Junk DNA R Us - 3

Which one is it?

I. Background

I criticized a practice concerning the current state of nomenclature detailing the storage of genome data in GenBank (The Doll As Metaphor, 2, 3, 4, 5, 6, 7, 8).

My recent research indicates that some of that mix-up still remains, but it was much worse in the previous century (e.g. 1980's):

"Whereas the use of, for example, the symbols R and Y to designate purine (A or G) and pyrimidine (C or T) ribonucleotides respectively is generally accepted, no agreed symbols exist for the other possible combinations. Indeed, a plethora of diverse systems has proliferated in the last few years. It is striking that, in one extreme case, the combination (C or G) has been represented by at least five different symbols. A standardized set of symbols is thus required to prevent confusion.  The symbols are intended to be applicable to both deoxyribonucleic and ribonucleic acids. Thus it is important to note from the outset that the recommended symbols will not discriminate between DNA and RNA, and the symbol T will be employed at all positions where U might appear in the RNA."

(Eur. J. Biochem. 150, 1-5 (1985),emphasis added, cf. Nomenclature for incompletely specified bases in nucleic acid sequences). The scientists had already instigated the mishmash, so a committee of sorts set out to sort it out.

Nevertheless, the cognitive mutations caused by the discord in the nomenclature had not completely subsided about three decades later:

"The genetic code is redundant with most amino acids using multiple codons. In many organisms, codon usage is biased toward particular codons. Understanding the adaptive and nonadaptive forces driving the evolution of codon usage bias (CUB) has been an area of intense focus and debate in the fields of molecular and evolutionary biology. However, their relative importance in shaping genomic patterns of CUB remains unsolved."

(Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift, 2011, emphasis added). The CUB of most amino acids "is what done it" eh?

The metaphorical practices in widespread use do not help.

For example, the sentence "The genetic code is redundant with most amino acids using multiple codons" implies that amino acids are making choices that they should not make, plus the amino acids are biased in their usage of codons.

Never mind that amino acids are molecules without consciousness or life, and that they are generally composed only of carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) atoms.

Blaming the amino acid molecules for what scientists have done in their august scientific pontificating is both humorous and absurd. 

Thus, "Houston, we have a problem":

"We already enjoy a broad array of often conflicting hypotheses for the mechanisms that induce codon-usage biases in nature, and for their effects on protein synthesis and cellular fitness. Until recently, we have been unable to systematically interrogate these hypotheses through large-scale experimentation. As a result, despite decades of interest and substantial progress in understanding codon-usage biases, there is an overabundance of plausible explanatory models whose relative, quantitative contributions are seldom compared."

(Synonymous But Not The Same). Starting off with a loose nomenclature has produced many a loose hypothesis.

II. Monkey Pox

Assuming CUB could be real does not clear up an interesting phenomenon concerning the similarity between SARS-CoV-2 & Omicron variants (Junk DNA R Us at Appendix One, Appendix Two, Appendix Three, Appendix Four, and Appendix Five).

Furthermore, it does not clear up the likeness of the up and coming Monkey Pox virus, as compared to those SARS-CoV-2 & Omicron variants.

Compare the Monkey Pox genomes in today's appendices (Codons, NonCodons, and NonACGT) with the data in those aforementioned five appendices and you will get my drift.

III. Closing Comments

Is scientific nomenclature dynamics the main player here, or is it the reverse planned obsolescence of big pharma's amok commercialism?

The next post in this series is here, the previous post in this series is here.