Pangenome - 3

Fig. 1 Look Ma!
Viruses Made of Atoms!

I. Background

When I was constructing the first post (Pangenome) of this series I derived a meaning for "pangenome" from the web/blog site "HPRC".

Possibly the better place to begin would have been to consider the operative word that frames the meaning of "genome" in context:

pan-

word-forming element meaning "all, every, whole, all-inclusive," from Greek pan-, combining form of pas (neuter pan, masculine and neuter genitive pantos) "all," from PIE *pant- "all" (with derivatives found only in Greek and Tocharian).

Commonly used as a prefix in Greek (before a labial pam-; before a guttural pag-), in modern times often with nationality names, the first example of which seems to have been Panslavism (1846). Also panislamic (1881), pan-American (1889), pan-German (1892), pan-African (1900), pan-European (1901), pan-Arabism (1930).

(Etymology, emphasis added). In other words "Pan-HumanGenome" might have been a better derivation than "Pangenome".

Now the HPRC has updated themselves with a "draft" (A draft human pangenome reference) that is said to be able to get improvements updated by, among other things, filling in the 'N' nucleotide gaps in existing human chromosome data.

That is a worthwhile start because there are hundreds of 'N' placeholders instead of 'A', 'C', 'G', 'T' and/or 'U' nucleotides in the chromosome genomes in current databases.

II. Pan-Atomic

The atomic nitty gritty was brought up in the second post of this series, that is, that DNA and RNA are composed of a small group of only four atom-types, i.e. Carbon, Hydrogen, Nitrogen, and Oxygen (Pangenome - 2, Fig. 1)!

In that post I presented almost fifty thousand DNA and/or RNA sequences that had been analyzed to determine the atomic content and percentages by type/quantity of atoms in those genomes.

The surprising thing about that was the similarities in the atomic make up (percentage of atom types) within many different types of creatures and viruses.

Today, that atomic analysis continues but I am using the new viruses discovered in the ocean fairly recently (Thousands of new viruses discovered in the ocean).

In Fig. 2 below, three complete DNA genomes (gathered by the folks who wrote the paper) are linked to.

The percentage/ratios of the atom types are also listed (Tables 1-3).

Finally, there is a summary featuring those three tables (Fig. 3)

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Fig. 2

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Table: 1

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Link and genome info: JAAOEI010000001.1
Viral metagenome NODE_1_length_147131_cov_7.178554

Nucleotide count: 147,131

Atom	Count	Percent
Carbon	693,535	32.06
Hydrogen	767,852	35.49
Nitrogen	554,824	25.65
Oxygen	147,164	6.80
Totals	2,163,375	100.00

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Table: 2

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Link and genome info: JAAOEI010000002.1
Viral metagenome NODE_2_length_79887_cov_6.251428

Nucleotide count: 79,887

Atom	Count	Percent
Carbon	386,320	32.65
Hydrogen	427,574	36.14
Nitrogen	288,788	24.41
Oxygen	80,521	6.81
Totals	1,183,203	100.00

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Table: 3

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Link and genome info: JAAOEI010000003.1
Viral metagenome NODE_3_length_78338_cov_84.761340

Nucleotide count: 78,338

Atom	Count	Percent
Carbon	370,586	32.09
Hydrogen	408,577	35.38
Nitrogen	298,821	25.87
Oxygen	76,957	6.66
Totals	1,154,941	100.00

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Fig. 3

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Summary information for above three tables:

Atom	High Percent	Entity	Low Percent	Entity	Variation Percent
Carbon	32.65	JAAOEI010000002.1	32.06	JAAOEI010000001.1	0.59
Hydrogen	36.14	JAAOEI010000002.1	35.38	JAAOEI010000003.1	0.76
Nitrogen	25.87	JAAOEI010000003.1	24.41	JAAOEI010000002.1	1.47
Oxygen	6.81	JAAOEI010000002.1	6.66	JAAOEI010000003.1	0.14

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III. Results

As you can see in Fig. 2 and Fig. 3, the percentages of atoms by type in recently found and previously unknown virus genomes are surprisingly close percentage matches (less than 2% variation).

The previous results in the previous post of this series were close too (Pangenome - 2).

IV. Closing Comments

I have stumbled upon another unknown.

The mixture of atoms in all those genomes is problematic:

"And we come up with this basic plot, which is the two first elements are hydrogen and helium, which are created about 13.8, 13.9 billion years ago in the big bang. And everything else on this plot the astronomers called metals, but everything else is created in a supernova, not our star. A very hot short life star ... and then there's carbon, nitrogen, and oxygen ... so these elements form the nucleic acids ... How did we get the nucleic acids? We don't really know."

(Dr. Falkowski, video below). We don't really know how a group of atoms of different origin locations and birthdays "got together" to become nucleic acids (The Doll As Metaphor - 6).

I have a suspicion that geneticists won't like my atomic percentages discovery because it really makes their teleological lives more difficult.

Enter the Shakespearean play spoken in the "teleology language" (On The Origin of The Containment Entity - 8).

The teleology as a reaction to "we don't know" goes back to a Latin speaking priest "Lemaître" who began the Big Bang hypothesis.

There are those who are still doubling down on that Big Bang 'sermon' (Universe will end with a bang, or a whimper, says Vatican astronomer). 

But it does not end there folks, no, it's a bigger bang than ever now, yep, Panbiggaboom Zen (Small Brains Considered - 7).

The previous post in this series is here.

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