Friday, February 20, 2015

The Uncertain Gene - 11

You are Epigenetic: an overview
In the previous post of this series I said it's "probably the final post in this series".

But, Tom (who is a regular commenter here at Dredd Blog) brought up some new research concerning epigenetics (Tom's Comment).

Then, I kept thinking about the implications until it dawned on me that one aspect of the uncertain gene concept, elucidated upon in this series, is that proton tunnelling is also technically "epigenetic."

I mean that in the sense that any gene itself, in all genetic circumstances, does not "control" itself or anything else.

Thus Epigenetics, a discipline in and of itself, is a realm that studies what utilizes the genetic molecules, where those genetic molecules are utilized, when those molecules are utilized, how they are utilized, and why those molecules are utilized.

Thus, this is another case where nomenclature is paramount (Good Nomenclature: A Matter of Life and Death).

The papers that Tom alluded to concern valid epigenetic dynamics, because the nomenclature of Epigenetics covers all activity that acts upon gene molecules, including those that decide whether, for example, to turn the gene on or off:
Geneticists study the gene; however, for epigeneticists, there is no obvious 'epigene'. Nevertheless, during the past year, more than 2,500 articles, numerous scientific meetings and a new journal were devoted to the subject of epigenetics. It encompasses some of the most exciting contemporary biology and is portrayed by the popular press as a revolutionary new science — an antidote to the idea that we are hard-wired by our genes. So what is epigenetics? - (Perceptions of Epigenetics)

Much work has been published on the cis-regulatory elements that affect gene function locally, as well as on the biochemistry of the transcription factors and chromatin- and histone-modifying complexes that influence gene expression. However, surprisingly little information is available about how these components are organized within the three-dimensional space of the nucleus. Technological advances are now helping to identify the spatial relationships and interactions of genes and regulatory elements in the nucleus and are revealing an unexpectedly extensive network of communication within and between chromosomes [cf. this]. A crucial unresolved issue is the extent to which this organization affects gene function, rather than just reflecting it. - (Nuclear organization of the genome and the potential for gene regulation)

(see following link for more ...)
(Nature Insight: Epigenetics, Vol. 447, No. 7143 pp 396-440). The point is that epigenetic dynamics involve multiple levels of analysis and subsequent operations to, among other
Figure 1
things, eventually activate processes whereby the gene molecules and their analysis will eventually be handled in a customized way in the ribosome and/or ribozyme.

So, let's use the format of a layered graphic (see Figure 1 graphic to the right - click to enlarge) to assist in visualizing some of these known, and some of the yet unknown, dynamics involved.

Some of these epigenetic dynamics, as the concept relates to humans, are behavioral, including cultural behavior that impacts the individual.

IOW, the level of individual behavior is not controlled by gene molecules (see e.g. The "It's In Your Genes" Myth, 2; One Man's Junk Gene Is Another Man's Treasure Gene?, Microbial Hermeneutics - 3, On The Origin of Genieology, 2, 3).

Let's take a working example by asking: "how could these epigenetic operatives be having an impact?"

In the context of "answers" ... please notice some "puzzling" research ... that was considered in one prior Dredd Blog post:
From biology class to “C.S.I.,” we are told again and again that our genome is at the heart of our identity. Read the sequences in the chromosomes of a single cell, and learn everything about a person’s genetic information — or, as 23andme, a prominent genetic testing company, says on its Web site, “The more you know about your DNA, the more you know about yourself.”

But scientists are discovering that — to a surprising degree — we contain genetic multitudes. Not long ago, researchers had thought it was rare for the cells in a single healthy person to differ genetically in a significant way. But scientists are finding that it’s quite common for an individual to have multiple genomes. Some people, for example, have groups of cells with mutations that are not found in the rest of the body. Some have genomes that came from other people.

Medical researchers aren’t the only scientists interested in our multitudes of personal genomes. So are forensic scientists. When they attempt to identify criminals or murder victims by matching DNA, they want to avoid being misled by the variety of genomes inside a single person.

Last year, for example, forensic scientists at the Washington State Patrol Crime Laboratory Division described how a saliva sample and a sperm sample from the same suspect in a sexual assault case didn’t match.
(On The Origin of Genieology). The piece which Tom linked to, echoed the common misconception that "The human genome is the sequence of all the DNA on chromosomes. The [human] DNA is identical in every cell, from neurons to hearts to skin."

The (newly discovered) variant genetic material (whether RNA or DNA) existing within an individual, may be due to a proton tunnelling type of mutation (PTM); and/or a viral-microbial lateral gene transfer (LGT); and/or other layers or levels of epigenetic processes.

