Eradicating Typological Thinking in Prokaryotic Systematics and Evolution
Bibliographic record
Abstract
In 1982, John Maynard Smith called for an evolutionary "New Synthesis" specific for prokaryotes, observing that "population thinking has been well developed for fully half a century, but has yet to be adopted by microbiology" (Maynard Smith 1982). Twenty-seven years later, typological thinking (population thinking's antithesis) still dominates the field. Evidence for this includes the continuing debates on the reality of prokaryotic species, the value of the term "prokaryote," and the significance of the tree of life (TOL). In each case, the unexpected prevalence of interlineage transfer of genetic information has been (or should now be) the catalyst for the final Darwinization of our discipline. With examples from phylogenomics, I argue that "species," "domains," and the "TOL" are reifications that we can do without, especially as genomics dissolves into metagenomics.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.004 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.004 | 0.004 |
| Science and technology studies | 0.001 | 0.008 |
| Scholarly communication | 0.003 | 0.008 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.003 | 0.006 |
| Insufficient payload (model declined to judge) | 0.003 | 0.003 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".