Wednesday, February 9, 2022

The Doll As Metaphor - 3

Fig. 1 Close up of a virus brain

The word 'accept' may be used when there is only one item offered to us, however, when there is a list of items we have to 'select' or 'choose' an item from two or more 'choices'.

This is a simple reality of language: 

"Definition of 'select'... If you select something, you choose it from a number of things ..." (Collins)

"Definition of 'select' ... chosen from a number or group ..." (Meriam-Webster)

This can be quite a chore in some instances: 

"Many times in life, we are forced to choose between two or more options. It's not easy to make a decision, because everything you choose imprints on your life. It's easy to be overwhelmed in the moment and make a choice you regret."

(How To Choose Wisely). That applies to human beings with vastly more capable brains and cognitive skills than viruses with no brain or similar cognitive skills.

Nevertheless some virologists, in playing with dolls mode (like children talking about their dolls), suggest to us that the virus has such selection skills.

Moving on, let's consider RNA examples from GenBank that were used in the following research paper, because the GenBank is where Dredd Blog examples are also selected:

"Complete genome sequences of the viruses from the Coronaviridae family were obtained from the GenBank database of the National Center for Biotechnology Information (NCBI, USA) ... A virus optimizes its codon usage to fit the host environment on which it savors ... the role and the extent of ... natural selection towards the codon usage pattern ... Each gene in the Coronaviridae family plays an essential role ... in determining its choice"

(Natural Selection ... the Coronaviridae Family, emphasis added). Here the 'family' which the SARS-CoV-2 virus is a member of is described as intelligent enough to 'savor' and 'optimize' usage of parts of its genome to decide by selecting for itself how to evolve (this kind of language has been discussed here and here).

Why are they confident of this? ... :

"Why are we confident of that? We're confident of that because we have a kind of metaphysical belief that there are laws of nature that are outside time and those laws of nature are causing the outcome of the experiment to be what it is. And laws of nature don't change in time. They're outside of time. They act on the system now, they acted on the system in the same way in the past, they will act the same way in a year or a million or a billion years, and so they'll give the same outcome. So nature will repeat itself and experiments will be repeatable because there are timeless laws of nature.

But that's a really weird idea [for scientists] if you think about it because it involves the kind of mystical and metaphysical notion of something that is not physical, something that is not part of the state of the world, something that is not changeable, acting from outside the system to cause things to happen. And, when I think about it, that is kind of a remnant of religion. It is a remnant of the idea that God is outside the system acting on it."

(If Cosmology Is "Off," How Can Biology Be "On?"). In contrast, other virologists state clearly that:

"An excellent place to ponder the realm of virus changes is the Virology Blog, where the question "are viruses living" is addressed:

'Viruses are not living things. Viruses are complicated assemblies of molecules, including proteins, nucleic acids, lipids, and carbohydrates, but on their own they can do nothing until they enter a living cell. Without cells, viruses would not be able to multiply. Therefore, viruses are not living things.'

(Are Viruses Living?, emphasis added). Viruses, then, are abiotic rather than being biotic (see e.g. The New Paradigm: The Physical Universe Is Mostly Machine, 2, 3; A Microbe's Machine Kills Intruders)."

(Omicron (OMC!) - 2). Viruses are replicated in their microbe hosts, which said microbe hosts are located within meta-hosts, i.e. humans/animals.

But ... but ... Dredd ... mutations!!!!:

"Viruses adapt to their hosts by evading defense mechanisms and taking over cellular metabolism for their own benefit. Alterations in cell metabolism as well as side-effects of antiviral responses contribute to symptoms development and virulence. Sometimes, a virus may spill over from its usual host species into a novel one, where usually will fail to successfully infect and further transmit to new host. However, in some cases, the virus transmits and persists after fixing beneficial mutations that allow for a better exploitation of the new host. This situation would represent a case for a new emerging virus ... A major difference is that genes involved in stress and pathogen response are not activated upon infection with the evolved virus, suggesting that selection has favored viral strategies to escape from host defenses."

