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.

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