Dredd Blog: 2022-11-13

Thursday, November 17, 2022

Small Brains Considered - 13

Fig. 1 Metaphorical Teleology

I. From A Distance

Morphology in biology is the branch of biology that deals with the form of living organisms, and with relationships between their structures:

"Understanding the basic structure and function of organisms is one of the oldest areas of research pertaining to the natural world. We are, quite simply, fascinated with how animals work."

(Functional Morphology). One virals' poster "Christoph I-Y-II" (aye wye 2) cites to the shape of a colleague's post which points out that:

"in biology one of the most important paradigms is that of structure-function"

(On Shape). Of course one of the major small thingy paradigms is "a worldview underlying the theories and methodology of a particular scientific subject", which is:

“Teleology is like a mistress to the biologist; he dare not be seen with her in public but cannot live without her.” —J. B. S. Haldane

In Fig. 1 the paradigm's graphic concept is presented. It's from a Berkeley post, which focuses on what Dredd Blog has been focusing on too:

[Eukaryotes] "show unbelievable diversity in form"

(Introduction to the Eukaryota). But, the Berkeleys focus only from a teleological distance.

II. Distant Shapes Considered

But the Dredd Blog view is a small brains considered view, which is not from a distance that is far away from the "containment entity" pointed out about functional morphology (in the Dredd Blog post Quantum Biology - 15).

The realm of shape, or as Dredd Blog puts it "containment entity", has been a failure in biology:

Fig. 2 Functional Atomic Morphology

"The modern age of metagenomics has ... failed to provide information about coincident cellular morphologiea [even though] ... morphology comprises a critical component of bacterial fitness, molded by natural selection into the many elaborate shapes observed across the bacterial domain."

(Diversity Takes Shape: Understanding the Mechanistic and Adaptive Basis of Bacterial Morphology). For example, note that the shape of the home planet of all relevant abiotic and biotic entities is the shape of the Earth, which happened way before "natural selection".

That shape, along with the shapes which this "modern age of metagenomics has ... failed to provide information about [even though] ... morphology comprises a critical component of bacterial fitness" is shown in Fig. 3.

Fig. 3 The "containment entity"

It (containment entity shape) is the blue circle of the Earth representing the globe shape of the Earth.

A globe shape that is an invisible, but well known "containment entity" which we can measure: F=G(m1*m2/d²).

That well-known yet invisible entity is called gravity (NASA, Why Are Planets Round?)

It is a factor in other shape realms too.

"A galaxy is a large group of stars, gas, and dust bound together by gravity"(NASA).

Galaxies composed of both "round" planets and stars that are shaped by gravity can vary in shape because of angular momentum (another invisible "containment entity") impact on them (Angular Momentum And Galaxy Formation Revisited).

Thus, we can say that the morphology of the celestial home of biological entities shown in Fig. 3 is the "containment entity" we call gravity.

But that is about it in terms of the shapes shown outside the blue circle shown in Fig. 3.

Some of those shapes could be confused with galaxies, but that would lead to Astrology, not functional morphology.

The post Quantum Biology - 15 quoted above included an appendix which shows that "from a distance" biologists know that Toxoplasma gondii codons are the same as human (homo sapiens) codons, and the "same old same old" goes for "Escherichia coli ... the model bacterium" of microbiologists:

Unique Escherichia coli codons:
GCT,GCC,GCA,GCG,GCU,TGT,TGC,UGU,UGC,GAT,GAC,GAU,GAA,GAG,
TTT,TTC,UUU,UUC,GGT,GGC,GGA,GGG,GGU,CAT,CAC,CAU,ATT,ATC,
ATA,AUU,AUC,AUA,AAA,AAG,CTT,CTC,CTA,CTG,TTA,TTG,CUU,CUC,
CUA,CUG,UUA,UUG,ATG,AUG,AAT,AAC,AAU,CCT,CCC,CCA,CCG,CCU,
CAA,CAG,CGT,CGC,CGA,CGG,AGA,AGG,CGU,TCT,TCC,TCA,TCG,AGT,
AGC,UCU,UCC,UCA,UCG,AGU,ACT,ACC,ACA,ACG,ACU,GTT,GTC,GTA,
GTG,GUU,GUC,GUA,GUG,TGG,UGG,TAT,TAC,UAU,UAC,TAA,TAG,TGA,
UAA,UAG,UGA

Unique Escherichia coli amino acids:
ACDEFGHIKLMNPQRSTVWYZ

(Generated by Dredd Blog software also used to generate Codons R Us). Compare the Escherichia coli codons with the human and toxo codons in the appendix Codons R Us in the Dredd Blog post Quantum Biology - 15.

UPDATE: I added an appendix (Codons R Us - 2) of 65 bacteria codons that match the previous (toxo, human, corona) codons.

"From a distance" we all look similar, eh?

III. Are We There Yet?

At "the 19th century telescopic distance" from Mars, scientists indicated that there were canals, etc. on Mars (NASA).

