Saturday, January 8, 2022

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).


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?


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).


3 comments:

  1. "DNA and RNA are totally different. DNA, stands for Deoxyribo Nucleic Acid, is a long polymer with a deoxyribose and phosphate backbone and four different bases: adenine, guanine, cytosine and thymine (A,G,C,T), while RNA,stands for Ribo Nucleic Acid, is a polymer with a ribose and phosphate backbone and four different bases: adenine, guanine, cytosine and uracil (A,G,C,U). DNA can only be found in nucleus, while RNA can either be found in cytoplasm or nucleus. Generally DNA is a double-stranded molecule with a long chain of nucleotides, while RNA is a single-stranded molecule with a short chain of nucleotides. DNA is a medium of long-term storage and is used in transmission of genetic information. RNA is not. Its job is to transfer the genetic code needed for the creation of proteins from the nucleus to the ribosome. To make protein, mRNA must first be sythesized from a DNA template. This step is called transcription. Then ribosomes will synthesize proteins using the mRNA transcript produced during the transcription process. By the way, mRNA is just one type of RNA, which stands for Messenger RNA, while the other two types of RNA are rRNA (Ribosomal RNA) and tRNA (Transfer RNA)." (link)

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    1. "The thymine-uracil exchange constitutes one of the major chemical differences between DNA and RNA ... uracil incorporation in DNA is usually a mistake that needs to be excised. There are two ways for uracil to appear in DNA: thymine replacement and cytosine deamination. Most DNA polymerases readily incorporate dUMP as well as dTMP depending solely on the availability of the d(U/T)TP building block nucleotides. Cytosine deamination results in mutagenic U:G mismatches that must be excised. The repair system, however, also excises U from U:A “normal” pairs. It is therefore crucial to limit thymine-replacing uracils." (Keeping Uracil Out of DNA)

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    2. "Why does the FASTA sequence for coronavirus look like DNA, not RNA?"

      ANSWER: It's HAARD WERK to do RNA rite ... (Stack Exchange)

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