Well, the main point I made in #45 was that the study described only found around 10 thousand short sequences of DNA (among the approximately 95 percent of mammalian that doesn't code for proteins) that, because their sequences are broadly "conserved" across mammalian taxa, presumably have some function. This leaves 99.whatever percent of "junk" DNA with no known function, and no specific reason to believe it has a function (or, more precisely, no function that depends on sequence specificity).
This reveals that your headline commentary -- "'Junk' DNA not junk at all" -- was highly misleading. Saying "at all" suggests that "junk" DNA in general has been found to have a function. But neither the current study, nor any other, has found anything of the sort. Finding that very small portions of previously presumed "junk" DNA aren't "junk" after all is nothing like undermining the notion that large portions of the DNA remain with no (sequence dependent) function. It's something like, indeed almost exactly like, finding a needle in a haystack and then claiming that there's no hay 'cause it's all needles.
The other point was that the only reason for presuming that these sequences have functions is that they are preserved across mammalian taxa, i.e. across VERY broad MACROevolutionary distances. IOW the entire force of this argument is based on assuming that ALL mammals are related by evolutionary descent. Which is a claim you utterly reject. So you have no basis for affirming this finding.
Finally, a subsidiary point I didn't make previously: The study described doesn't actually demonstrate any particular function for these sequences. It hypothesizes a function for a few thousand of these 10 thousand sequences based primarily on their proximity to coding regions and their resemblance to transposons.
In any other context you would ridicule this as gratuitous and even dishonest evolutionary speculation. Your use of it then is hypocritical as well as baseless.
ping to preceding...
“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.”
http://www.sciencedaily.com/releases/2007/06/070613131932.htm
Neither did you respond to the fact that the Church of Darwin has been using the idea of junk DNA to disparage ID scientist, whereas IDers have been predicting this turn of events for years. I will post it here again for your convenience:
I think a little history is in order. First, let me quote two high priests from the Church of Darwin on “junk” DNA:
“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 there’s lots more DNA that doesn’t 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 doesn’t 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.”
—Michael Denton
“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