Friday, September 27, 2013

The Uncertain Gene - 2

The Red-Rectangle Nebula
It is Friday so we are going to talk some science, even though the title does not contain the phrase "Weekend Rebel Science" as it often does.

In this series we are focusing on one area of the general history of the theory of evolution in its current dogmatic format, following "the synthesis" (Modern Evolutionary Synthesis).

That "one area" is the area where one of our most celebrated "hard sciences", Physics, intersects and impacts upon the theories of the evolutionary biological sciences.

The specific area of inquiry and intersection we focus on in this series is quantum mechanics.

The specific phenomenon within quantum mechanics which we are looking at is quantum tunneling.

The first post demonstrated an undisputed phenomenon, the dynamics of proton tunneling, together with its impact on DNA replication and/or mutation.

Yes, DNA replication in the context of proton tunneling's very real potential for initiating genetic mutation (The Uncertain Gene).

Around the Dredd Blog System, over the years, we have generally considered this subject matter area primarily to come under the heading of abiotic evolution:
The Earth is said to have formed "around 4.54 billion ... years ago" (History of Earth).

Therefore The Big Bang happened about 9.21 billion years before the Earth formed (13.75 - 4.54 = 9.21).

Biological organisms formed on the Earth about a billion years later, which would be ~10.21 billion years after The Big Bang.

Humans, e.g. homo sapiens,  are said to have evolved about 200,000 years ago, which would be ~13.7498 billion years after The Big Bang (13.7498 + 00.0002 = 13.75 billion years). Homo sapien evolution is a very tiny 0.0002 billion years of the 13.75 billion year story.

The abiotic epoch which preceded the biotic epoch involved a vast amount of "time" as we know it, populating vast areas of space with the atoms that make up chemicals, the subject of the scientific discipline Chemistry ...
(Putting A Face On Machine Mutation - 3, cf. Did Abiotic Intelligence Precede Biotic Intelligence?). In terms of time, the major portion of evolution, then, is abiotic evolution.

The modern human evolution portion of that time-line is: .2m / 13.75bn = 0.000014545, or  0.0015% (i.e. way, way less than 1%) of the time involved in the complete evolutionary time-line since the Big Bang.

Total biotic evolution is: 3.54 / 13.75 = .257, or ~26% of the total evolutionary time-line since the Big Bang.

Microbial evolution takes up about 3 billion years (~85%) of that total 3.54 billion year time-line of biotic evolution on Earth.

Thus, the minor portion of the evolutionary time-line is biotic evolution, (i.e. the events following the advent of carbon atoms, as well as the subsequent advent of carbon based life forms) while by far the major portion of the evolutionary time-line is abiotic evolution.

