For anyone who didn't actually read the article, it does NOT suggest, or infer, or justify, or provide any evidence regarding any claim that "junk" DNA is functional in general. Or even that MOST of it is functional. Or even that a significant percentage of it is functional. Or even that 10 or 5 or 2 percent of it is functional.
The study discussed found around 10,000 short DNA sequences in the approximately 95 percent of "non-coding" mammalian DNA that were found to be "conserved" across mammalian lineages generally. Conserved means they varied little among diverse mammalian groups. The logic is that if the sequences were preserved by evolution, then they must have some function. If they didn't have a function then evolution wouldn't be able to prevent them changing randomly over time, LIKE MOST OF THE "JUNK" DNA INDEED DOES.
IOW the whole logic of this result ASSUMES evolution. So why would you -- an antievolutionist -- be justified in drawing any conclusion (even a false and misleading one) from it?
“the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, in contrast, can easily explain them as nothing more than failed experiments in a random process”
--Ken Miller 1994
“...And theres lots more DNA that doesnt even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, tandem repeats, and other nonsense which may be useful for forensic detectives but which doesnt seem to be used in the body itself. Once again, creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA. ... Can we measure the information capacity of that portion of the genome which is actually used? We can at least estimate it. In the case of the human genome it is about 2% - considerably less than the proportion of my hard disc that I have ever used since I bought it.”
--Richard Dawkins 1998
Now let see what Intelligent Design scientists were saying on the subject of “junk” DNA:
“If it is true that a vast amount of DNA in higher organisms is in fact junk, then this would indeed pose a very serous challenge to the idea of directed evolution or any teleological model of evolution. Junk DNA and directed evolution are in the end incompatible concepts. Only if the junk DNA contained information specifying for future evolutionary events, when it would not in a strict sense be junk in any case, could the finding be reconciled with a teleological model of evolution. Indeed, if it were true that the genomes of higher organisms contained vast quantities of junk, then the whole argument of this book would collapse. On any teleological model of evolution, most, perhaps all, the DNA in the genomes of higher organisms should have some functions.”
"Finally, Science reports “Hints of a Language in Junk DNA” (25 November, p. 1320). Those supposedly meaningless strands of filler DNA that molecular biologists refer to as “junk” don’t necessarily appear so useless to those of us who have designed and written code for digital controllers. They have always reminded me of strings of NOP (No OPeration) instructions.. . .Perhaps the “junk DNA” puzzle would be solved more rapidly if a few more computer scientists would make the switch to molecular biology."
—Forrest Mims III 1994
“A couple of potential uses that spring to mind as I sit here at my desk include bonding to active hemoglobin genes during DNA replication in order to stabilize the DNA; guiding DNA recombination events; and aligning protein factors relative to active genes.”
—Michael Behe 1996
an ID theorist, reckoning that an intelligent designer would not fill animals’ genomes with DNA that had no use, predicted that much of the “junk” DNA in animals’ genomes — long seen as the detritus of evolutionary processes — will someday be found to have a function.
—John G. West 1998
“But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through along, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how “non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development.” Design encourages scientists to look for function where evolution discourages it.”
—William Dembski 1998
Many other ID and Creation Scientists have repeated these predictions, and they now being vindicated. Having said that, I suggest that you read the following CAREFULLY, as it does indeed demonstrate that these New Findings Challenge Established (Darwinian) Views On the Human Genome (while at the same time vindicating the IDers, some of which were mentioned above):
“The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. Our perspective of transcription and genes may have to evolve, the researchers state in their Nature paper, noting the network model of the genome poses some interesting mechanistic questions that have yet to be answered."
"Other surprises in the ENCODE data have major implications for our understanding of the evolution of genomes, particularly mammalian genomes. Until recently, researchers had thought that most of the DNA sequences important for biological function would be in areas of the genome most subject to evolutionary constraint that is, most likely to be conserved as species evolve. However, the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution, at least when examined by current methods used by computational biologists."
"According to ENCODE researchers, this lack of evolutionary constraint may indicate that many species genomes contain a pool of functional elements, including RNA transcripts, that provide no specific benefits in terms of survival or reproduction.”