(SARS-CoV-2 ... mutations, emphasis added). Yes, but considering actual mutations of genes necessitates including data from some of the hard sciences; data which mandate consideration of the actual 'brain' (see Fig. 1) behind such 'mutations':

"The analysis of the original proton wave packet involves an interesting phase problem, and, since the energy distribution is temperature dependent, the whole phenomenon is also temperature dependent."
"The tunneling times will depend essentially on the height and the form of the barrier. In DNA, the form of the double-well potentials regulating the hydrogen bonds depend not only on the base pair involved but also on neighboring pairs, their net charges, and the entire electric environment. The tunneling time is hence not only characteristic for a certain biological specimen but is also a function of the position in the DNA molecule involved. The tunneling time is very likely also temperature dependent, even if the protons are well shielded in the double helix. The main problem is whether the tunneling time is very short in comparison to the replication time, or whether there exist organisms where the penetration of the barrier is slow in comparison to the replication."
"It should always be remembered that, in Born's interpretation of quantum mechanics, the quantity |¥|² represents the probability density for finding the proton in a specific position. The tunneling of the wave packet is hence a time-dependent process which is going to influence the properties of the genetic code."
"In this connection, it should be observed that the tunneling probabilities depend not only on the base pair involved but also on the electrostatic environment, the neighboring base pairs, etc., which may explain the occurrence of "hot spots."
At a DNA replication, the protons have to "choose sides," and the proton code immediately after a DNA replication represents actually a nonstationary state from the quantum-mechanical point of view. The time evolution of the system and particularly the penetration of the potential barrier in the double-well potential represents a loss of the genetic code which should perhaps be considered as the primary cause of aging.

Proton Tunnelling induced mutation

The aging is thus a process which goes on continuously in the DNA molecule but gets "manifested" at the replications.


Proton tunneling may finally be of importance in connection with the occurrence of spontaneous tumors.

The growth of an individual is a highly refined balance between factors which enhance the cell duplication and other factors which limit this duplication so that the organism takes a specific shape. The entire process is stimulated and controlled by various enzymes, and there is a feedback from the environment about which we know, at present, very little. If there is a somatic mutation, i.e., a change of the genetic code in a DNA molecule in the body of an organism, the change may influence the protein synthesis and the balance between the enhancing and controlling enzyme actions in the growth cycle. Actually, the new genetic code may lead to the development of a "new individual" within the individual, i.e., a tumor."
"In this paper we have pointed out that, since the protons are not classical particles but "wave packets" obeying the laws of modern quantum theory, the genetic code cannot --in spite of all precautions-- be 100% stable. Due to the quantum-mechanical "tunnel effect," there is always a small but finite probability that the protons will change place, alter the genetic code, and give rise to mutations. This implies also that this transfer of protons over a distance of about 10-8 cm may be one of the driving forces in the evolution of living organisms on the earth."

(The Uncertain Gene, quoting "Proton Tunneling in DNA and its Biological Implications", by Per-Olov Löwdin; Journal: Review of Modern Physics, Vol 35, No. 3). Yikes, this could ruin the opportunity to learn How To Enjoy The End Of Bad Choices (/snark).

Seriously, it behooves researchers to closely examine the microbes that replicate the SARS-CoV-2 viruses (they haven't yet specified exactly which microbes those are).

So, I have searched hundreds of thousands of the genomes in the gut microbiomes of the "mass-production-of-animals-for-food-industry" cattle and swine stored in GenBank (see the Appendices to The Doll As Metaphor, 2).

It is incredible how many SARS-CoV-2 gene segments are found in the genomes of those microbes in those animals (many such segments existed prior to the discovery of SARS-CoV-2 in December of 2019).

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

A friendly virus reports back to us about what it is like to enter into a vastly larger single-celled host [in doll magic language: "to take control over its highly complex machines"] (The New Paradigm: The Physical Universe Is Mostly Machine).

1 comment:

  1. Congressman on the way to see the Wizzard of Odds about viruses (link)