With that in mind, in the first post I indicated that:
In the next episode of this series, then, we will zoom in on the book "Quantum Aspects of Life", a scientific textbook, to further explore the impact of The Uncertain Gene on the evolution of carbon based life ("us").
(The Uncertain Gene). That book, Quantum Aspects of Life, offers several monumental efforts to bridge the great mysterious gap (where the things we do not know about "life" or how it first formed) stand out:
When the remarkable book What is Life? was published in 1944, written by the great quantum physicist Erwin Schrödinger and based on lectures that he had given at Trinity College Dublin in February 1943, it had a very considerable influence on several key figures in the development of molecular biology.
One of the basic questions that Schrödinger raised was whether the ideas of classical physics, as normally employed by biologists in their understanding of the behaviour of the physical world, can be sufficient for explaining the basic features of life.
[Schrödinger] pointed out that a key feature of the Darwinian/Mendelian nature of inheritance is its basis in discreteness, which could only be explained through a quantum discreteness and stability, in the basic carriers of genetic information. He argued that these carriers had to be molecules of some nature—the molecules that we now know as DNA.
Schrödinger argues [that] it is certainly possible that new physical ingredients, going beyond those of 20th century physics, might be needed for a full understanding of the physical underpinnings of life. There are probably not many biologists today who would argue for the necessity of such new physical ingredients in order to explain life.
The possible physical need for going beyond this framework had already been raised by Schrödinger himself some eight years before his Dublin lectures, when he introduced his famous “cat paradox”. Although he did not refer to this paradox explicitly in What is Life? (presumably because he had no desire to confuse his lay audience by introducing such unsettling issues into his descriptions of quantum mechanics), this unsatisfactory state of affairs in the foundations of quantum theory no doubt led him to be sceptical of the current dogma that the rules of quantum mechanics must hold true at all levels of physical description. (It may be pointed out that three others of the key figures in the development of quantum mechanics, namely Einstein, de Broglie, and Dirac, have also expressed the opinion that existing quantum mechanics must be a provisional theory.) There is, indeed, a distinct possibility that the broadening of our picture of physical reality that may well be demanded by these considerations is something that will play a central role in any successful theory of the physics underlying the phenomenon of consciousness.
These deep matters are still subject to much controversy, and the present volume provides a multitude of closely argued opinions on the issues that Schrödinger raised concerning the relation of biology to quantum physics.
Does life in some way make use of the potentiality for vast quantum superpositions, as would be required for serious quantum computation? How important are the quantum aspects of DNA molecules?
It would be too optimistic to expect to find definitive answers to all these questions, at our present state of knowledge ...
(Quantum Aspects of Life, "Foreward by Roger Penrose", p. vii-ix, emphasis added). I am reminded of the recent Dredd Blog post quote where a noted physicist became as candid as Dr. Penrose can be:
This is said to be the golden age of cosmology and it is from an observational point of view, but from a theoretical point of view it's almost a disaster. It's crazy the kind of ideas that we find ourselves thinking about.
(If Cosmology Is "Off," How Can Biology Be "On?"). Let's take a look, then, at how important Dr. Penrose's statement was when he wrote that there "are probably not many biologists today who would argue for the necessity of such new physical ingredients in order to explain life."

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.

Let me do so by first referring to a section contained in the first post of this series:
Today, then, we offer you a much more recent paper (6/7/13) which focuses on, and details, that same phenomenon a bit more:
By treating the proton as a quantum ”wave packet” it becomes possible to model the hydrogen bond as a quantum body problem. Due to quantum tunneling, however, there is a small but finite probability that the protons will change place within the hydrogen bond, altering the genetic code, and giving rise to mutations.
(Quantum Tunneling in DNA, by Megan Wolfe). That "small but finite probability" gets much more probable by happening millions of repetitions per short amount of time (like a second or a minute) in the trillions of cells inside us.
(The Uncertain Gene). The author Megan Wolfe goes on to then write:
Mutations of this type have been called transitions and they are characterized by the fact that they are reversible, meaning the mutant DNA strands may continue replicating and if a transition happens again, they will revert back to their original ordering. Most often though in this type of mutation the once functioning DNA strand turns into junk DNA and so fails to pass on its
Proton tunneling into Life?
encoded information and directions, or even worse, turns into malfunctioning DNA which gives destructive information.

In the case of bases with unequal charge, one of the bases in a nucleotide pair has obtained an extra charge, changing the shape of the double well potential. The tunneling of a proton occurs only in one direction in this case. This results in transitions of the type A-T to A+ -T− or A− -T+ which does not appear in the Watson-Crick model. There is no nucleotide which can or will combine with the transitioned A+ and G+ so the genetic code is lost, deleted from the larger DNA strand. This means that this type of mutation is irreversible–once lost, the genetic information can never be recovered.
(ibid, Quantum Tunneling in DNA, pp. 7-8, emphasis added). The use of the term "junk DNA" is one of the types of things that The Modern Synthesis sought to eradicate.

Interdisciplinary as well as intra-disciplinary misunderstandings and loose language were targets, because they generate confusion rather than clarity and consistency.

