Former “Junk DNA” Now Considered Essential

The term “junk DNA” seems to be fading with each new discovery.  Helen Pearson, reporting for Nature Science Update, leads with the line “‘Junk’ DNA reveals vital role: Inscrutable genetic sequences seem indispensable.”  They don’t know what it does yet, but the assumption is it must be important for evolution to hang onto it for so long.  Pearson writes,

If you thought we had explored all the important parts of our genome, think again.  Scientists are puzzling over a collection of mystery DNA segments that seem to be essential to the survival of virtually all vertebrates.  But their function is completely unknown.
    The segments, dubbed ‘ultraconserved elements’, lie in the large parts of the genome that do not code for any protein.  Their presence adds to growing evidence that the importance of these areas, often dismissed as junk DNA, could be much more fundamental than anyone suspected.

Researchers found 480 sequences that are identical between humans, mice and rats, and “largely match up with chicken, dog and fish sequences too,” but do not exist in invertebrates such as sea squirts and fruit flies.
    Scientists can only guess what these sequences do.  One idea is that they “control the activity of indispensable genes.”  Another is that they may slice and splice RNA into different forms.  Or perhaps they may control embryo growth.  Pearson describes the initial reactions to the discovery that junk DNA is not junk after all:

To solve the conundrum, experts predict a flurry of studies into the enigmatic DNA chunks.  “People will be intrigued by this [finding],” says Kelly Frazer who studies genomics at Perlegen Sciences in Mountain View, California.  “It is the kind of stuff that blows people away.”

She quotes one researcher who said, “It absolutely knocked me off my chair.”  It was hard to believe these sections could be 100% identical.  Some thought they must have contaminated their samples.  “The presence of exact copies in different animals suggests that even tiny changes in the sequence of these segments destroy whatever they do,” Pearson surmises, “and have been weeded out during evolution” whereas other parts have been free to accumulate mutations.
    Clearly there is a lot of work ahead, Pearson says.  Finding the function of the ultraconserved elements is just the tip of the iceberg.  There are other vast tracts of similar so-called “junk DNA” whose functions await discovery.
    On a related subject, Current Biology has news on introns (see 09/03/2003 headline).  A dispatch by Arlin Stoltzfus begins, “The evolutionary origin of spliceosomal introns remains elusive.  The startling success of a new way of predicting intron sites suggests that the splicing machinery determines where introns are added to genes.”  New techniques show the splicing sites are not random, because observers can predict where they will be found with uncanny accuracy.  The “putative benefits” of introns that “justify their existence” are still unknown.  Apparently, the cell has “mechanisms of targeted intron gain.”
See also the May 12 BBC News report on this finding.

Researchers could have had a big head start by approaching this topic from an intelligent design perspective.  Just because these stretches of DNA don’t code for proteins, and just because they have unknown functions, doesn’t mean they are junk.  It was evolutionary presuppositions that treated them as useless leftovers of evolutionary ancestry.  Now Darwinian scientists are surprised and have a lot of catching up to do.  A design perspective would begin by assuming that these stretches are there for a reason.  Let’s find out, therefore, what they are there for.