Junk DNA, Junky PR

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A week ago, a huge, painstakingly orchestrated PR campaign was timed to coincide with multiple publications of a long-term study by the ENCODE consortium in top-ranking journals.  The ENCODE project (EP) is essentially the next stage after the Human Genome Project (HGP).  The HGP sequenced all our DNA (actually a mixture of individual genomes); the EP is an attempt to define what all our DNA does by several circumstantial-evidence gathering and analysis techniques.

The EP results purportedly revolutionize our understanding of the genome by “proving” that DNA hitherto labeled junk is in fact functional and this knowledge will enable us to “maintain individual wellbeing” but also miraculously cure intractable diseases like cancer and diabetes.

Unlike the “arsenic bacteria” fiasco, the EP experiments were done carefully and thoroughly.  The information unearthed and collated with this research is very useful, if only a foundation; as with the HGP, this cataloguing quest also contributed to development of techniques. What is way off are the claims, both proximal and distal.

A similar kind of “theory of everything” hype surrounded the HGP but in the case of the EP the hype has been ratcheted several fold, partly due to the increased capacity for rapid, saturating online dissemination.  And science journalists who should know better (in Science, BBC, NY Times, The Guardian, Discover Magazine) made things worse by conflating junk, non-protein-coding and regulatory DNA.

Biologists – particularly those of us involved in dissecting RNA regulation – have known since the eighties that much of “junk” DNA has functions (to paraphrase Sydney Brenner, junk is not garbage).  The EP results don’t alter the current view of the genome, they just provide a basis for further investigation; their definition of “functional” is “biochemically active” – two very different beasts; the functions (let alone any disease cures) will require exhaustive independent authentication of the EP batch results.

 

Written By: Athena Andreadis 
continue to source article at blogs.scientificamerican.com

7 COMMENTS

  1. As I read this and from what little I’ve heard before the following analogy occurs to me:

    if a Martian were to inspect the memory of your average computer, she would think at first that a fairly large part was “junk” memory. Its not related to any documents, video, or other content that the user sees. This would be things like the Operating System and the Java Virtual Machine, things needed to make the other programs run but seldom invoked directly by the average user. It seems to me that some of this “junk” DNA is analogous, its the engine that is used to do the copying, splicing, etc. required so that for example a few cells can eventually grow into an adult human.

    Does that make sense or am I completely misunderstanding the junk DNA?

  2.   A similar kind of “theory of everything” hype surrounded the HGP but in
    the case of the EP the hype has been ratcheted several fold, partly due
    to the increased capacity for rapid, saturating online dissemination. 
    And science journalists who should know better (in Science, BBC, NY Times, The Guardian, Discover Magazine) made things worse by conflating junk, non-protein-coding and regulatory DNA.

    Well journalists do love their hype and “scoops”!

    (There are some who really should borrow spare scoops from dog owners for their writings.)

  3. That *could* be how DNA works, but don’t assume you have an argument for it being so; it’s more of an intuition pump. We *know* that junk DNA is copy-pasted many, many times; we also know much of it is ancient viruses. While there’s a possibility something we call “junk” may somehow be more than just a free rider, the operating system looks unlikely to be the right analogy in practice. Bear in mind also that, because functions are what serves the genes et al which cause them, DNA itself should not be thought of as “functional” anyway.

  4.  Thanks for the feedback. The interesting thing about computers is if you drop down enough levels of abstraction there really isn’t much of a difference between functions and data. Its all just ones and zeroes at the machine level.

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