The Junk DNA myth strikes again (next up: media hype).

Here’s the abstract of a paper set to be published in Molecular Biology and Evolution. Now, I think this kind of study is interesting and important. But it’s predictable that they start out with the standard (and historically false) claim that “non-coding DNA was long dismissed as junk” (seriously, do reviewers require authors to insert this line or something?). It’s also predictable that the amount of non-coding DNA that they report as showing signs of constraints (about 5% of the genome) will be reported in science news as “junk DNA functional after all!”.

Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes.
Eory L, Halligan DL, Keightley PD

Protein-coding sequences make up only about 1% of the mammalian genome. Much of the remaining 99% has been long assumed to be junk DNA, with little or no functional significance. Here we show that in hominids, a group with historically low effective population sizes, all classes of non-coding DNA evolve more slowly than ancestral transposable elements, and so appear to be subject to significant evolutionary constraints. Under the nearly neutral theory, we expected to see lower levels of selective constraints on most sequence types in hominids than murids, a group that is thought to have a higher effective population size. We found that this is the case for many sequence types examined, the most extreme example being 5′ UTRs, for which constraint in hominids is only about one-third that of murids. Surprisingly, however, we observed higher constraints for some sequence types in hominids, notably four-fold sites, where constraint is more than twice as high as in murids. This implies that more than about one-fifth of mutations at four-fold sites are effectively selected against in hominids. The higher constraint at four-fold sites in hominids suggests a more complex protein-coding gene structure than murids, and indicates that methods for detecting selection on protein coding sequences (e.g., using the d(N) /d(S) ratio), with four-fold sites as a neutral standard, may lead to biased estimates, particularly in hominids. Our constraint estimates imply that 5.4% of nucleotide sites in the human genome are subject to effective negative selection, and that there are three times as many constrained sites within non-coding sequences as within protein-coding sequences. Including coding and non-coding sites, we estimate that the genomic deleterious mutation rate U = 4.2. The mutational load predicted under a multiplicative model is therefore about 99% in hominids.

Update: See BIOpinionated for a silly critique and Sandwalk for a fine reply.


2 comments to The Junk DNA myth strikes again (next up: media hype).

  • troglodyte

    Seems your old buddy Pellionisz took the title of this post and ran with it:

    http://forums.carm.org/v/showthread.php?p=5611435#poststop

    Junk DNA – a myth


    Since at least September 18th, 2009, even T. Ryan Gregory calls “Junk DNA” a “myth”.

    This left a Lonely Moron as the last named “scientist” who still keeps is head in the sandwalk and clings to the silly notion (even against the majority of his bloggers – see his extreme left marginal poll) that “the majority of human DNA is junk”.

    When it was pointed out that this post did nothing of the sort, Pellionisz ignored it, until he was reminded several times, upon which he did what he usually does:

    http://forums.carm.org/v/showpost.php?p=5662776&postcount=584
    As I comment over there I mention, that young and talented T. Ryan Gregory tried to launch his early career on “Junk DNA” (minimizing that Ohno declared a majority of human DNA to be there “for the importance of doing nothing”).

    Now, realizing that such a crass mistake is scientifically untenable, TRG is trying to “fuzz up” his formerly rigid stance. Earlier, TRG bunched up with a Lonely Moron full of junk, who still clings in his sandbox (better than rubber box) to that silly notion. TRG and Lonely Moron are no longer joint in the hips – moreover TRG also dropped “anonymous bloggers”. While trying to salvage his career launched on “junk DNA” TRG is now playing both sides of the fence. A a result, his recent entries are rather confusing. He is welcome to clarify.

    On his famed youtube posting, he writes:

    http://www.youtube.com/watch?v=WJMFuc75V_w

    Young T. Ryan Gregory launched a career on “Junk DNA” (minimizing that Ohno declared a majority of human DNA “to do nothing”). Now TRG is trying to “fuzz up” his stance. Formerly, TRG bunched up with a Lonely Moron full of junk, who still clings to that silly notion. No longer -´╗┐ TRG also dropped “anonymes”. While trying to salvage his career launched on “junk DNA” TRG is now playing both sides of the fence; thus his recent entries are rather confusing. He is welcome to clarify. – Principals Only

    Shameless self-promotion at the expense of others seems his forte.

      (Quote)

Leave a Reply

 

 

 

You can use these HTML tags

<a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <strike> <strong>

*