all six existing sources; 2019 full XML/main body read. Existing cached main bodies of the 2002 expression, 2005 pathway and 2006 phenotype papers read in full; fresh full XML retrieval returned HTTP500 and PMC browser retrieval challenged access. 1997 and 2000 sources are abstract-bounded. The 2001 formate partner-comparison abstract was read on the publisher site, not its full paper. Original figure pixels, supplements and raw data were not reviewed. No new publication bodies or caches will be committed.

All-state issue-title/body dedup and ignored/hidden-inclusive local path search recorded; matching #800 is unrelated. Local search excludes .git, generated docs/site, reference caches and .env files; it is not an exhaustive historical PR-comment review.

Lifecycle

Address in batch114; close only after protected-main merge. Self-adversarial review is not independent approval.