From the paper quoted above:

"Imagine a bacterium. Did you imagine asymmetric, multicellular filaments of curved bacteria ... Or perhaps instead you imagined a photosynthetic, ovoid ... Or did you imagine ... coccoid, rod shaped, or spirillar types, there are also dendroid, coryneform, cylindrical, bulbiform, fusiform, and vibrioid types" ... [etc.]

("Diversity Takes Shape"). What do you mean "imagine" ... do you mean shaped by the invisible "containment entity" gravity/angular momentum that shapes most cosmic matter, or perhaps you mean the imaginative astrological charts of ancient Babylon that have some familiarity to microbe shapes?

Anyway, no, I did not imagine anything of the sort because imagination is not evidence.

Gravity is not the containment entity that shapes microbes, nor is their likeness to some of the ancient astrological charts a clue to the containment entities that form their shapes.

The "Conclusion" section of that paper states:

"Decades after an initial surge in environmental microbiology described a vast array of different bacterial shapes, we are left with an impressive body of knowledge describing what is out there, but relatively little in the way of how and why."

(ibid, p. 11). Well, I guess that does leave us with the mistress, the teleological imagination, that J. B. S. Haldane pointed out (Metaphor and Meaning in the Teleological Language of Biology).

But I digress.

Even though the paper (Diversity Takes Shape: Understanding the Mechanistic and Adaptive Basis of Bacterial Morphology) does not contain the word "atom" or the word "molecule" or the word "codon" or the word "RNA" or the word "DNA" (but "R-factor DNA" is in the title of a paper listed at reference 10), Dredd Blog posts and series indicate an awareness of codons, DNA, RNA, atoms, and molecules, so let's go there.

IV. Let's Get Down To The Small
Atomic Shapes To Be Considered

But first, let's remember that:

"The reason that bacteria have certain shapes remains unclear; we can only surmise that certain shapes have adaptive value or have been produced by other selective forces since they are under genetic control and are maintained from generation to generation." (p. 4) [But] "all these guesses may be off the mark" (p. 5). "Although microbiologists have long appreciated the impressive morphological diversity among bacteria, we still have much to learn. Modern technologies provide access to unprecedented quantities of data, particularly microbial genome sequences." (p. 6)

(ibid, emphasis added). As I wrote above, the paper does mention Escherichia coli which has been featured on Dredd Blog (in terms of its codons, molecules, and atoms; e.g. Appendix SBC-5(E)).

Here again, the "containment entity" i.e. origin of the shape is not revealed in the molecules and atoms that make up the DNA, RNA, codons, amino acids, nucleotides, and genes.

V. Closing Comments

So, the most-honest we can be with our words is "we don't know":

Fig. 4 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

(emphasis added, link @ Fig. 4).

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

Appendix Codons R Us - 2

This is an appendix to: Small Brains Considered - 13

Unique Staphylococcus debuckii Codons:

Unique Staphylococcus debuckii Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Mycoplasma mycoides Codons:

Unique Mycoplasma mycoides Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Staphylococcus haemolyticus Codons:

Unique Staphylococcus haemolyticus Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Rathayibacter tanaceti Codons:

Unique Rathayibacter tanaceti Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Rathayibacter festucae Codons:

Unique Rathayibacter festucae Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Staphylococcus aureus Codons:

Unique Staphylococcus aureus Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Moraxella bovis Codons:

Unique Moraxella bovis Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Pseudomonas aeruginosa Codons:

Unique Pseudomonas aeruginosa Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Pseudomonas brassicacearum Codons:

Unique Pseudomonas brassicacearum Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Psychrobacter alimentarius Codons:

Unique Psychrobacter alimentarius Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Pseudomonas amygdali Codons:

Unique Pseudomonas amygdali Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Candidatus Pseudomonas Codons:

Unique Candidatus Pseudomonas Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Acetobacter ascendens Codons:

Unique Acetobacter ascendens Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Mycoplasma capricolum Codons:

Unique Mycoplasma capricolum Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Pasteurella canis Codons:

Unique Pasteurella canis Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Shewanella aestuarii Codons:

Unique Shewanella aestuarii Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Pasteurella dagmatis Codons:

Unique Pasteurella dagmatis Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Staphylococcus equorum Codons:

Unique Staphylococcus equorum Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Xylanimonas cellulosilytica Codons:

Unique Xylanimonas cellulosilytica Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Staphylococcus hominis Codons:

Unique Staphylococcus hominis Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Candidatus Hepatoplasma crinochetorum Codons:

Unique Candidatus Hepatoplasma crinochetorum Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Pseudomonas allokribbensis Codons:

Unique Pseudomonas allokribbensis Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Staphylococcus auricularis Codons:

Unique Staphylococcus auricularis Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Pseudomonas alvandae Codons:

Unique Pseudomonas alvandae Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Staphylococcus felis Codons:

Unique Staphylococcus felis Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Isoptericola variabilis Codons:

