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Junk DNA Not Junk After All September 9, 2012

Posted by Metabiological in Genetics.
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A big new study out of the Human Genome Research Group has just been released to the public.  This is probably the biggest study in genetics since the Human Genome project a decade ago and the results coming out seem to be just as fascinating.

“The ENCODE project not only generated an enormous body of data about our genome, but it also analyzed many issues to better understand how the genome functions in different types of cells. These insights from integrative analyses are really stories about how molecular machines interact with each other and work on DNA to produce the proteins and RNAs needed for each cell to function within our bodies,” explains Ross Hardison of Pennsylvania State University, one of the JBC authors…

The human genome consists of about 3 billion DNA base pairs, but only a small percentage of DNA actually codes for proteins. The roles and functions of the remaining genetic information were unclear to scientists and even referred to as “junk DNA.” But the results of the ENCODE project is filling this knowledge gap. The findings revealed that more than 80 percent of the human genome is associated with biological function.

The status of junk DNA has been a thorn in biology’s side for a while now so it’s nice to have that question at least somewhat resolved.  What’s most interesting for me is how this changes our view of the complexity of the human body.

It’s been becoming apparent for some time now that while what genes an organism possess are very important in determining organism functioning how those genes are activated and deactivated is just as (or possibly more) important.  The field of epigenetics has been hot in recent years as scientists have begun to examine how regulation of gene expression rather then the actual structure of DNA determines the phenotype of individuals.  If what this study tells us is correct it would seem that the vast majority of DNA is devoted to this regulation and while I’m not one to say that size always matters the sheer amount of this non-coding DNA speaks volumes about it’s likely importance.

It also makes the job of predicting the development of phenotypes a bit more tricky.  “Junk DNA” may regulate gene expression but many other factors, including environmental, can affect junk DNA.  Furthermore there is some evidence that changes in gene expression can actually be passed on to descendents, a form of non-Darwinian evolution.  Will Lamark make a comeback?  Hard to say but we do seem to be on the edge of a major shift in our understanding of the basics of life.

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Artificial DNA Created April 20, 2012

Posted by Metabiological in Beyond Earth, Genetics.
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In what appears to be a first scientists have created the first synthetic genetic material that can store information and evolve in a similar way to DNA.

Researchers at the MRC Laboratory of Molecular Biology, in Cambridge, developed chemical procedures to turn DNA and RNA, the molecular blueprints for all known life, into six alternative genetic polymers called XNAs.

The process swaps the deoxyribose and ribose (the “d” and “r” in DNA and RNA) for other molecules. It was found the XNAs could form a double helix with DNA and were more stable than natural genetic material.

Cool news by anyone’s standard.

I will however take issue with one things stated by the authors.

“There is nothing Goldilocks about DNA and RNA,” Holliger told Science. “There is no overwhelming functional imperative for genetic systems or biology to be based on these two nucleic acids.”

That is overstepping bounds to me.   While this has certainly proved the possibility of other molecules forming the basis of genetic material it says nothing about the probability of said molecules actually forming on their own.  As of right now the only truly concrete thing we can say is that despite a very long time to try out different options the only type of genetic material to evolve are DNA and RNA.  Their prevalence, and the lack of any competitors, are the only evidence we have for how successful different types of genetic material are.  DNA may no longer be the only possible configuration but it still may be the most likely one and therefore the most likely basis for life on other worlds.    Far more work needs to be done in order to knock DNA off it’s pedestal.

1000 Genomes To Be Sequenced By End Of Year April 4, 2012

Posted by Metabiological in Genetics.
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Ambitious?  Yes.  Plausible?  Absolutely.

The 1000 Genomes Project, as its name suggests, is a joint public-private effort to sequence 1000 genomes. Begun in 2008, the Project’s main goal is to create an “extensive catalog of human genetic variation that will support future medical research studies.” The 1000 Genomes Consortium is headed by the NIH’s National Human Genome Research Institute which in turn is collaborating with research groups in the US, UK, China and Germany.

That might not sound like much. Thanks in large part to companies like Silicon Valley start up Complete Genomics perhaps as many as 30,000 complete genomes around the world have already been sequenced. But what is unique about the 1000 Genomes Project is that their genomes will be made available to the public for free, and stored in a place where the world can access the data easily and interact with it.

I’ve been critical in the past of Kurzweil applying his law of accelerating returns to non-computer science fields but when he sticks to what he knows he’s usually pretty accurate and genome sequencing is probably the best current example of that.  Prices have been plummeting and power has been increasing pretty much just as he predicted and the explosion of companies like 23&Me is testament to that.  I look forward to hearing about this project in the future.