Saturday, July 11, 2015

Hypothesis: Toxins of Power Originate in Molecular Machines - 2

Universe of molecular machines
I. Introduction

A recent post at Dredd Blog points out that the physical universe, including the human brain and body, is composed substantially of molecular machines (The New Paradigm: The Physical Universe Is Mostly Machine - 3).

That post draws from, among other things, two books mentioned in the New York Review of Books, and a long list of Dredd Blog posts on the subject of molecular machines going back to 2009 (The New Paradigm: The Physical Universe Is Mostly Machine).

Those two books are: "Life’s Engines: How Microbes Made Earth Habitable", and "A New History of Life: The Radical New Discoveries About the Origins and Evolution of Life on Earth."

II. The Revolutionary Context

In a previous Dredd Blog post, the latter book had been discussed a bit, even featuring a video of the author, at a book signing in Seattle.

There, Dr. Peter Ward talked about the book contents, which indicated that the book was revolutionary (Weekend Rebel Science Excursion - 42).

The first chapter of the first book I mentioned, the other book in the review, Life’s Engines, discusses how scientists missed the full picture of evolution:
The concept of genes and the basis of the physical inheritance of traits were totally unknown to Darwin, or anyone else at the time. [p. 19]
The concept of origin, as in the origin of life, was in the back of Darwin’s mind but not explicitly discussed in the book. [p. 20]
Even if Darwin had observed fossil microbes, he would almost certainly not have understood what their relationship to plants or animals was. Darwin, and virtually every other scientist in the nineteenth century, would have been profoundly surprised to learn that plants and animals had all descended from microbes over a period of time that was completely unimaginable in the nineteenth century ... [p. 21]
(Life’s Engines, Chapter 1, cf. Princeton University Press). The book also takes a revolutionary look at microbes, in terms of their part in evolutionary unfolding.

It pointis out how the establishment's scientific and religious communities at large missed the big little picture by not considering microbial life as the first order of inquiry:
In sum, the oversight of microbes, in both the literal and figurative senses, distorted our worldview of evolution for more than a century, and including microbes in our understanding of evolution is still a work in progress. [p. 12]
Microbes were missed because of our observational biases. They had been on this planet for billions of years before the first animal arose. Let’s meet the missing microbes and see how they played an outsized role in making this planet function. Without microbes, we would not be here. [p. 22]
(Life’s Engines, Chap. 1). Thus, the book points out, the two major sources for the science (Darwin) and faith (Bible) of origins had not discussed microbes (in fact Darwin was not even aware of either microbes or genes).

I don't want to be a spoiler, but I will address your attention to the second half of the title of the book "How Microbes Made Earth Habitable."

That indicates a revolution in scientific hypotheses and theories.

III. Ok, So What About The Molecular Machines?

The title of the New York Book Review piece, mentioned in Section I above, sets the molecular machine stage: "How You Consist of Trillions of Tiny Machines."

A concept that has been discussed on Toxins of Power blog for years:
Dr Clarke said: “There are a lot of fundamental questions about the origins of life and many people think they are questions about biology. But for life to have evolved, you have to have a moment when non-living things become livingeverything up to that point is chemistry.”
“Our cells, and the cells of all organisms, are composed of molecular machines. These machines are built of component parts, each of which contributes a partial function or structural element to the machine. How such sophisticated, multi-component machines could evolve has been somewhat mysterious, and highly controversial.” Professor Lithgow said.
Many cellular processes are carried out by molecular ‘machines’ — assemblies of multiple differentiated proteins that physically interact to execute biological functions ... Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.
The most complex molecular machines are found within cells.
Writing in the journal PLoS Pathogens, the team from Queen Mary's School of Biological and Chemical Sciences show how they studied the molecular machine known as the 'type II bacterial secretion system', which is responsible for delivering potent toxins from bacteria such as enterotoxigenic E. coli and Vibrio cholerae into an infected individual.

Professor Richard Pickersgill, who led the research, said: "Bacterial secretion systems deliver disease causing toxins into host tissue. If we can understand how these machines work, then we can work out how it they might be stopped."
(Do Molecular Machines Deliver Toxins of Power?). That there are molecular machines in organisms has been carried forward, on this blog, to also consider whether viruses may also have molecular machine components:
When is a life form not a life form? When it's a virus.