Which are symbolically depicted in Figure 1, and verbally described (at least in the abstract) in the scientific papers discussed above (Nature Insight: Epigenetics, Vol. 447, No. 7143 pp 396-440).

A lot of the lunacy that has manifested in the biological sciences, from Eugenics to The Selfish Gene myth of Dawkins, is due in whole or in part, to our scientific culture's failure to have a discipline I call "Abiology 101" (see Weekend Rebel Science Excursion - 27).

The extent of the impact of that failure is discussed in another Dredd Blog series (On the Origin of the Genes of Viruses, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12) and in previous posts of this series (The Uncertain Gene, 2, 3, 4, 5, 6, 7, 8, 9, 10).

The previous post in this series is here.

See if you can pick out some of the errors in this video, which is ~99% correct:


  1. "See if you can pick out some of the errors in this video, which is ~99% correct"

    One thing is that the video does not mention proton tunnelling which can have an impact on the gene directly.

    1. Yes.

      Not mentioned in the video also is that the epigenome project has the same ideology as the human genome project.

      False enthusiasm for drugs to fix this and that, when big pharma is actually the cause of most related problems.

      In the lead up to the human genome project there was such a load of hoopla it was embarrassing.

      In the end it was embarrassing too ... human genes were about the equivalent of a grape genome.

      Until they study abiology they will not even think of abiotic dynamics like proton tunnelling as a source of epigenetics.

  2. Perhaps you could suggest the idea to someone further up the research chain, Dredd.


    1. LOL.

      Big Pharma has access to the journals even more so than we do.

      And they have research staff.

      I discovered the phenomenon in a paper "Proton Tunneling in DNA and its Biological Implications, by Per-Olov Löwdin; Journal: Review of Modern Physics, Vol 35, No. 3, July 1963".

      I quoted it first, I think, in this post: Stem Cell Malfunction A Quantum Toxin Source?.

      That was about two years ago.

      Big Pharma has some of the epigenome of climate change deniers.

      Per-Olov Löwdin is well known for his quantum physics work that paved the way for, among other things, certain electronics.

  3. Dredd:

    In your essay, you state that epigenetics concerns the what, when, where and why, but i don't see it answering the why.

    So my question is "What's driving this?" Is it Evolution, Life, Quantum Mechanics, 'God,' or what? Is it a reaction on the atomic level to signals from the environment?

    It seems the more we find out about this stuff, the more interesting 'life' seems to be, and the more mysterious it becomes as far as "direction" or "purpose." Is it just randomness in the system that begins as exploding stars (and even before that, actually)?

    It's amazing.


    1. Tom,

      You commented: "i don't see it answering the why."

      Good observation.

      The why, in the narrowest sense, is basically the dynamics that make one gene active in one person, but not in another.

      Or makes one gene active at one time in an individual's life, but turns it off at another time.

      The simple answer is: some "epigenetic function" does that.

      In another post, I wrote the following to try to clarify epigenetic:

      "And finally, for the purposes of this post, 'epigovernment' means the layer above government that actually sets the policy and direction of government.

      Thus, epigovernment is a concept like epigenetics in the sense that epigenetics is 'above genetics,' because epi means 'above' or 'over' in this context, which is a context declaring that genes are no more controlling ... than government is ...

      Thus, epigovernment is to government what epigenetics is to genetics.
      " (Epigovernment: The New Model).

      We know that there are behind-the-scene machinations by non-government powers which manipulate and/or control government officials, but we don't know enough.

      Same with epigenetics, in that, we know epigenetic functions are there manipulating and/or controlling the application of the DNA construct, the genes, to do or not do this and that.

      But we don't know enough to say why in several senses.

      It would be much simpler if the genes just controlled everything.

      If you want more of something in an entity, add more genes.

      But, instead, there is a sort of bureaucracy level of ribosomes and ribozymes that parse the genetic material using, by one estimate, some 180,000 molecular machines to do the work of transcription.

      Go figure eh?

    2. Tom,

      You commented further:
      So my question is "What's driving this?' Is it Evolution, Life, Quantum Mechanics, 'God,' or what? Is it a reaction on the atomic level to signals from the environment?

      It seems the more we find out about this stuff, the more interesting 'life' seems to be, and the more mysterious it becomes as far as "direction" or "purpose." Is it just randomness in the system that begins as exploding stars (and even before that, actually)?
      It is so complicated that Robert Jastrow, a famous scientist, said that the principles of probability made the notion of the evolution of carbon based life, here on Earth, so improbable that he did not buy it any more.

      He concluded, then, that life came here from another place. I don't know what he finally came up with.

      For a comprehensive grasp of it abiological evolution must be factored in, because if there is no abiotic evolution there is no biological evolution either.

