Dredd Blog: 2023-11-05

Saturday, November 11, 2023

On The Origin Of A Genetic Constant - 9

If you haven't read the previous posts in this series (On The Origin Of A Genetic Constant, 1, 2, 3, 4, 5, 6, 7, 8) then this post will be a primer.

To determine the genetic constants for DNA and RNA we begin with the basic Chemical Formula concept:

"In chemistry, a chemical formula is a way of presenting information about the chemical proportions of atoms that constitute a particular chemical compound or molecule, using chemical element symbols, numbers ... [example glucose:] C₆H₁₂O₆ (12 hydrogen atoms, six carbon and oxygen atoms)."

(Wikipedia, Chemical Formula). Now we apply it to the molecules of DNA and RNA:

"I. Where Did The ~(32/35/25/6) Originate?

That is a fair question, so this post will answer the question and will provide the updated exact values and where "~(32/35/25/6)" originated.

Let's start with the nucleotide, atom, and their quantities that are in BOTH DNA and RNA:

Nucleotides(ACG), atoms, and counts in both DNA and RNA:

A: (Adenine) 15 atoms (5 carbon, 5 hydrogen, 5 nitrogen, 0 oxygen)

C: (Cytocine) 13 atoms (4 carbon, 5 hydrogen, 3 nitrogen, 1 oxygen)

G: (Guanine) 16 atoms (5 carbon, 5 hydrogen, 5 nitrogen, 1 oxygen)

44 total atoms (14 carbon, 15 hydrogen, 13 nitrogen, 2 oxygen)

Percentages:
(carbon 31.8181, hydrogen 34.0909, nitrogen 29.5455, oxygen 4.5455)

Now let's add the missing ingredient ("T") needed to make the nucleotide group complete for DNA:

Additional nucleotide(T), atoms, and count (only in DNA):

T: (Thymine) 15 atoms, (5 carbon, 6 hydrogen, 2 nitrogen, 2 oxygen)
59 total atoms (19 carbon, 21 hydrogen, 15 nitrogen, 4 oxygen)

Percentages:
(carbon 32.2034, hydrogen 35.5932, nitrogen 25.4237, oxygen 6.7797)

That is the source for the DNA (ACGT) ~(32/35/25/6) genetic constant.

It is 19, 21, 15, and 4 divided by 59 (x 100.0) which determines those percentages of those atoms in the genomes of DNA."

(On The Origin Of A Genetic Constant - 5). To top it off, we note that RNA does not have "T" thymine, instead it has "U" uracil:

"Now let's add the missing ingredient ("U") needed to make the nucleotide group complete for RNA:

Additional nucleotide(U), atoms, and count (only in RNA):
U: (Uracil) 12 atoms, (4 carbon, 4 hydrogen, 2 nitrogen, 2 oxygen)
56 total atoms (18 carbon, 19 hydrogen, 15 nitrogen, 4 oxygen)

Percentages:
(carbon 32.1429, hydrogen 33.9286, nitrogen 26.7857, oxygen 7.1429)

That is the source for the RNA (ACGU) ~(32/33/26/7) genetic constant.

It is 18, 19, 15, and 4 divided by 56 (x 100.0) which determines those percentages of those atoms in the genomes of RNA."

(On The Origin Of A Genetic Constant - 6).

You may be wondering where the projected constant "~(32/35/25/6)" of DNA nucleotide carbon, hydrogen, nitrogen, and oxygen atoms came from, so here are the relevant Chemical Formulas:

Screen shots
from Wikipedia links above

The calculations concerning the atomic genetic constant are accomplished by simple arithmetic (no algebra or high math or calculus is necessary).

To apply it to a GenBank single genome file (.gbff or .fasta):

1) load the ACGT nucleotides (Origin section of a GenBank .gbff file, or the second line through the end of the file for a GenBank FASTA file); 2) determine the total individual nucleotide count of ACG and T in that genome; 3) multiply those nucleotide counts by the individual carbon('C'), hydrogen ('H'), nitrogen('H') and oxygen('O') atom counts specified in the Chemical Formula for each nucleotide type (ACGT), example: 'A' nucleotide count times carbon count (5), 'C' nucleotide count times carbon count (4), etc.; 4) add up (sum) the 'C' 'H' 'N' and 'O' quantities for each individual atom type ; 5) add up (sum) all atoms ; and 6) divide each atom category count ('C', 'H', 'N' and 'O') by the sum of all atoms, then multiply by 100 to derive the percentage of each atom type in that genome:

Example genome totals:

Atom	Atom Count	Percent
Carbon	1,071,062	32.3550
Hydrogen	1,178,966	35.6146
Nitrogen	847,036	25.5875
Oxygen	213,284	6.4429
Totals	3,310,348	~100.00

Total carbon atoms (1,071,062 divided by total genome atoms 3,310,348) = 0.32355 (times 100 = 32.3550%) and so forth.

Today's appendix gives an example of how the numbers come about (Example Appendix).

If you like, enjoy this arithmetic applied to over a million genomes in the previous appendices to the previous post (Appendix Low, Appendix High, and Appendix Average).

