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More Functions For “Junk DNA”

A new paper has just been published in the journal Genome Biology by John Rinn and David Kelley, identifying a role for transposable elements in gene regulation in stem cells. Science Daily reports on the paper:

Over a decade after sequencing the human genome, it has now become clear that the genome is not mostly ‘junk’ as previously thought. In fact, the ENCODE project consortium of dozens of labs and petabytes of data have determined that these ‘noncoding’ regions house everything from disease trait loci to important regulatory signals, all the way through to new types of RNA-based genes.

Yet over 70 years ago, it was first proclaimed that all this junk wasn’t so junky. Barbara McClintock discovered the first utility of all of this junk DNA: jumping genes, also known as transposable elements. These genes serve only one purpose, which is to replicate themselves and reinsert randomly in the genome, or do they? Ironically, at the same time two other scientists (Roy Britten and Eric Davidson) proposed that jumping genes may be involved in regulating cell specificity. Indeed, in an exciting new study published in Genome Biology, John Rinn and David Kelley based at Harvard University and the Broad Institute in Boston, USA, provide genome-wide evidence that jumping genes may shape when a gene is turned on or off in stem cells.

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3 Responses to More Functions For “Junk DNA”

  1. I liked this part:

    The study published by Rinn and Kelley finds a striking affinity for a class of hopping genes known as endogenous retroviruses, or ERVs, to land in lincRNAs. The study finds that ERVs are not only enriched in lincRNAs, but also often sit at the start of the gene in an orientation to promote transcription. Perhaps more intriguingly, lincRNAs containing an ERV family known as HERVH correlated with expression in stem cells relative to dozens of other tested tissues and cells. According to Rinn, “This strongly suggests that ERV transposition in the genome may have given rise to stem cell-specific lincRNAs. The observation that HERVHs landed at the start of dozens of lincRNAs was almost chilling; that this appears to impart a stem cell-specific expression pattern was simply stunning!”
    http://www.sciencedaily.com/re.....192838.htm

    The reason that something that was thought to be randomly drifting junk in the Genome is now found to be “stem cell-specific” would be ‘simply stunning’ is because:

    Mutations expressed early in embryonic development are the least likely to be tolerated by organisms – Paul Nelson – video
    http://www.metacafe.com/watch/5548184/

    Understanding Ontogenetic Depth, Part II: Natural Selection Is a Harsh Mistress – Paul Nelson – April 7, 2011
    http://www.evolutionnews.org/2.....45581.html

  2. The important lesson to be learned, in my opinion, from recent studies published in Nature and other journals comprising the ENCODE studies, is a broader appreciation of how complex the genome is. The more we peel away the layers the more functionally interactive it all becomes. It is no longer meaningful to ask how many genes we have because we can no longer define a gene by the geographic location of bases, and we can no longer define how evolutionarily advanced an organism is by how many genes it has. It is becoming evident that the order in which genes are expressed, their post transcription modifications, etc. are vastly more important in determining the final outcome. This level of mind-boggling series of controls and counter-controls leads me and, increasingly, eminent scientists from around the world, to begin to re-examine the basic tenets of evolution. It is becoming clearer with each discovery that the sheer complexity of the genome and its regulatory mechanisms needs a more robust theory than the simplistic model of spontaneous mutations and natural selection, even though, on a local level, these mechanisms have a very important role. People like Simon Conway Morris, Cambridge Professor of evolutionary biology, and John Kearns, Harvard geneticist, have each expressed doubt about the standard evolutionary model for different reasons and join hundreds of other eminent scientists who are calling for a more robust model. Evan Olsen has even proposed a model based on chaos theory by which DNA is a fractal attractor which guides the evolutionary process toward a defined goal. If all this sounds like blasphemy, let us not be tempted to give Michael Behe’s infantile Intelligent Design model any more due than to admit that his concerns over the ever-increasing complexity of the genome are seeping into the mainstream scientific community.

  3. Off topic, at least in specifics, for which I apologise, but re the concluding point made in an article in ‘The New Republic by Plantinga on Nagle’, in the Faith and Science section of Evolution News, the author concludes:

    ‘The probability, with respect to our current evidence, that life has somehow come to be from non-life just by the working of the laws of physics and chemistry is vanishingly small.’

    It is not ‘probability’ that is the issue, but the very question of ‘possibility’. How often do we set these two concepts merged in this kind of ‘evaomalutionst’ context? No wonder Pauli was concerned that they hadn’t ‘done the math’!

    In the meantime, others have done it for them, and ought to have roundly declared: ‘No! it is NOT improbable. It is IMPOSSIBLE! We’re talking about science today. If in the future someone can indicate a verifiable pointer towards the currently-perceived impossible being possible, fine, but right now, that is UNICORN territory. And it does not go with the territory. Science doesn’t go with Unicorn territory! Period. Get over it, and start acknowledging that the only successful science you perform confounds your metaphysical position, posturing as a scientific one.’

    Since the laws of physics and chemistry are, in fact, simply, codifications of observed regular patterns in nature, precisely which such regular patterns in physics and or chemistry have served to explicate for us the origin of life, however, primitive, on this planet?

    I mean, we’re not talking about conjectures here; with a scientific establishment in thrall to corporate finance and insisting on absolute dereliction of the empirical norms of scientific research, ‘evomalutionists’ had better come up with some hard science. Their comprehensive disgrace already is only a matter of time, and a brief time, at that.’

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