The Conditional Refinement, Part I: Two Resolutions of the Standard and Mitochondrial Codes, and the Insufficiency of Block Data

Abstract

Our preceding paper seeds a codon block, propagates, and divides once at the third base, and its output is the vertebrate mitochondrial code at every codon. It describes the standard code as that output with two further divisions. That is two thirds of the distance: the two codes differ at four codons spanning three half-blocks, and at the third of them, the purine half of AG, both codes are uniform and no division occurs — an absence in the output is arginine in the standard code.

We remove the second operation by widening the first. The outcome at a half is three-valued — release a residue uniformly, release nothing, or resolve the two codons differently — and which value it takes is conditional on the environment, through a pair of thresholds on an effective vessel volume. Normal form is the case where the third value never occurs, the two codes are two settings, and the preceding paper is recovered entire as the mitochondrial case, with no operation added. The direction is fixed by the code data against the chemistry one would try first: at AG the low-pH compartment releases and the high-pH one terminates, so the limiting step is engagement and not escape.

The scheme then predicts a third setting neither code uses, and four published tables occupy it, three of them among the four the preceding paper finds in normal form; one monotone parameter, with thresholds shared across all sixteen purine halves, orders tables 1, 3, 5, 13 and 2 in that sequence. Nothing required a third regime to be occupied. This, and not the two-code fit, is the paper's evidence.

Widening the outcome set also widens the range, and the score moves with it. All twenty-seven published translation tables lie inside the range against four of twenty-seven inside its predecessor's. That is a weaker prediction with a perfect score and not a better result, and the one surviving prohibition — a pyrimidine half is uniform, satisfied at 432 of 432 — is third-position synonymy. A conjecture of the paper's own, that the two codes are the two fixed points of the implied feedback circuit, is withdrawn: the record occupies at least four settings. Part II supplies all three from one object, the chrysene-adenosine reaction cell, in which reachability of a carve is a maximum over reaction words of a minimum over cage margins, and so a step function of a continuous environment.