The medium is the experiment, and the guess fails twice (#183, #543) - #550
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The medium is the experiment, and the guess fails twice (#183, #543)#550realmarcin wants to merge 1 commit into
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Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom: the fungus as an 8 mm plug and B. altitudinis B4 at 50 μL of OD600 0.4, co-cultured in P20 liquid medium made WITHOUT thiamine, with single-partner treatments as controls; plate assays at 28 °C in the dark. The omission is the point. S. clintonianus is a thiamine auxotroph, so a medium lacking thiamine is what makes it dependent on the bacterium. Recording "P20" without "without thiamine" would describe a system in which the interaction cannot be observed at all — the same shape as the fumarate deliberately kept out of the syntrophy record, where one component decides whether the partnership is necessary. No system_type or working_volume: the source gives neither for the co-culture, and both liquid co-culture and 60 mm plate assays appear, so one vessel value would misdescribe half the work. Second failure of the "likely refuse" group in #543, and it failed differently from the first. ORNL_PMI_Populus was assembled in liquid and never met a plant; here the two partners are co-cultured in liquid with the plant simply absent from the assay. Two falsifications from two readings means the remaining three in that group are not being classified without reading either. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Network integrity findingsWarnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build. The full report is attached to the workflow run as an artifact. |
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What
Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom— the fungus as an 8 mm plug and B. altitudinis B4 at 50 μL of OD₆₀₀ 0.4, co-cultured in P20 liquid medium made without thiamine, with single-partner treatments as controls. Plate assays at 28 °C in the dark.The omission is the experiment
S. clintonianus is a thiamine auxotroph. A medium lacking thiamine is what makes it dependent on the bacterium. Recording "P20" without "without thiamine" would describe a system in which the interaction cannot be observed at all.
Same shape as the fumarate deliberately kept out of the syntrophy record (#539): one component decides whether the partnership is necessary, so getting it wrong doesn't just misstate a condition — it describes a different experiment.
No
system_typeorworking_volume: the source gives neither for the co-culture, and both liquid co-culture and 60 mm plate assays appear, so one vessel value would misdescribe half the work.Second failure of the #543 "likely refuse" group
I predicted this a refusal on the assumption that a plant-associated SynCom lives on the plant. Wrong again — and differently from the first failure, which is the informative part:
ORNL_PMI_Populus_PD10_SynComwas assembled and passaged in liquid and never met a plant.Two readings, two falsifications. The remaining three in that group (
Lotus_LjSC3,PSY_Transgenic_Rice,hCom2) are not being classified without reading either.My first pass on this paper also nearly got it wrong in the other direction: the visible methods are all exudate collection and supernatant transfer, which reads as a design where the partners never meet. The co-culture is stated once, in a single sentence about "the combined system". A keyword sweep for "co-culture" found it; a summary of the methods would not have.
Running tally on #543
Seven of thirteen candidates read: 2 refused, 1 partial, 5 curated. Every wrong call so far has been a prediction made without reading, and every one has been corrected by reading a single sentence.
Checks
just validate— no issuesjust validate-references— 0 issues; both snippets verbatimjust validate-strict,just lint,just check-docs-current— exit 0uv run pytest tests/— 2375 passed, 16 skippedPart of #183. Corrects #543 again.
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