Junk DNA R Us

Shudders and Shocks

I. Background

According to our daddy's and mommy's DNA Guy (they preceded our Cable Guy) we had more DNA than we knew what to do with.

Now we know, according to the numbers of our DNA guy, that we have about as much "human" (homo) DNA as a grape like Gilbert Grape (The Human Microbiome Congress), but more magically it's like:

"What your daddy and mommy were taught about genetics, like most old skool mommy and daddy skoolin', is wrong.

Don't feel bad, Charles Darwin knew nothing of genes, yet said he knew all about how we got here.

He had a lot of genies to help, though.

But now, the age of conflating genies with genes is over, however, the new genetic reality is not yet catching on well enough.

So, today we will review the difference between the understanding during "early genetics" (The Eugenics Review Vols. 1 to 60; 1909 to 1968) with the current state of affairs for understanding genetics (The Uncertain Gene, 2, 3, 4, 5, 6, 7, 8, 9, 10).

Once upon a selfish gene ("The Selfish Gene" age) in a discipline long ago, genes were thought to be genies in the sense of being able to draw the map of your everything.

Determinism (genetic essentialism) on steroids, as it were, taking you along for the virtual magic carpet ride.

Everyone was unique with an "isn't that special" set of genies down under the hood, genies that were like Jack's magic beans, which took you and everyone else up, up, up, rapturously along their own special, unique Highway 61, to selfish gene heaven.

That is, if you had a special gene maker genie who was selfish enough, but if not, well then it's Eugenics for you.

Then came the Human Genome Project, those damn scientists, who wrecked the daydream with this:

More problematic is the reality that the human genome is still a vast catalogue of the unknown and scarcely known. The Human Genome Project’s most startling finding was that human genes, as currently defined, make up less than 2 percent of all the DNA on the genome, and that the total number of genes is relatively small. Scientists had predicted there might be 80,000 to 140,000 human genes, but the current tally is fewer than 25,000 — as one scientific paper put it, somewhere between that of a chicken and a grape. The remaining 98 percent of our DNA, once dismissed as “junk DNA,” is now taken more seriously.Researchers have focused on introns, in the gaps between the coding segments of genes, which may play a crucial role in regulating gene expression, by switching them on and off in response to environmental stimuli.

 

(One Man's Junk Gene Is Another Man's Treasure Gene?). What do you mean ... human genes fit somewhere between "a chicken and a grape" (What's Eating Gilbert Grape?)."

(On The Origin of Genieology). What, genetically speaking we were 98% junk genes ("The remaining 98 percent of our DNA, once dismissed as 'junk DNA'")?

Eugenics in the USA perhaps? ... but what about that epigenetics stuff (The Epigenetics of Viruses)?

II. Foreground

What was "junk DNA" not very many years ago is now considered to be super DNA (after the advent of the trons), but still one wonders if the war being waged against microbes is being considered in the serious way that it should be:

The concept has been discussed in scientific journals since at least 1957 (Penicillin-Induced Lysis of Escherichia coli) and as recently as this year:

"Bactericidal antibiotics kill bacteria by perturbing various cellular targets and processes. Disruption of the primary antibiotic-binding partner induces a cascade of molecular events, leading to overproduction of reactive metabolic by-products. It remains unclear, however, how these molecular events contribute to bacterial cell death. Here, we take a single-cell physical biology approach to probe antibiotic function. We show that aminoglycosides and fluoroquinolones induce cytoplasmic condensation through membrane damage and subsequent outflow of cytoplasmic contents [including virus RNA] as part of their lethality.
...
Previous work has shown that the intracellular accumulation of promiscuously reactive metabolic by-products induces widespread cellular dysfunction and contributes to antibiotic lethality [microbe death]. However, the mechanisms underlying how reactive metabolic by-products, and the accompanying phenotypic changes, [variants, mutants] contribute to cell death have remained unclear."

(Cytoplasmic ... Damage ... Antibiotic Lethality, emphasis added). The words highlighted in red, and the words highlighted in bold, help focus on the Dredd Blog hypothesis that antibiotic chemicals used promiscuously in the mass-production-of-animals-for-food industry is causing viruses to be changed by the indiscriminate killing of microbe hosts ("around 70% of the world's total production of antibiotics is used in animal husbandry and agriculture").

(Omicron (OMC!) - 3). When we extract genetic material (from the realm where 70% of the antibiotics being made by big pharma that are killing microbes in the animals we eat; [see second video below]) we must consider the damage that has been done or is being done to the genomes of those microbes by the mass-production-of-animals for food industry.

It is now ho-hum science to examine waste water and other sources which point out that chimera (more than one chimeric) genomes are everywhere (It's In The GenBank - 4, On The Origin Of The Home Of COVID-19 - 19, In New York City Sewage, a Mysterious Coronavirus Signal).

III. Appendices

Today I have prepared some evidence and placed it into several appendices.

The effort I have put forth is directed at discovering any anomalies in the GenBank files.

These anomalies I will talk about in today's post are real in the sense that they should not be there.

Some of them take place at the microbe destruction phase, others take place at the collection of the DNA/RNA phase, and most may take place during the analysis phase.

