Modified Nucleosides Always Were: an Evolutionary Model
Why this work is in the frame
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Bibliographic record
Abstract
This chapter evaluates the distribution of modified nucleosides in certain RNA species of the three domains of life (archaea, bacteria, and eukaryotes). Fourteen modifications are present in all three domains and of these several are found at comparable positions in tRNAs . First, most of the conserved modified nucleosides are in or near the anticodon loop. There is strong phylogenetic evidence for the early appearance of modified nucleosides. The incorporation of modified nucleosides into nucleic acid polymers is quite plausible, and the use of a particular nucleoside may depend only on its concentration in the primordial soup. Again, considering the chemistry of nucleosides, it would seem that the moderately modified nucleosides would be present in the highest concentrations in the primordial soup along with the standard nucleosides. In parallel, the phylogenetic evidence suggests that some simple modified nucleosides existed at the point when the major organismal groups diverged. In the case of tRNAs, there is no evidence for present-day RNA guiding, although such a system could be imagined early in the evolution of replicating cells. The current evidence of the enzymes involved in RNA-guided modification leaves the door open to speculation that RNA has a greater role in this process than simply guiding modification.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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 it