Viruses are strange things that straddle the fence between living and non-living. On the one hand, if they're floating around in the air or sitting on a doorknob, they're inert. They're about as alive as a rock. But if they come into contact with a suitable plant, animal or bacterial cell, they spring into action. They infect and take over the cell like pirates hijacking a ship.
Viruses are a curious lot. The standard drawing of the tree of life, the one you find on the inside back cover of biology textbooks, is divided into three branches: Archaea, Bacteria and Eukarya. Viruses don’t make it onto the page.

That makes sense, some scientists argue, because they’re not alive. They can’t reproduce on their own; they require the cozy environment of living cells for their survival. Others disagree. Not only are viruses alive, they say, but genetic evidence indicates that they may have been the first forms of life on Earth, predating cellular life.
The processes responsible for the evolution of key innovations, whereby lineages acquire qualitatively new functions that expand their ecological opportunities, remain poorly understood. We examined how a virus, bacteriophage λ, evolved to infect its host, Escherichia coli, through a novel pathway. Natural selection promoted the fixation of mutations in the virus’s host-recognition protein, J, that improved fitness on the original receptor, LamB, and set the stage for other mutations that allowed infection through a new receptor, OmpF. These viral mutations arose after the host evolved reduced expression of LamB, whereas certain other host mutations prevented the phage from evolving the new function. This study shows the complex interplay between genomic processes and ecological conditions that favor the emergence of evolutionary innovations.
If not for a virus, none of us would ever be born.

In 2000, a team of Boston scientists discovered a peculiar gene in the human genome. It encoded a protein made only by cells in the placenta. They called it syncytin.
What made syncytin peculiar was that it was not a human gene. It bore all the hallmarks of a gene from a virus.

Viruses have insinuated themselves into the genome of our ancestors for hundreds of millions of years.
It turned out that syncytin was not unique to humans. Chimpanzees had the same virus gene at the same spot in their genome. So did gorillas. So did monkeys. What’s more, the gene was strikingly similar from one species to the next.
(Are Toxins of Power Machines or Organisms?). We are getting closer all the time, but, we must consider how molecular machines make, and then deliver, toxins of power.

IV. What About The Toxins of Power In Molecular Machines?

There is one ironclad and well known phenomenon deep down in any molecular machine, or any molecule for that matter, which can deliver what we can call a potential toxin of power:
"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. 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."
(Stem Cell Malfunction A Quantum Toxin Source?, quoting the journal: Reviews Of Modern Physics, Vol. 35, No. 3, by Per-Olov Lowden, 1963). That is a purely abiotic dynamic, in terms of the core physics (cf. The Uncertain Gene).

Proton tunnelling can happen to any atom or molecule that is part of an utterly lifeless rock on planets, a steel beam in a skyscraper, a virus, a microbe, or other biological entities.

V. A Curious Example

Let's look at the corruption of a powerful group, which is ostensibly the most aware and knowledgeable group concerning human cognition.

They are the mind doctors.

Yet, it is coming to light that:
The largest association of psychologists in the United States is on the brink of a crisis, the Guardian has learned, after an independent review revealed that medical professionals lied and covered up their extensive involvement in post-9/11 torture. The revelation, puncturing years of denials, has already led to at least one leadership firing and creates the potential for loss of licenses and even prosecutions.

For more than a decade, the American Psychological Association (APA) has maintained that a strict code of ethics prohibits its more than 130,000 members to aid in the torture of detainees while simultaneously permitting involvement in military and intelligence interrogations. The group has rejected media reporting on psychologists’ complicity in torture; suppressed internal dissent from anti-torture doctors; cleared members of wrongdoing; and portrayed itself as a consistent ally against abuse.

Now, a voluminous independent review conducted by a former assistant US attorney, David Hoffman, undermines the APA’s denials in full – and vindicates the dissenters.
(Guardian: Psychologists and ‘Enhanced’ Interrogation; Full report: PDF). Some of the minds in the group became corrupted by toxins of power.

That infection then spread through the organization's governors under the meme complex dynamics which groups tend to foster (A Structure RE: Corruption of Memes - 3).

VI. Conclusion

This post is getting way to long for a single post, so I will close now and continue this series another day.

The next post in this series will consider the advent of wireless communication, propaganda, and other signalling.

That is, communication of various sorts as both a source of toxins of power, and as a remedial dimension for neutralizing toxins of power (a teaser is here).

For those readers who want to follow the overall evolutionary hypotheses about how the molecular machines evolved, consider (On the Origin of the Genes of Viruses, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13; The Uncertain Gene, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11).

The previous post in this series is here.