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)

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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)

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(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.

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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.

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

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