      When I look at it scientifically I subscribe to: The Tenets of Ecocosmology.

      Species that are well suited to being good cosmic citizens will (once they discover the nature of their Sun/Star) work together.

      To survive and thrive long enough to learn to migrate into space and settle on a habitable planet with a more stable star (e.g. a white dwarf).

      Our species does not seem to pass that Test, so we will be evaporated into abiotic quanta eventually.

    3. Tom,

      You commented further:
      So my question is "What's driving this?' Is it ... 'God,' ...

      It seems the more we find out about this stuff, the more interesting 'life' seems to be, and the more mysterious it becomes as far as "direction" or "purpose."
      Creationism comes in many flavors.

      For example, the Gnostics:

      "All religious traditions acknowledge that the world is imperfect. Where they differ is in the explanations which they offer to account for this imperfection and in what they suggest might be done about it. Gnostics have their own -- perhaps quite startling -- view of these matters: they hold that the world is flawed because it was created in a flawed manner.

      Like Buddhism, Gnosticism begins with the fundamental recognition that earthly life is filled with suffering. In order to nourish themselves, all forms of life consume each other, thereby visiting pain, fear, and death upon one another (even herbivorous animals live by destroying the life of plants). In addition, so-called natural catastrophes -- earthquakes, floods, fires, drought, volcanic eruptions -- bring further suffering and death in their wake. Human beings, with their complex physiology and psychology, are aware not only of these painful features of earthly existence. They also suffer from the frequent recognition that they are strangers living in a world that is flawed and absurd.

      Many religions advocate that humans are to be blamed for the imperfections of the world. Supporting this view, they interpret the Genesis myth as declaring that transgressions committed by the first human pair brought about a “fall” of creation resulting in the present corrupt state of the world. Gnostics respond that this interpretation of the myth is false. The blame for the world’s failings lies not with humans, but with the creator. Since -- especially in the monotheistic religions -- the creator is God, this Gnostic position appears blasphemous, and is often viewed with dismay even by non-believers.

      Ways of evading the recognition of the flawed creation and its flawed creator have been devised over and over, but none of these arguments have impressed Gnostics. The ancient Greeks, especially the Platonists, advised people to look to the harmony of the universe, so that by venerating its grandeur they might forget their immediate afflictions. But since this harmony still contains the cruel flaws, forlornness and alienation of existence, this advice is considered of little value by Gnostics. Nor is the Eastern idea of Karma regarded by Gnostics as an adequate explanation of creation’s imperfection and suffering. Karma at best can only explain how the chain of suffering and imperfection works. It does not inform us in the first place why such a sorrowful and malign system should exist.

      Once the initial shock of the “unusual” or “blasphemous” nature of the Gnostic explanation for suffering and imperfection of the world wears off, one may begin to recognize that it is in fact the most sensible of all explanations. To appreciate it fully, however, a familiarity with the Gnostic conception of the Godhead is required, both in its original essence as the True God and in its debased manifestation as the false or creator God.
      ." (Gnostic World View)

  4. That's fantastic Dredd. i'm very familiar with Gnosticism from college where i minored in philosophy. Since i don't think we can know the 'why,' i've categorized my own thinking as Agnostic. We can discover the mechanisms by which the universe functions and the nuts and bolts of biologic life, but not the intent, if there even is one.

    Great subject.


  5. Trouble-maker Tom here, with another article you might like Dredd:

    Has a sixth DNA base been discovered?

    Most text books talk of four DNA bases. Later research has shown there to be five. No, wait, cross that out, there could be six. Scientists suggest that the methyl-adenine is the sixth base and that it is medically important.

    DNA (deoxyribonucleic acid) is the main component of genetic material, found in humans and all other animals. DNA is formed by combining four parts or bases. These are coded A, C, G and T (representing adenine, cytosine, guanine and thymine).

    The combination of these leads to thousands of possible sequences. This variation explains the genetic variability found across and throughout living creatures.

    Use of the word base is historical, in reference to the chemical properties of 'nucleobases' in acid-base reactions; the term does not really describe their biological functions.

    There are, in addition to the four main bases, two other bases. These are methylated forms of other DNA bases. Methylation is a form of alkylation with a methyl group. These have epigenetic implications. Epigenetics is essentially additional information layered on top of the sequence of letters that makes up DNA.

    A fifth base was identified a few years ago. Called methyl-cytosine (mC), this is derived from cytosine. The find was of significance because mC can switch genes on or off depending on the physiological needs of each tissue. There is a probable link between alterations to this base and the risk of developing cancer.

    Now comes the news, via the University of Barcelona, that there could be a sixth base: methyl-adenine (mA). This base could be key in the life of the cells. The base was identified using advanced screening methods.

    [read the rest]