Thursday, October 3, 2013

The Uncertain Gene - 4

Molecular Machine Work
I began this series with a look at human genetic mutation through the abiotic quantum mechanical dynamic called "proton tunneling" (The Uncertain Gene).

I used the word abiotic because proton tunneling is machine-like, rather that being life-like.

In short, this type of mutation in DNA is not an organic event at the onset.

In other words, the result of proton tunneling is not life, it is molecular, i.e. a mutation of molecules rather than being a direct mutation into a carbon based life form.

To be very clear, recall that in the second post of this series (The Uncertain Gene - 2) we looked once again at the history of evolution, finding that what is quite notable in that regard is that the great bulk of evolution, in terms of time, has been abiotic evolution (i.e. the evolution of molecular machines) rather than having been biotic evolution (the evolution of carbon based life forms).

That being the case, molecular machine evolution and/or mutation, a.k.a. abiotic evolution, needs more attention than it gets, thus, the focus in this series is on a purely abiotic dynamic, which is proton tunneling induced mutation.

In the previous post I indicated that we would look at how "150,000 initiation machines" in the "non-gene" or "non-coding" portion of DNA could be utilized by various types of RNA and their operations promoted by the "molecular machine" known as a ribosome:
The ribosome ... is a large and complex molecular machine, found within all living cells, that serves as the primary site of biological protein synthesis (translation).
(Wikipedia, emphasis added). That protein synthesis or translation is where the ribosomes perform the critical task of bridging the gap from abiotic to biotic, by processing the proton tunneling mutation.

The ribosomes, using RNA, do so by perpetuating that mutation into molecules containing carbon atoms --into molecular arrangements called amino acids from which proteins are then made.

Both amino acids and proteins are organic compounds:
An organic compound is any member of a large class of gaseous, liquid, or solid chemical compounds whose molecules contain carbon.
(Wikipedia, "Organic Compound", emphasis added). But until recently that translation has been known to take place only in the area of genes, not in the area of "junk DNA" or "dark matter."

But new research tells us that in fact is precisely what takes place in what is becoming known as an area of treasure, not of junk:
The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation.
(ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome," Nature, Vol. 489:57-74, September 6, 2012, emphasis added). Those operations by RNA etc. in that region were totally unexpected by pop science writers who unfortunately expressed themselves in undesirable teleological terms:
"It stretches even their creative ingenuity to make a convincing reason why an intelligent designer should have created a pseudogene -- a gene that does absolutely nothing and gives every appearance of being a superannuated version of a gene that used to do something -- unless he was deliberately setting out to fool us ...

Leaving pseudogenes aside, it is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes."
(The Greatest Show on Earth, by Richard Dawkins, pp. 332-33). That area in the human genome and/or microbiome is the target for today's post, because in the previous post I said:
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 Uncertain Gene - 3). If a quantum proton tunneling induced mutation took place, and the results of that mutation are placed, for any reason, into the "junk DNA" or "dark matter" section of the human genome and/or microbiome, it is clear that it could still be included in subsequent biological protein synthesis or translation.

In conclusion for today, the results of purely quantum-mechanical proton tunneling could cross the bridge spanning the gap from abiotic to biotic at the time of translation --a non-carbon-based-machine-component could thereby become part of a biological component --part and parcel of the DNA of some carbon based life form.

In the next post of this series, we will look into the operation of microbes in and on both sections of the human genome and/or microbiome, in terms of inducing mutations or other genetic related events.

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

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