Monday, July 25, 2022

Quantum Biology - 11

Fig. 1 Close up of a cell's brain?

I. Preference Appendices

I read two doll-oriented papers recently; one from western civilization scientists (Germany & Russia), the other from near-eastern civilization scientists (India).

The papers reveal how cultural/religious beliefs impact scientific research. 

The western civilization versions focus on anthropomorphic selections in the brains of microbes (cells with DNA/RNA):

"Translational pressure means preference towards codons [prefer: "to like, choose, or want one thing rather than another" (dictionary)] that are most suitable for translation in a given context ... a growing body of evidence suggests that [Translational pressure] is not the main driver of synonymous codon preference. [IOW 'preference' means that a single cell prefers some codons more than other codons]" (p.1)

"A predominant factor ... is believed ... Additional factors ... might contribute ... could also be produced by ... however, the extent of such ... is still a matter of controversy ... speculated to ... no proof has been presented ... remains to be proven" [yet ...] "The concept of synonymous and non-synonymous genetic variation is central to evolutionary studies." (p. 7)

(Causes and Implications of Codon Usage Bias in RNA, emphasis added). This honesty ("no proof ... remains to be proven") seems clumsy, as far as I am concerned.

It seems to me that it is more scientific to know the 'what' and the 'where' before stumbling over the 'why' when one considers DNA/RNA dynamics.

Mentioning the 'why' in scientific papers, especially when 'the why' is unknown, is a bit clumsy and it detracts from the honesty.

The 'what', the Codons and the viruses listed in that paper, are discussed in today's appendices (Appendix_01, Appendix_02, Appendix_03, Appendix_04, Appendix_05, Appendix_06, Appendix_07, Appendix_08, Appendix_09, Appendix_codons, Appendix_combo_counts, Appendix_CUB_counts). 

The "01 - 09" appendices detail the Codon positions within 54 viruses specified in the paper (each virus genome is linked to; click on the link for GenBank virus information).

The "Appendix_codons" appendix is a list of the Codons in the DNA Codon and RNA Codon Tables along with the counts of atoms in the nucleotides of each Codon.

Notice the difference between the two (emphasized by bold), in terms of atomic weight and the impact that could have on the Löwdin hypothesis (The Doll As Metaphor - 4). 

I tried to point this out to "the powers that be" (It's In The GenBank - 4).

The "Appendix_combo_counts" details the Codon counts (by family) of the 54 viruses discussed in the paper.

The "Appendix_CUB_counts" details the number of codons in each of the 54 viruses, from most to least contained in the virus (links to each virus included).

II. Western Cells Have Brains?

This is especially so when one is on the edge of saying that a cell can contemplate which codon out of the 64 available is a better choice than the other 63, and therefore that cell somehow prefers (i.e. "to like, choose, or want one thing rather than another") the chosen one.

One of the appendices in today's post includes a list of those 64 codons, the atoms which each nucleotide (molecule) in each codon is made of, and a "Total Atoms" column listing all of the atoms in the three nucleotides (molecules) of that codon:

"Atomic Composition of Codons

Codon Atoms 1 Atoms 2 Atoms 3 Total Atoms
GCT C5H5N5O1 C4H5N3O1 C5H6N2O2 C14H16N10O4
GCC C5H5N5O1 C4H5N3O1 C4H5N3O1 C13H15N11O3


(List of Codon Atoms, sample). The "Atoms 1" applies to the first nucleotide in the Codon, the "Atoms 2" applies to the second nucleotide in the Codon, and "Atoms 3" applies to the third nucleotide in the Codon (they are the quanta of the the codon's three molecules).

The "Total Atoms" column is the total of, for example, the 'C' (carbon), 'H' (hydrogen), 'N' (nitrogen), and 'O' (oxygen) atoms in that Codon.

I am pointing out that what the CUB club scientists are really talking about "deep down", is a myth, i.e a myth that a cell makes a choice as to the molecules/atoms that make-up that Codon (The Doll As Metaphor - 3).

III. Near-Eastern Cells Have Magic?

The paper from India is an another, but more extreme, example of animism usage in science:

"In the Indian-origin religions, namely Hinduism, Buddhism, Jainism, and Sikhism, the animistic aspects of nature worship ... are part of the core belief system."

(Wikipedia, Animism). What is a bit strange about this, for one thing, is that they nevertheless are full-on chemical genetic engineering aficionados (e.g. GMO):

"Today, Genetic Engineering is one of the top career choices made by students in engineering courses.

What is Genetic Engineering?

Genetic Engineering is also referred as genetic modification. It is a process of manually adding new DNA to a living organism through artificial methods." 

(Sarvgyan, emphasis added). Note that "The headquarters of Ananda Marga Gurukula (an unincorporated international Neohumanist university in the making) is located at Ananda Nagar in the Purulia District of West Bengal, India" (AMGK; cf. Wikipedia: Prabhat Ranjan Sarkar).

