Some Of My Best Friends Are Germs

Some of my best friends are germs

I. Forward !

The issue of whether or not viruses are alive, like the issue of whether or not rocks are alive, my computer is alive, Dredd Blog is alive, etc., depends on the quality of a language's nomenclature (Good Nomenclature: A Matter of Life and Death).

One would, at first blush, think that scientists would be the first professionals to develop a professional nomenclature without defects, but think again (Are Viruses Alive?).

Whether or not viruses have brains capable of doing what most humans cannot do is also up for cognitive grabs:

"Will virologists try to explain the haphazard genetic changes in those appendices with 'magic words' or will they consider that the microbes hosting these viruses around the world are being damaged and destroyed with antibiotic chemicals? 

(Yes to magic words: "For a virus to evolve, it needs to develop a strategy to fuse itself with the cell membrane of the host and/or to induce host cell–cell fusion." link;  WTF ... "it NEEDS to ... DEVELOP A STRATEGY" ... without a brain, eyes, ears, laboratory ... how does that explain the haphazard percents of change?)"

(The Epigenetics of Viruses). The teleological and/or teleonomical and/or orthogenetic approaches are not an improvement.

Attributing intelligence to a virus that "on their own they can do nothing" (ibid) is beyond absurd (see video below for one viruses experience).

But I digress.

II. UGH! The Missing "U"

The most abundant entities in the universe could be said to be viruses (Are There 10³¹ Virus Particles on Earth, or More, or Fewer?).

And most of them are RNA viruses, not DNA viruses.

One basic difference between RNA and DNA viruses is uracil vs thymine ('U' vs 'T'):

"Uracil (U) is one of four chemical bases that are part of RNA. The other three bases are adenine (A), cytosine (C), and guanine (G). In DNA, the base thymine (T) is used in place of uracil."

(NIH, uracil). What I am UGH!ing about is that in the nucleotide databases "the powers that be" do not use 'U' for uracil (example RNA virus nucleotide data) [go to 'ORIGIN' section @ bottom of the file].

Instead, they use 'T' for thymine in both RNA and DNA sequences even though "In RNA, uracil [U] binds to adenine via two hydrogen bonds. In DNA, the uracil nucleobase is replaced by thymine [T]" (see thymine & uracil links below).

I am not the only one to wonder why they do it that way (Is mRNA sequence on NCBI the actual mRNA with thymine in place of uracil?).

There is "a simple answer" why they tell us about "U" but always use "T" rather than "U": "some of their best friends are germs" (The Genetic Code).

UPDATE: Using 'U' in RNA nucleotide sequencing can be done (Direct RNA Sequencing of the Complete Influenza A Virus Genome; cf. here).

---

adenine (A) [C₅H₅N₅]

cytosine (C) [C₄H₅N₃O]

guanine (G) [C₅H₅N₅O]

thymine (T) [C₅H₆N₂O₂]

uracil (U) [C₄H₄N₂O₂] "Uracil is rarely found in DNA"

---

carbon (C)

hydrogen (H)

nitrogen (N)

oxygen (O)

---

III. Appendices

Anyway, today's appendices detail the variations of "ATGCU" counts in thousands of SARS-CoV-2 viruses around the globe.

The (AC, DI, JM, NR, SZ, USA, UU) appendices contain country data that is alphabetized by the first letter of the country's three letter abbreviation.

Each country has a maximum of 100 SARS-CoV-2 virus data listed.

Each virus is distinguished by a count of the number of adenine (A) [C₅H₅N₅], cytosine (C) [C₄H₅N₃O], guanine (G) [C₅H₅N₅O], thymine (T) [C₅H₆N₂O₂], and uracil (U) [C₄H₄N₂O₂] molecules in their genes.

The count columns (A,C,T,G,U) are the total number of adenine, cytosine, thymine, guanine, and uracil molecules in the genes of that SARS-CoV-2 virus (it does not include A,C,T,G,U counts outside of the genes in the spaces before, between, or after the genes in the nucleotide sequence.

The 'genes' column has the number of genes in that virus.

Note that none of these viruses are [erroneously] said to contain the RNA feature 'U' which represents uracil in the genomes (nucleotides) located in the government GenBank repository.

That (error) even though ("Uracil is a natural base of RNA ... The common RNA base uracil (U)"; I mentioned that above in Section II). 

IV. Closing Comments

Notice also that the changes in A,C,T,G counts are haphazard, i.e., no rhyme nor reason.

Is the missing 'U' component the result of the mass killing of DNA based hosts of the RNA based SARS-CoV-2 viruses? ("Coronaviruses have fewer genetic mutations compared to other RNA viruses" Uracil switch in SARS-CoV-2 genome).

Or, is the missing 'U' thingy just another result of bad nomenclature?

The next post in this series is here.

---

A friendly virus reports back to us about what it is like to enter into a vastly larger single-celled host "to take control over its highly complex machines" (The New Paradigm: The Physical Universe Is Mostly Machine).

---