The physicist Megan Wolfe, in her paper (quoted from above) shows that she has a very good handle on her specialty, Physics, yet does not adequately grasp current genetics:
In genomics and related disciplines, noncoding DNA sequences are components of an organism's DNA that do not encode protein sequences. Some noncoding DNA is transcribed into functional noncoding RNA molecules (e.g. transfer RNA, ribosomal RNA, and regulatory RNAs), while others are not transcribed or give rise to RNA transcripts of unknown function. The amount of noncoding DNA varies greatly among species. For example, over 98% of the human genome is noncoding DNA, while only about 2% of a typical bacterial genome is noncoding DNA.

Initially, a large proportion of noncoding DNA had no known biological function and was therefore sometimes referred to as "junk DNA", particularly in the lay press. Some sequences may have no biological function for the organism, such as endogenous retroviruses. However, many types of noncoding DNA sequences do have important biological functions, including the transcriptional and translational regulation of protein-coding sequences. Other noncoding sequences have likely, but as-yet undetermined, functions. (This is inferred from high levels of homology and conservation seen in sequences that do not encode proteins but, nonetheless, appear to be under heavy selective pressure.)
(Wikipedia, emphasis added). Thus, even if she is correct that proton tunneling induced mutant DNA is placed in the non-coding section, along with the other 98% of the human genome, that does not mean that RNA of various sorts will not later utilize it or that it will not be passed on to future iterations of that DNA molecule (to be covered exhaustively in next post of this series).

The mistake, in the sense that it reads like she presumes that "natural selection" would cause the mutation to somehow become extinct, gets a bit into teleology:
A teleology is any philosophical account that holds that final causes exist in nature, meaning that, analogous to purposes found in human actions, nature inherently tends toward definite ends.
Some disciplines, in particular within evolutionary biology, are still prone to use language that appears teleological when they describe natural tendencies towards certain end conditions ...
(Teleology). Now, let's reverse the scenario to show that physicists also labor under some fundamental teleological pulls at times:
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?", emphasis in original). So, let's get back to the book (Quantum Aspects of Life) to further emphasize that physicists also can get loose with their discipline, i.e. can get off into the weeds of teleology, unless they are careful:
Expressed differently, how does a quantum superposition recognize that it has “discovered” life and initiate the said collapse? There seems to be an unavoidable teleological component involved: the system somehow “selects” life from the vastly greater number of states that are nonliving ... But this implies the environment somehow favours life—that life is “built into” nature in a preordained manner. So an element of teleology remains. (p. 11) ... an element of teleology is required; namely that the molecule must somehow know before hand what it is aiming for. (p. 42) There is no teleology needed here since we describe the measurement as a two-step process ... (p. 45) ... there’s the teleological point that, hey, we search for something ... (p. 357) ... As far as the teleological aspects are concerned (p. 360) ... Teleological aspects and the fast-track to life ... there is a teleological issue here ... (p. 392)
(ibid, Quantum Aspects of Life, emphasis added). The point being made is that "natural selection" discussions by either evolutionary biologists or physicists can become fundamentally teleological unless great care and focused technical language skills are employed:
"The concept of natural selection was originally developed in the absence of a valid theory of heredity; at the time of Darwin's writing, nothing was known of modern genetics. The union of traditional Darwinian evolution with subsequent discoveries in classical and molecular genetics is termed the modern evolutionary synthesis. Natural selection remains the primary explanation for adaptive evolution."
(Natural Selection, emphasis added). What we are attempting to grasp in this series is that various scientists realize that teleological factors are at the very foundation of our current scientific understanding, because, so far the modern synthesis has not filtered it all out.

Heretofore in this series, the only "pure" dynamic we have discussed, in the sense of trying to be free from teleological influences, is genetic molecular mutation through proton tunneling.

This real impact that teleological impurity has in natural selection discussions will continue to be pointed out in future posts of the series.

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

Country sex genes explained in Teleological terms:

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