I pointed out some of this conundrum ("why artificial-ize the gods?") in a previous post:

"Examples of Intelligence ... For a remarkably long time, the atoms keep some ‘memory’ of their previous quantum mechanical origin ... These, what are called ‘intelligent molecules’ ... Some mysterious traveler is hiding in the background ... Viruses can choose their victims ... a virus cooperates ... How could the trees think of this practical solution and implement it? ... Plants may have intelligence, but are they also able to learn? ... Remarkably, the plants remembered their training ... How do plants transmit their intelligence, learn and remember, since they don’t have brains and a neural system? ... Cooperation is a widely spread phenomenon ... To go with the flow may be a sign of intelligence, but the conscious choice to sometimes cheat and sometimes cooperate hints at intelligence... we know by research, that both human beings and insects have brains and are smart"

(The Doll As Metaphor - 5, quoting from "Evolving Intelligence").

Thus, the characterization of "cells intelligently choosing their Codons" (like humans choosing their favorite liver, heart, lungs, etc.) is but one illogical deduction from the word salad rhetoric in the India paper (Codon usage bias).

Is nothing sacred?

IV. Back To Non-Teleological, Non-Anthropomorphic Science

Can you see that I see a drift in molecular biology from "just the facts ma'am" to "playing with dolls",  i.e. using play pretend on inanimate objects that become like "selfish genes" (what next "my lawnmower is so selfish"?).

There are even scientists now in word battles where both use teleological, anthropomorphic ideology to try to cancel each other out (see e.g. The Unselfish Gene vs The Selfish Gene).

Hopefully, soon their dolls will soon have no stuffing in them.

But I digress.

The issue of "codon usage bias" (CUB) was discussed in a recent series (Junk DNA R Us, 2, 3, 4).

Today, let's take a look at CUB from the perspective of atoms while remembering that a codon is:

"A sequence of three consecutive nucleotides in a DNA or RNA molecule that codes for a specific amino acid." 

(Codon Definition). The codons are made of nucleotides, and those nucleotides are  ... drum roll ... molecules ... and those molecules are made up of ... drum roll .... inanimate objects we call atoms.

V. Closing Comments

That is what quantum science is about, that is what quantum biology is about (Quantum Biology, 2, 3, 4, 5, 6, 7, 8, 9, 10).

The nucleotide's atoms are not alive, the molecules of the Codon are not alive, the Codons are not alive, and the DNA is not alive.

They are quantum mechanical machines (The New Paradigm: The Physical Universe Is Mostly Machine - 2).

IMO, it is about time for virologists and microbiologists to develop and use a realistic nomenclature and stop playing with dolls:

My interpretation of that statement is that Dr. Penrose thinks that evolutionary biologists utilize too much teleological language, and other observers agree with Penrose:

Since at least the 17th century (and mostly because of Newton), natural scientists have stopped using formal or final causes to explain natural phenomena ... except in biology. This was first pointed out by Colin Pittendrigh (Pittendrigh, C. S. Behavior and Evolution) (ed. by A. Rose and G. G. Simpson), Yale University Press, 1958), who coined the term "teleonomy" to refer to the kind of teleological phenomena observed in biological processes.
(Teleological Explanations in Biology, emphasis added). The piece "Teleological Notions in Biology" adds further insight.

This teleological factor lingers in the literature even after many years have passed since "the modern synthesis":
The modern evolutionary synthesis is a 20th-century union of ideas from several biological specialties which provides a widely accepted account of evolution. It is also referred to as the new synthesis, the modern synthesis, the evolutionary synthesis, millennium synthesis and the neo-Darwinian synthesis.

The synthesis, produced between 1936 and 1947, reflects the consensus about how evolution proceeds. The previous development of population genetics, between 1918 and 1932, was a stimulus, as it showed that Mendelian genetics was consistent with natural selection and gradual evolution. The synthesis is still, to a large extent, the current paradigm in evolutionary biology.

The modern synthesis solved difficulties and confusions caused by the specialisation and poor communication between biologists in the early years of the 20th century.
(Wikipedia, emphasis added). That has led me to zero in on 1) teleology, 2) the modern synthesis, and 3) the issue of the impact of quantum mechanical concepts on evolutionary biology.

(On The Origin of Genieology - 2; cf. Quantum Biology - 7).

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


  1. What could go wrong ... "A chess-playing robot broke its seven-year-old opponent's finger" (Link)

  2. Just about everything could go wrong: "A number of studies over the past decade have revealed that genetically engineered foods can pose serious risks to farmers, human health, domesticated animals, wildlife and the environment. Despite these long-term and wide-ranging risks, Congress has yet to pass a single law intended to manage them responsibly. The haphazard and negligent agency regulation of biotechnology has been a disaster for consumers and the environment. Unsuspecting consumers by the tens of millions are purchasing and consuming unlabeled GE foods, despite a finding by U.S. Food & Drug Administration scientists that these foods could pose serious risks." (Center For Food Safety)