Saturday, April 10, 2021

The Coronaviridae - 7

DNA/RNA molecules are NOT alive

A fairly recent article (Oct. 2020) introduced something I ran across and wrestled with over the past week or so.

That something is "Overlapping Genes" [OLG] in the genome of corona viruses.

At first I though I had a bug in my software or "they" GenBank had a bug in theirs.

The article I mentioned solved the mystery and pointed out some interesting factors:

"OLGs are known entities but remain inconsistently reported in viruses of the species Severe acute respiratory syndrome-related coronavirus (subgenus Sarbecovirus; genus Betacoronavirus; Coronaviridae Study Group of the International Committee on Taxonomy of Viruses et al., 2020). For example, annotations of ORF9b and ORF9c are absent or conflicting in SARS-CoV-2 reference genome Wuhan-Hu-1 (NCBI: NC_045512.2) and genomic studies (e.g. Chan et al., 2020; Wu et al., 2020b), and OLGs are often not displayed in genome browsers (e.g. Flynn et al., 2020). Further, ORF3b, an extensively characterized OLG within ORF3a that is present in other species members including SARS-CoV (SARS-CoV-1) (McBride and Fielding, 2012), has sometimes been annotated in SARS-CoV-2 even though it contains four early STOP codons in this virus. Such inconsistencies complicate research, because OLGs may play key roles in the emergence of new viruses."

(Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic, emphasis added; cf. Viruses: Essential Agents of Life).

I had mentioned to the GenBank folks that GenBank Flat Files (GBFF) had gene specifications where beginning positions and ending positions were indicating that some genes were overlapped. 

Out of about 70,000 genomes I identified a total of about 1,034 of overlapped-gene genomes from a lot of countries (see Appendix).

I still maintain my hypothesis that, since mutations are damages "from exposure to a multitude of endogenous and exogenous insults" (The Coronaviridae - 6), the "variants" we hear about lately in the corporate news media are merely victims of other victims (their microbe hosts).

The overuse and misuse of chemicals in the mass-production-of-animals-for-food industry are still prime suspects (On The Origin Of The Home Of COVID-19, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21).

The previous post in this series is here.

An interesting video of an interesting TED talk:

Video Index (time - subject)

00:21 - microbes are oldest life forms on Earth
01:03 - 10 times more microbes than human cells in us
01:31 - 100 times more microbial genes than human genes in us
02:00 - microbes are 99% of our make-up; they keep us alive
02:20 - microbes are vital for keeping us alive and healthy
04:20 - microbes talk with a molecular language
07:50 - quorum sensing (like a census) to know population count
08:20 - Intra species communication (shape of words) dialects
10:50 - microbes communicate with other microbes (multi-lingual)
11:20 - they take a census of all other microbes around them
12:30 - synthetic molecules-words interrupt communication
13:50 - synthetic molecules-words confuse the microbes
15:00 - they have collective, community behaviors
15:20 - microbes made the rules for multi-cellular development
16:00 - microbes invented multi-cellular behavior inside us
17:15 - the team

Dr. Bonnie L. Bassler, Princeton University:

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