First, remember that only 'A', 'C', 'G', or 'T' letters should appear in the base pairs of the about thirty thousand letter nucleotide data (IUPAC nomenclature allows "it could be this,that, or the other" letters into the nomenclature because the equipment used is not flawless).

IV. Appendix One 

Appendix One is the list of Unique Codons for the SARS-CoV-2 variety, followed by the Codon Count in each virus on the list.

The total viruses in the list is 528.

Most viruses in the list (519) have 61 codons, but 7 of them have 62 codons, 2 of them have 60 codons.

V. Appendix Two

Appendix Two is the list of Unique Codons for the Omicron variety, followed by the Codon Count in each virus on the list.

The total viruses in the list is 353.

Most viruses in the list (351) have 61 codons, but 2 of them have 62 codons. 

VI. Appendix Three

Appendix Three shows us that an 'N' shows up to indicate a bad read or translation of the DNA material, and it shows us that alien letters show up as well.

The following six examples are from that appendix:

SARS-CoV-2 [ version: Link, about: Australia/AUS/VIC23/2020 ]
Unique Non-ACGT erata: N, total count: 1

SARS-CoV-2 [ version: Link, about: Australia/AUS/VIC27/2020 ]
Unique Non-ACGT erata: K, total count: 1

 ...

Omicron [ version: Link, about: United States/USA/2021]
Unique Non-ACGT erata: N, total count: 141

Omicron [ version: Link, about: United States/USA/2021]
Unique Non-ACGT erata: N, total count: 92

Omicron [ version: Link, about: United States/USA/2021]
Unique Non-ACGT erata: N,Y, total count: 91

Omicron [ version: Link, about: Vietnam/VNM/2022]
Unique Non-ACGT erata: N, total count: 25

(from Appendix Three). The "SARS-CoV-2" indicates a non "Omicron" sample, "Omicron" indicates a "variant"; the "version: Link" is an URL link to the GenBank data of a particular virus sample (click on it if you are online and the GenBank data will be loaded into your browser); the "about: ..." indicates the country (e.g. "Australia/AUS") which the sample is from, and ("/2020") tells us the year the sample was acquired; the "Unique Non-ACGT erata: K" tells us that the letter 'K' is an error in the DNA record; the "total count" tells us the total number  of erroneous letters which are in that DNA record; in other words, "total count" is not the number of different letters, it is the total number of illegitimate letters.

So, if is says "Z" is the only unique letter, but the total number is "25" that means there are 25 illegitimate 'Z' letters in the sample).

The Omicron viruses listed above are an example of one illegitimate letter type, with multiple ('141', '92') quantities of that one letter.

The "Unique Non-ACGT erata: N,Y, total count: 91" indicates two illegitimate letters with 91 being the total count (the individual counts for each letter are not provided).

If you want to know where each letter is located in the nucleotide list, load the FASTA or GenBank (GBFF format) version into your word processor and do a search for each letter.

VII. Appendix Four

Appendix Four is a list of Omicron variants with malformed letters that are not three letter codons, instead, they are one or two letters in length.

While those letters are either 'A' or 'C' or 'G' or 'T' letters (the valid letters), there must be three to make up a valid codon.

The total count is the number of letters (about 10% of the total number of base pairs).

VIII. Appendix Five

Appendix Five is a list of SARS-CoV-2 viruses with malformed letters that are not three letter codons, instead, they are one or two letters in length.

While those letters are either 'A' or 'C' or 'G' or 'T' letters (the valid letters), there must be three to make up a valid codon.

The total count is the number of letters (about 10% of the total number of base pairs). 

IX. RNA Codons vs. DNA Codons

The difference in RNA and DNA is real, as indicated by the Genetic Code.

That makes the RNA codons different from DNA codons in that DNA has thymine, RNA does not, and RNA has uracil, DNA does not.

Notice the 'U' for uracil in the following RNA codon appendices from the recent Dredd Blog post On The Origin Of The Home Of COVID-19 - 30:

Countries (Alphabetical)

Appendix: A-C

Appendix: D-G

Appendix: H-L

Appendix: M-O

Appendix: P-T

Appendix: U-Z

The way RNA codons are formulated from DNA is shown in the first video below.

That is not the way the DNA codons were determined in today's appendices.

Instead, the Genetic Code was used (DNA and RNA codon tables). 

In the next post of this series I will illustrate these concepts further by processing the same genomes processed in this post, but using 'U' rather than 'T'.

That is, the 'T' letters in the genomes will first be changed into 'U' ('T'=thymine, 'U'=uracil) before the codons are generated.

Stay tuned if you wish.

X. The Process

The process I used to isolate the DNA in today's appendices is as follows:

1) Identify and remove non-ACGT letters (e.g. 'N');

2) Identify and list valid codons, using the Genetic Code;

3) Identify and remove non-valid sequences of ACGT letters.

That differs from the process I used to isolate RNA codons, which as I said, is depicted in the first video below.

XI. Closing Comments

Scientists have warned about the problems with genome construction.

There are a lot of things to sort out since we are destroying the microbes (with antibiotics and other chemicals) that are hosts of both beneficial and harmful viruses (see the second and third videos below).

The next post in this series is here.

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