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I. My Favorate Format
Dredd Blog posts have discussed the advent of "gene overlap" as evidence of damage to viruses caused by damage to the microbe hosts of those viruses (e.g The Coronaviridae - 7).
In other words Dredd Blog hypothesizes that gene overlap is a "bug" rather than a "feature" because there is a lot of room for more research and more than one hypothesis as to the why of many aspects of the realm of virus gene overlap.
There are alternate hypotheses to the Dredd Blog theory, hypothesizing that "gene overlap is not a bug, it's a feature", nevertheless there is room for the damage hypothesis:
"Despite their importance, the evolution and function of overlapping genes are often not well understood, in part due to difficulties in their detection."
"Gene overlap occurs when two or more genes share the same region of a nucleotide sequence in a genome."
(A Simple Method, Mol. Biol. Evol., 2018, p.2572, emphasis added). The "difficulties in their detection" statement leads me to inform readers that Dredd Blog uses GenBank flat file format (GenBank Flat File Format).
II. Gene Overlap Designations
In other words, when one downloads genomes of viruses there is a choice of what type of file you want the data stored in.
I like the comprehensive GBFF format because the genes are specified by a beginning nucleotide location as well as an ending nucleotide location for each gene (the "ORIGIN" section of a GBFF file contains the nucleotides list).
For example, let gene_one be "204..807", which would mean that the gene begins at position 204 and extends to position 807.
And let gene_two be "800..904", which would mean that gene_two begins 7 positions prior to gene_one's "807" ending position.
The overlap situation is a 7 position overlap.
Those who do not take damage into consideration, generate a lot of pretzel logic in an attempt to make the "overlapping genes are often not well understood" reality "nothing to see here folks, it's a feature, not a bug" (Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic).
That post advances a notion or hypothesis that viruses self-evolve by choosing to save space by overlapping their genes.
For one thing, that is subject to valid criticism just as many hypotheses are (The Memes of Penrose, On The Origin of Genieology, 2, 3).
For another thing, the data in the major virus databases does not bear that hypothesis out, rather, the data falsifies it (e.g. Appendix Coronaviridae-7).
III. Closing Comments
The "Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic" paper linked-to above is a classic example of "Biologist Teleology", an infamous practice in the virology section of the biological realm (On The Origin of Genieology - 2).
"Magic words" ... they are not just for faux religionists and politicians anymore.
In the next post or so in this series I will document the realm of "overlapping genes" a bit more.
Stay tuned.
The next post in this series is here, the previous post in this series is here.