A Unified Model of Codon Reassignment in Alternative Genetic Codes
Bibliographic record
Abstract
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment, based on the observation that reassignment involves a gain and a loss. The loss could be the deletion or loss of function of a tRNA or release factor. The gain could be the gain of a new type of tRNA for the reassigned codon, or the gain of function of an existing tRNA due to a mutation or a base modification. In the codon disappearance mechanism, the codon disappears from the genome during the period of reassignment. In the other mechanisms, the codon does not disappear. In the ambiguous intermediate mechanism, the gain precedes the loss; in the unassigned codon mechanism, the loss precedes the gain; and in the compensatory change mechanism, the loss and gain spread through the population simultaneously. We present simulations of the gain-loss model and demonstrate that all four mechanisms are possible. The frequencies of the different mechanisms are influenced by selection strengths, number of codons undergoing reassignment, directional mutation pressure and the possibility of selection for reduced genome size.
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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 | 0.001 | 0.004 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.002 | 0.003 |
| Scholarly communication | 0.003 | 0.004 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.004 | 0.002 |
| Insufficient payload (model declined to judge) | 0.006 | 0.001 |
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".