From GEN (Genetic Engineering & Biotechnology News) :
“What Junk DNA? It’s an Operating System”
In the August 1 issue of CELL, researchers from the Gene and Stem Cell Therapy Program at Sydney’s Centenary Institute revealed another function of introns, or noncoding nucleotide sequences, in DNA. They reported that gene-sequencing techniques and computer analysis allowed them to demonstrate how granulocytes use noncoding DNA to regulate the activity of a group of genes that determines the cells’ shape and function.
Their report adds to growing experimental support for the idea that all that extra stuff in the human genes, once referred to as “junk DNA,” is more than functionless, space-filling material that happens to make up nearly 98% of the genome. The paper adds to a growing body of knowledge establishing a considerable role for this material in the regulation of gene expression and its potential role in human disease.
Now just watch Darwin’s followers claim that they never used the existence of masses of junk DNA as an important support to their theory, that they haven’t been trying to discredit ENCODE for that very reason.
File facts for any who care:
Brown University biologist Kenneth R. Miller, Oxford University zoologist Richard Dawkins, University of Chicago biologist Jerry A. Coyne, and University of California–Irvine biologist John C. Avise have all argued that most of our DNA is junk, and that this provides evidence for Darwinian evolution and against intelligent design.
So, as with vestigial organs, Darwinians claimed that one way you could know that their theory is true is that most DNA is junk. But it was not junk. That should count against their theory. How have Darwinists responded? In three ways: first by claiming that they never said it was junk. As Wells points out, that claim is easily disproved. Second, by ignoring the growing problem. British physicist David Tyler observes,
Instead of alerting popularisers of science to be cautious, these writers treated the new data as unrepresentative exceptions. They pressed on with their claim that the bulk of the genome is useless. The trickle of challenging research findings became a stream, but the “consensus” about junk DNA was not corrected. The stream became a river, but still the much-needed correction was lacking.
Third, some just doubled down on their story like a political party caught in a scandal. Richard Dawkins announced in 2004, “DNA differs from written language in that islands of sense are separated by a sea of nonsense, never transcribed.” By 2004, he should have known that the evidence suggests otherwise. And in 2006, Skeptic Magazine publisher Michael Shermer wrote: “ … we have to wonder why the Intelligent Designer added to our genome junk DNA, repeated copies of useless DNA, orphan genes, tandem repeats, and pseudogenes, none of which are involved directly in the making of a human being.” New atheist Darwinist Jerry Coyne claimed in 2009, “Our genome—and that of other species —are truly well populated graveyards of dead genes.” By then, there was no particular reason, apart from faith in Darwin, to believe this.
In 2010, one research group went so far as to directly contradict the findings of the ENCODE Project. Foul-mouthed Darwinist blogger PZ Myers was happy (“Well score one for the more cautious scientists, and give the creationists another big fat zero”), but his colleagues were less happy. The dissenting research group was criticized for using a method that is “certain to leave gaping holes in [our] understanding of the transcriptome.”
In any event, attacks on ENCODE have continued from Darwin’s camp, the gist being that it can’t be true because then Darwinism wouldn’t be true. ID theorist Jonathan Wells sums up this response to ENCODE among Darwin’s followers: “they have forfeited any claim they might have had to be speaking for science.” 
So did ID theorists have anything to say about junk DNA? Yes, they predicted that it was not junk. For example, William A. Dembski spoke for most when he wrote in The Design Revolution (2004),
For years now evolutionary biologists have told us that the bulk of genomes is junk and that this is due to the sloppiness of the evolutionary process. That is now changing. For instance, researchers at the University of California at San Diego are finding that long stretches of seemingly barren DNA sequences may form a new class of noncoding RNA genes scattered, perhaps densely, throughout animal genomes. Design theorists should be at the forefront in unpacking the information contained within biological systems. 
All the while Coyne and Shermer were still proclaiming that most DNA is junk (look at the dates). And the former two continued to claim it for years after they should have wised up. Darwin does that to his followers.
I could go on but why bother? A single eagerly accepted pronunciamento from a senior Darwinist will transform myth into fact and vice versa, eagerly accepted by anyone who seeks advancement.
Soon we will be hearing from all quarters that Darwin’s followers never really said it was junk. If this blog disappeared, would you know any different?
– O’Leary for News
 Richard Dawkins, The Ancestor’s Tale (Houghton Mifflin Harcourt, 2004), p. 22
 Michael Shermer, Why Darwin Matters: The Case Against Intelligent Design (Times Books, 2006), p. 75.
 Jerry Coyne, Why Evolution Is True (Viking Adult, 2009), p. 81.
 Jonathan Wells, The Myth of Junk DNA, (Discovery Institute Press, 2011): pp. 82-84.
 Jonathan Wells, The Myth of Junk DNA (Discovery Institute Press, 2011), pp. 97-98.
 William A. Dembski and Charles W. Colson, The Design Revolution: Answering the Toughest Questions about Intelligent Design (InterVarsity Press, 2004), p. 317.
Hat tip: Matthew Cochrane