Tuesday, November 8, 2022

Quantum Biology - 15

Fig. 1 Artwork by Celeste Roberge

I. Art

Today let's understand that art and science can work hand in hand to help us understand what we are (Fig. 1).

II. Science

In episode five of this series I presented some  atomic data concerning the codons in homo sapiens at chromosome 1 (Appendix One, Appendix Two), but today we take a look at the unique lists of DNA/RNA codons found in Toxoplasma gondii ("toxo") and Homo sapiens ("human") genomes from a different perspective.

What is shown is that the unique codons of toxo and humans are identical.

They are presented in today's Codons R Us appendix for your perusal.

I downloaded both toxo and human chromosomes from GenBank, then processed the nucleotides using the technique shown in the last video below.

They were extracted from an SQL data base with the following contents:

mysql> select count(*) from strands;
 | count(*)|
 | 543507 |
1 row in set (1.36 sec)

mysql> select count(*) from strands where celltype='toxo';
 | count(*)|
 |   4766   |
1 row in set (1.17 sec)

mysql> select count(*) from strands where celltype='homo';
 | count(*)|
 | 538741 |
1 row in set (1.20 sec)

In other words, there are 4,766 rows of toxo data, 538,741 rows of human data, and a grand total of 543,507 rows in the SQL database table 'strands'.

Fig. 2 Artwork by Celeste Roberge
This data in my SQL database came from GenBank as usual.

III. Technique

The technique required that I make segments of the human chromosomes into 5' (five prime), 3' (three prime), and mRNA segments because the human chromosomes are from ~60 megabytes up to ~350 megabytes in disk drive size (GBFF format).

The toxo chromosomes are smaller (as shown by the resulting 4,766 toxo genome segments compared to the 538,741 human genome segments) requiring less segmentation.

I loaded one toxo 5', 3', and mRNA row along with one human 5', 3', and mRNA row of nucleotides (base pairs) at a time, then used my genetic code software to extract valid codons from each segment.

I retained only one codon type, i.e. did not allow multiple copies of a codon type for either toxo or human (so, "unique" in this case means only one codon type sample is retained for toxo and for human).

Fig. 3 Artwork by Celeste Roberge

IV. Results

The resulting unique codon list is shown in the sequence they were extracted, along with the amino acid match in the sequence they too were extracted (see Codons R Us).

These results tell us that our human eucaryotic cells are composed of the same unique genome codons that toxo eucaryotic cells are composed of (which also means that they are of the same atomic composition, see Appendix QB.7.1, Appendix QB.7.2, Appendix QB.7.3, Appendix QB.7.4, Appendix QB.7.5, Appendix QB.7.6, Appendix QB.7.7, Appendix QB.7.8, in Quantum Biology - 7).

The human genome has many more codons than the toxo genome has, but they each have the same number of unique codons.

V. Analysis

Fig. 4 Artwork by Celeste Roberge

This is where we focus on the art shown in Fig. 1, Fig. 2, Fig. 3, and Fig. 4, because what holds humans and toxo together comes into focus.

The art at Fig. 1 and Fig. 3 shows that what holds the artwork together is not the rocks or stones within "the containment entity". 

We can liken the rocks or stones within the containment entity to the atoms that humans and toxo have within their containment entity.

Their shape is not determined by the atoms within, rather it is a result of their containment entity.

VI. Closing Comments

The shapes of a great number of things that can be seen are determined by containment entities that can not be seen.

For example the containment entity we call gravity:

"A planet is round because of gravity. A planet's gravity pulls equally from all sides. Gravity pulls from the center to the edges like the spokes of a bicycle wheel. This makes the overall shape of a planet a sphere, which is a three-dimensional circle."

(NASA, Why Are Planets Round?). Another stellar containment entity is "COAM", a member of the containment entity family called angular momentum:

"This effect is due to conservation of angular momentum, and it’s true for galaxies, too."

(NASA, Conservation of Angular Momentum). Once we realize how many planets, stars, and galaxies are shaped by containment entities, not to mention the number of toxo and virus containment entities there are, it's way past the time to focus on containment entities.

That focus, however late, is coming in a future Dredd Blog post in this series.

So, prepare for it by remembering that DNA and RNA are not alive (The New Paradigm: The Physical Universe Is Mostly Machine - 2).

And watch the Dr. Falkowski video below which makes "we don't know" great again, because, the most-honest we can be with our words is "we don't know":

Dr. Paul Falkowski

"Andy. Thank you very much, Andy, and thanks for inviting me here. It's a pleasure. So I just want to begin this by thinking about a bridge. In this particular case, it's an obvious bridge. And if you think about evolution, you know where we've come to, but you don't know where we began. So origins of life is one of the most challenging problems facing science. Actually, as my friend and colleague Nick Lane says, it's the black hole of science. It's an embarrassment. And it's a very complicated problem." -Dr. Falkowski

(From the transcript, emphasis added).

The next post in this series is here, the previous post in this series is here.

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