Continuation Capacity in DNA Sequence Space: Genetic Code Structure and the Mutation Rate as a Selectivity Parameter

Temporal Rate Ontology (TRO) treats ordered succession as primitive and defines a selection rule, the Principle of Maximal Freedom, that weights admissible continuations by their finite-horizon continuation multiplicity. This paper applies that construction at the molecular level, treating DNA sequence space as a succession structure in which genotypes are states, single-base substitutions are admissible extensions, and viability determines which extensions are admitted. Three computational results are reported. First, the standard genetic code is an extreme outlier in continuation capacity: 24.4 percent of single-base changes in sense codons are synonymous, against 4.5 percent for degeneracy-preserving random codes, and the standard code ranks first among 2001 codes tested. Its missense substitutions are also more hydropathy-conserving than 99.25 percent of block-preserving random codes. Second, a negative result is reported. In rugged NK landscapes where viability is defined by a fitness threshold, continuation rate and fitness are substantially correlated and continuation rate does not predict survival of environmental perturbation better than fitness does. Continuation capacity is therefore not a universal improvement on fitness as a predictor. Third, in a two-region landscape contrasting a narrow high peak with a broad lower plateau, exact quasispecies dynamics exhibit a sharp crossover at a per-site mutation rate of approximately 0.044. Below it, fitness ordering governs the outcome; above it, continuation ordering governs. This suggests that the mutation rate plays the role that the selectivity parameter plays in the physical framework, where that parameter is currently undetermined. The paper argues that these results are consistent with established population genetics rather than in competition with it, and states explicitly that TRO does not yet make a prediction that standard theory does not.