Monday, September 30, 2013

The Uncertain Gene - 3

Genetic Transcription Mysteries Solved?
In this series we are exploring the old concept of "junk DNA", which is beginning to now be called "dark matter" by evolutionary biologists.

That is because daily discoveries in research are showing that the 98% of the human genome that has been very erroneously called "junk DNA" is anything but that.

The use of the term "dark matter" by biologists is interesting, because for one thing, here at Dredd Blog we feel that so far "dark matter" is a prime example of scientific teleology which is affecting the cosmology discipline whereby imagination gets way ahead of scientific data, then goes off into places where competent science would not go.

It is Freudian that evolutionary biologists would grab that phrase which cosmologists have been using to dogmatically tell us that some 96% of the universe is "dark matter/energy":
Let's remember that the subject is not only "dark matter", but is also the Dredd Blog scientifically rebellious binding of that subject with "faith," because this dark matter is more "scientific faith" than it is provable science.

The big deal in cosmology at the moment is "dark matter", so let's cut to the chase, and let one of the foremost experts explain why this dark matter subject is so hot to trot:
‘We are on the verge of finding out what dark matter is’, Professor Carlos Frenk told the British Science Festival in Bradford. Frenk, director of Durham University’s Institute for Computational Cosmology, predicts that within the next few months, ‘Either dark matter will be discovered, or our model of the universe is not quite right.’
(Subsequent Paper: Dark Matter). The professor said we will soon be "finding out what dark matter is", "dark matter will be discovered", "or our model of the universe is not quite right"?

What the hell, we don't know what 96% of the universe is, nor have we discovered it yet, but he hope to discover it soon?
(Heretics Deny The Dark Matter of Faith - 3). In that vein, let's get ready to zero in on the
Proton Tunneling Into Dark Matter?
specific purpose of today's post, which was explicitly stated in the last post of this series:
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 - 2). Let's quickly gather our thoughts before we move on, and reflect once again on where the wrong headed notion of "junk DNA" came from, not to mention the years of damage done to science by that faulty scholarship and faulty research:
The 1960s discovery that much nuclear DNA in eukaryotic cells does not code for proteins was quickly interpreted as evidence for the evolution of eukaryotic genomes. Papers were published suggesting a nomenclature reflecting evolutionary assumptions about this “junk DNA.” Noncoding DNA was also used as evidence for the selfish gene theory popularized by Richard Dawkins and others. As many important functions played by noncoding DNA have come to light, the assumption can no longer be made that it represents DNA potsherds of evolution. Now the assumption of functionality in what was once called junk DNA is widespread, but its interpretation within a Darwinian framework remains. Thus, what was once touted as evidence of life’s evolutionary history because of its lack of function is now interpreted as evidence of the same thing because it is functional. This experience calls into question how much data actually unambiguously support Darwinian evolution, what evolutionary theory actually predicts, and how data can be used to check its predictive power.
(Tel Aviv University, "Rushing To Judgment", PDF, emphasis added). Once researchers looked into the packages and all the traffic in the "junk" pile, they began to realize that the bed time stories about junk DNA were teleological imaginings outside of competent scientific reasoning:
Snippets of information contained in dark matter, or “junk DNA,” can alter the way a gene gets put together, according to new research.

These small sequences of genetic information tell the gene how to splice, either by enhancing the splicing process or inhibiting it. The research opens the door for studying the dark matter of genes. And it helps us further understand how mutations or polymorphisms affect the functions of any gene,” says study senior author Zefeng Wang, assistant professor of pharmacology in the University of North Carolina School of Medicine.

Published in the current issue of Nature Structural & Molecular Biology, the findings may be viewed in terms of the film industry’s editorial process where snippets of celluloid are spliced, while others end up unused on the proverbial cutting room floor.

Taken from a DNA point of view, not every piece of it in each human gene encodes for a functional protein; only about 10 percent does, in coding regions called “exons.” The other 90 percent of the stuff that fills the intervening regions are longer stretches of dark matter known as “introns.”

But something mysterious happens to introns during the final processing of messenger RNA (mRNA), the genetic blueprint that’s sent from the cell’s nucleus to its protein factory. Only particular exons may be included within the final mRNA produced from that gene, whereas the introns are cut out and destroyed.

It’s therefore easier to understand why more scientific attention has been given to exons. “When people are looking at the genetics of a disease, most of the time they’re looking for the change in the coding sequence,” Wang says.

“But 90 percent of the sequence is hidden in the gene’s introns. So when you study gene variants or polymorphisms that cause human disease, you can only explain the part that’s in the exon. Yet the majority remains unexplainable because they’re in the introns.”
(Univ. South Carolina, ‘Junk’ DNA Assembly Instructions, emphasis added). The genetic movie starring you, me and everyone else, we now know, is being made by also using the information in "the junk DNA or dark matter" of the human genome and/or microbiome.

In the previous post of this series we discussed the book Quantum Aspects of Life, a science textbook, which calls some of this activity "quantum choreography", while at the same time cautioning against teleology.

So, how is all that cutting, pasting, and organizing done so that the genetic movie is a hit, and not a disaster?

The answer is thousands of specialized molecular machines, not made of junk, but made of various atoms which comprise a sophisticated genetic factory of such machines.

Here is what "junk DNA" or "dark matter" really is:
"We took this approach because so many RNAs are rapidly destroyed soon after they are made, and this makes them hard to detect," Pugh said. "So rather than look for the RNA product of transcription we looked for the 'initiation machine' that makes the RNA. This machine assembles RNA polymerase, which goes on to make RNA, which goes on to make a protein." Pugh added that he and Venters were stunned to find 160,000 of these "initiation machines," because humans only have about 30,000 genes. "This finding is even more remarkable, given that fewer than 10,000 of these machines actually were found right at the site of genes. Since most genes are turned off in cells, it is understandable why they are typically devoid of the initiation machinery."

The remaining 150,000 initiation machines -- those Pugh and Venters did not find right at genes -- remained somewhat mysterious. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant ["junk"] since they did not code for proteins." Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylation -- a long string of genetic material, adenosine bases -- that protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.
(Scientists Discover the Origins, emphasis added). One wonders why this was not contemplated prior to going off into junk science, especially since molecular machines are found elsewhere in cells.

Other molecular machines are doing other types of work necessary for cell existence (see e.g. Putting A Face on Machine Mutation, Do Molecular Machines Deliver Toxins of Power?, Weekend Rebel Science Excursion - 17,  and Did Abiotic Intelligence Precede Biotic Intelligence?).

In the next episode of this series we will take a look at the participation of microbes within the realm of the human genome and/or microbiome previously wrongly presumed to be just a junk yard (preview The Human Microbiome Congress for a taste of what is coming).

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

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