Unique Isoptericola variabilis Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Rathayibacter tritici Codons:

Unique Rathayibacter tritici Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Mannheimia haemolytica Codons:

Unique Mannheimia haemolytica Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Staphylococcus caprae Codons:

Unique Staphylococcus caprae Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Staphylococcus agnetis Codons:

Unique Staphylococcus agnetis Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Mannheimia varigena Codons:

Unique Mannheimia varigena Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Pseudomonas anuradhapurensis Codons:

Unique Pseudomonas anuradhapurensis Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Psychrobacter arcticus Codons:

Unique Psychrobacter arcticus Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Rathayibacter rathayi Codons:

Unique Rathayibacter rathayi Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Staphylococcus argenteus Codons:

Unique Staphylococcus argenteus Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Cellulosimicrobium cellulans Codons:

Unique Cellulosimicrobium cellulans Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Psychrobacter arcticus_2 Codons:

Unique Psychrobacter arcticus_2 Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Alteracholeplasma palmae Codons:

Unique Alteracholeplasma palmae Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Staphylococcus epidermidis Codons:

Unique Staphylococcus epidermidis Amino acids:
ADEFGHIKLNPQRTYZCMSVW

Unique Rathayibacter iranicus Codons:

Unique Rathayibacter iranicus Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Pseudomonas azerbaijanoriens Codons:

Unique Pseudomonas azerbaijanoriens Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Isoptericola dokdonensis Codons:

Unique Isoptericola dokdonensis Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Pseudomonas alkylphenolica Codons:

Unique Pseudomonas alkylphenolica Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Pseudomonas atacamensis Codons:

Unique Pseudomonas atacamensis Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Acholeplasma hippikon Codons:

Unique Acholeplasma hippikon Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Xylanimonas allomyrinae Codons:

Unique Xylanimonas allomyrinae Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Histophilus somni Codons:

Unique Histophilus somni Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Staphylococcus condimenti Codons:

Unique Staphylococcus condimenti Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Pseudomonas asgharzadehiana Codons:

Unique Pseudomonas asgharzadehiana Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Shewanella algae Codons:

Unique Shewanella algae Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Pasteurella atlantica Codons:

Unique Pasteurella atlantica Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Unique Pseudomonas alcaligenes Codons:

Unique Pseudomonas alcaligenes Amino acids:
ACDEFGHIKLMNPQRSTVWYZ

Monday, November 14, 2022

Quantum Biology - 16

A matter of size

In the previous post of this series I questioned how it is that the tininess of atoms (see video below), compared to "rock art atom counts" would allow anyone to believe that just a few atoms could "think".

Also, in the previous post of this series I pointed out that:

"... 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."

(Quantum Biology - 15). Can a million atoms "think", even if less than a hundred can't "think", is where this post is going, because of the many hypotheses which boil down to "everything is in fact a matter of size".

Now, I have done the same thing with Coronaviridae database rows so as to compare their RNA codons to the Toxoplasma gondii mRNA codons.

Here are the results:

The coronaviridae types in my SQL database were "alpha", "beta", "delta", "gamma", "mers", and "sars" types, as follows:

mysql> select count(*) from corona;
+----------+
| count(*) |
+----------+
|    13788 |
+----------+
1 row in set (0.02 sec)

mysql> select count(*) from corona where type = 'alpha';
+----------+
| count(*) |
+----------+
|     1278 |
+----------+
1 row in set (0.00 sec)

mysql> select count(*) from corona where type = 'beta';
+----------+
| count(*) |
+----------+
|      100 |
+----------+
1 row in set (0.00 sec)

mysql> select count(*) from corona where type = 'delta';
+----------+
| count(*) |
+----------+
|      203 |
+----------+
1 row in set (0.01 sec)

mysql> select count(*) from corona where type = 'gamma';
+----------+
| count(*) |
+----------+
|      514 |
+----------+
1 row in set (0.01 sec)

mysql> select count(*) from corona where type = 'mers';
+----------+
| count(*) |
+----------+
|      611 |
+----------+
1 row in set (0.01 sec)

mysql> select count(*) from corona where type = 'sars';
+----------+
| count(*) |
+----------+
|    11082 |
+----------+
1 row in set (0.01 sec)

What this shows, again as in the previous post, is that the unique codon components of any corona virus, toxoplasma gondii, and homo sapiens genomes is fundamentally the same.

Any difference is in quantity of codons, not type of codons.

The same goes for the atoms that make up the codons in those genomes (see e.g. 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).

Thus, the same can be said again:

"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."

(ibid, Quantum Biology - 15, at section "V. Analysis"). The first video below explains how this mystery involves a small number of types of atoms, and that the most-honest we can be with our words is "we don't know":

Dr. Paul Falkowski

(From the transcript, emphasis added). Atoms are not alive, so how a group of atoms can decide anything (as many science writers are wont to say they can) is a love affair with imaginary dolls:

It is not that complicated: