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Junk-of-the-Gaps Argument Shrinks Again

Jonathan Wells's book The Myth of Junk DNA has reduced defenders of the Junk DNA thesis to making "junk of the gaps" arguments, hoping that some of the DNA we don't yet understand will turn out to be useless evolutionary garbage after all. But with the direction that research is trending, as we discover more and more functions for non-coding DNA, the gaps keep getting smaller and smaller.

Back in July, we saw that multiple new papers have reported functions for "junk" DNA, including pseudogenes, showing that "the presumption that noncoding DNA is 'junk' hinders biological and medical research from moving forward." Now, the journal Nature has published the results of groundbreaking research that finds extensive evidence of function for junk-DNA.

The study sequenced and then compared the genomes of 29 eutherian (placental) mammals and sought to find sections that were highly similar, or "conserved," implying they have some kind of function that has been preserved over time. According to a Science Daily news release, 'Dark Matter' of the Genome Revealed Through Analysis of 29 Mammals, the study's results imply "the regulatory information that controls genes dwarfs the information in the genes themselves" as and "revea[l] almost 3 million previously undetectable elements in non-coding regions that have been carefully preserved across all mammals." The article explains that the functional elements discovered in the study include:

  • Almost 4,000 previously undetected exons, or segments of DNA that code for protein
  • 10,000 highly conserved elements that may be involved in how proteins are made
  • More than 1,000 new families of RNA secondary structures with diverse roles in gene regulation
  • 2.7 million predicted targets of transcription factors, proteins that control gene expression.

In humans, the conserved elements amount to over 4% of our genome. Again, the paper detected these functional DNA elements by comparing conserved, or highly similar sequences, across many diverse species of eutherian mammals ranging from humans to mice, to cows, elephants, and rabbits. Now of course if a sequence wasn't conserved across all of these species, then the study didn't count it as conserved. That doesn't necessarily mean that particular stretch of DNA isn't functional. It just means that it doesn't entail a common functional sequence ubiquitous across all placental mammals.

Obviously such diverse mammal groups have many unique differences, and so you wouldn't expect all functional mammalian DNA to be conserved across all mammals -- if that were the case, there would be no diversity. Any only-order-specific, only-family-specific, or only-genus- or species-specific functional DNA within eutherian mammals (which undoubtedly exists in great amounts) wouldn't necessarily be detected by the techniques used in this study. So the fact that most DNA isn't conserved across all eutherian mammals doesn't therefore mean that it isn't functional.

Indeed, this comparative study uncovered many new stretches of DNA that previously weren't known to have any function. As the Science Daily article noted, it offered "a clear view of once indiscernible genomic regions." Who knows what other vast tracts of functional DNA yet remain to be discovered? Indeed, it is turning out that the genetic differences between humans and chimps encode our many differences. As Jonathan Wells explains here, dissimilarity in non-coding DNA between humans and chimps helps produce our differences. So non-conserved "junk DNA" also plays vital roles.

Clearly we're still just beginning to uncover the workings of the genome, but it looks like both conserved and non-conserved DNA can have function. So how does one address the objection that "there may yet be junk hiding in some unstudied portion of the genome"? Jonathan Wells addressed this question in a recent article in Salvo Magazine:

There may be, but saying that some of our DNA might be junk is a far cry from claiming that most of our DNA is junk -- and that this junk provides evidence for Darwinism and against intelligent design. I would add: Calling something in a living cell "junk," just because no one knows its function, is a science-stopper. Biologists make progress not by closing their eyes to "junk" but by looking for new functions.
Wells responded in The Receding Myth of "Junk DNA" to writer John Farrell on the same point:
Farrell states that my chapter about them leaves the reader "with the misleading impression that biologists are well on their way to finding functions for the entire human genome." Of course, my book also includes chapters about functions in various other forms of non-protein-coding DNA. In any case, I never claim that functions have been found for most non-protein-coding DNA, though as I stated above the list grows longer every week. It is the trend, more than the current total, that should worry any defender of junk DNA.
Now another prominent paper has continued this trend, pushing defenders of junk DNA into yet smaller gaps in the genome.