Bibliographic record
Abstract
Whether or not the notion that “everything is everywhere” is “taken for granted by most” (Fenchel and Finlay 2004) remains to be seen, but one cannot deny that the proposition has had stifling effects on microbial community ecology in the last century. and Tom Fenchel and Bland Finlay seem determined to perpetuate the myth of ubiquity despite all evidence to the contrary. They simply brush away serious criticisms of ubiquity (Foissner 1999, Coleman 2002, Whitaker et al. 2003) and disregard reports of endemism or vicariant distributions in microorganisms (Cho and Tiedje 2000, Curtis et al. 2002, Bohonak and Jenkins 2003, Darling et al. 2004). The idea that small organisms are randomly spread over the planet, first formulated by Baas-Becking (Quispel 1998) and recently acclaimed by Finlay (2002), has enormous implications. According to the ubiquity dogma, microbial biogeography is a futile pursuit. Microbiologists “need not travel to exotic places,” as “most microorganisms can be found at the local seashore.” If “local extinction [of microorganisms] rarely, if ever, takes place,” then microorganisms should never play a meaningful role in conservation and a microbial species would never become globally extinct. The first fundamental flaw in the ubiquity theorem is the acceptance of the morphological species as a meaningful concept (“the only viable operational approach”) in microbiology. This flies in the face of the recent DNA sequencing revolution in microbial systematics, which provides clear identification tools and demonstrates widespread species crypticity and genetic structuring of regional populations. It is not surprising that an identification system that fails to discern species should give rise to flat species–area curves and break every other rule of biodiversity theory. Bacteriologists and yeast systematists have been aware for quite some time that microbial classifications based on morphotypes are rather meaningless. Fenchel and Finlay (2004) further fail the reader through their unrestrained proclivity for generalization. Let us for a moment grant that some aquatic protozoa may be truly “free-living,” that some can be identified correctly by simple microscopy (but see Nanney 2004), and that the global distribution of some species may be random. Extending such propositions to all small organisms, however, as Fenchel and Finlay do, is indeed a colossal leap.
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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 | 0.005 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.003 |
| Science and technology studies | 0.003 | 0.010 |
| Scholarly communication | 0.006 | 0.011 |
| Open science | 0.000 | 0.002 |
| Research integrity | 0.004 | 0.003 |
| Insufficient payload (model declined to judge) | 0.019 | 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".