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

Once upon a time a polymath visited Harvard:

Appendix Genetic Constant - 9

This is an appendix to: On The Origin Of A Genetic Constant - 9

Genetic Constant ~(32/35/25/6) file analysis

Genbank File Genome link: CP002988.1

Nucleotide Counts:

Adenine ('A') count: 527,444
Cytosine ('C') count: 930,774
Guanine ('G') count: 931,003
Thymine ('T') count: 524,468

Total Nucleotide content: 2,913,689 bp

ACGT Atom Percents:

Adenine ('A'):

Carbon: 6.17, Hydrogen: 6.17, Nitrogen: 6.17, Oxygen: 0.00,

Cytosine ('C'):

Carbon: 8.70, Hydrogen: 10.88, Nitrogen: 6.53, Oxygen: 2.18,

Guanine ('G'):

Carbon: 10.88, Hydrogen: 10.88, Nitrogen: 10.88, Oxygen: 2.18,

Thymine ('T'):

Carbon: 6.13, Hydrogen: 7.36, Nitrogen: 2.45, Oxygen: 2.45,

For totals: (see Atom percent sums below)

Atom percent sums (from Atom Data/Counts above):

Carbon: 31.8825% (6.17%+8.70%+10.88%+6.13%)
Hydrogen: 35.2846% (6.17%+10.88%+10.88%+7.36%)
Nitrogen: 26.0282% (6.17%+6.53%+10.88%+2.45%)
Oxygen: 6.80474% (0.00%+2.18%+2.18%+2.45%)

Total percent: 100%

Atom variation-from-constant percents:

Carbon: 0.320903%
Hydrogen: 0.308601%
Nitrogen: 0.604465%
Oxygen: 0.0250394%
total: 1.25901%

Friday, November 10, 2023

On The Origin Of A Genetic Constant - 8

Sketchfab

What it the big deal about a "genetic constant" you might wonder.

Well, the answer is the same as for any "fundamental physical constant or universal constant":

There are many physical constants in science, some of the most widely recognized being the speed of light in vacuum c, the gravitational constant G, the Planck constant h, the electric constant ε₀, and the elementary charge e. Physical constants can take many dimensional forms: the speed of light signifies a maximum speed for any object and its dimension is length divided by time; while the proton-to-electron mass ratio, is dimensionless.
The term "fundamental physical constant" is sometimes used to refer to universal-but-dimensioned physical constants such as those mentioned above.^[1] Increasingly, however, physicists reserve the expression for the narrower case of dimensionless universal physical constants, such as the fine-structure constant α, which characterizes the strength of the electromagnetic interaction.

(Wikipedia, Physical Constant). The concept is simple enough, however there is another part of the story to consider.

One thing about all constants is that they are measurements.

The quality of everything used to make measurements as well as the one doing the measuring, involves activities that can vary in degree of accuracy.

In the case of DNA gathering, analyzing, storing, and use:

"Despite how it is often portrayed, in the media and in courts, the forensic science of DNA is far from infallible." (Nature)

"It is extremely important to remember that DNA can easily be damaged even when it has been properly collected and packaged. Damage to DNA can occur from improper storage, exposure to direct sunlight, or simply by becoming too warm." (How To)

(cf. Guidelines for DNA Collection, The Atlantic, Puritan, DNA Evidence).

Measuring the length of a pencil is not the same in terms of difficulty as counting the atoms in a genome.

But even more difficult than that is accurately gathering those atoms.

It is well known that even gathering the nucleotide count ('A','C','G,','T','U') is difficult because they are so tiny.

Those are some of the reasons that the genetic constant ~(32/35/25/6) discovered and discussed in this series is compelling.

The genomes where it is found come from around the globe, from the air, water, and land, and from many different scientists.

In today's appendices over a million such genomes documented in the GenBank are analyzed for three variation dimensions (Appendix Low, Appendix High, and Appendix Average).

The technique used is to gather the counts of the carbon, hydrogen, nitrogen and oxygen atoms in each 'A','C','G,','T' nucleotide in each genome.

The variations from the ~(32/35/25/6) genetic constant are then detailed by the percentages of lowest percents of variation, highest percents of variation, and average percents of variation.

That is carbon variation from 32.2034%, hydrogen variation from 35.5932%, nitrogen variation from 25.4237%, and oxygen variation from 6.7797% (NOTE: The locus of the genetic constant values for DNA are calculated here and for RNA here.)

These genome values are considered in sections of 100,000 (one hundred thousand) genomes and a final smaller quantity, the sum of all of the sections being 1,052,789 (one million fifty two thousand and seven hundred eighty nine) genomes.

Sample HTML tables are displayed in each section with a link to the GenBank record for user perusal.

What is so convincing about this ~(32/35/25/6) genetic constant is that it is found in so many different plants, animals, fish, humans, and microbes from so many different scientists, and from so many different countries.

In practical terms, one can detect collection and/or processing and/or storage complications to the degree that the ACGT atom percentages vary from the ~(32.2034/35.5932/25.4237/6.7797) constant a significant amount.

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

GC-8 Appendix LOW

This is an appendix to: On The Origin Of A Genetic Constant - 8

GenBank Genome Files
Low Variations
Analysis Report

after processing 100,000 genomes:

Sample genome HTML tables
showing LOW variation
summaries for this section:

GenBank Genome
Table: 1
(v= <1 [0.0210%])
**URL Link:** LR862133.1

**Genome info for LR862133.1**:

LR862133 18411140 bp DNA linear PLN 28-JUL-2020 Ananas comosus var. bracteatus genome assembly
chromosome: 5.

**Nucleotide count:** 18,405,240
Non-Nucleotide Count: 5,900
Atom	Atom Count	Percent
Carbon	88,541,178	32.4808
Hydrogen	97,752,075	35.8597
Nitrogen	67,878,531	24.9008
Oxygen	18,424,038	6.7587
Totals	272,595,822	~100.00