Little evidence the standard genetic code is optimized for resource conservation

Shenhav & Zeevi (Science, 2020, 370:683-687) propose nitrogen and carbon conservation as optimization principles in the standard genetic code that are not confounded by the established optimizations for polar requirement and hydropathy. We show their results for nitrogen conservation are highly sensitive to their choice of null model and their results for carbon conservation are confounded by molecular volume.

Golden and Harmonic Mean in the Genetic Code

In previous two works (Rakočević, 1998; 2013), we have shown the determination of genetic code by golden and harmonic mean within standard Genetic Code Table, i.e. nucleotide triplet table, whereas in this paper we show the same determination through a specific connection between two tables – of nucleotide doublets Table and triplets Table, over polarity of amino acids, measured by Cloister energy in general, and by hydropathy and polar requirement, partialy. [This is the expanded version of the article published in Proceedings of the 2nd International Conference “Theoretical Approaches to BioInformation Systems” (TABIS.2013), September 17–22, 2013, Belgrade, Serbia. That first version is also stored, as Version 1, in OSF Preprints.]

A unified model of the standard genetic code

The Rodin–Ohno (RO) and the Delarue models divide the table of the genetic code into two classes of aminoacyl-tRNA synthetases (aaRSs I and II) with recognition from the minor or major groove sides of the tRNA acceptor stem, respectively. These models are asymmetric but they are biologically meaningful. On the other hand, the standard genetic code (SGC) can be derived from the primeval RNY code (R stands for purines, Y for pyrimidines and N any of them). In this work, the RO-model is derived by means of group actions, namely, symmetries represented by automorphisms, assuming that the SGC originated from a primeval RNY code. It turns out that the RO-model is symmetric in a six-dimensional (6D) hypercube. Conversely, using the same automorphisms, we show that the RO-model can lead to the SGC. In addition, the asymmetric Delarue model becomes symmetric by means of quotient group operations. We formulate isometric functions that convert the class aaRS I into the class aaRS II and vice versa. We show that the four polar requirement categories display a symmetrical arrangement in our 6D hypercube. Altogether these results cannot be attained, neither in two nor in three dimensions. We discuss the present unified 6D algebraic model, which is compatible with both the SGC (based upon the primeval RNY code) and the RO-model.