Not really. As more study & testing continues, junk DNA is not junk...as it was predicted to be.
You keep flogging this dead horse. You must just keep reading the same creationist tripe about it or something, and never once bothering to check on the veracity of their claims..
And you clearly ignore what you are shown on here.
RE: the predictions of function in junkDNA
I won't bother with the history of the name 'junkDNA' - suffice it to say that the term originally referred to a specific subset of noncoding DNA.
As best I can determine, creationists claim that people like Dembski and Forrest Mims "predicted" function in junkDNA in the early 1990s.
This despite the fact that actual researchers had been predicting - and finding - function in some types of noncoding DNA 15 years earlier:
Cell. 1975
Feb;4(2):107-11
…. We propose that "junk" DNA in eucaryotes functions to maintain total DNA at an optimum concentration.
Or Zuckerkandl from 1981:
A general function of noncoding polynucleotide sequences
Abstract
It is proposed that a general function of noncoding DNA and RNA sequences in higher organisms (intergenic and intervening sequences) is to provide multiple binding sites over long stretches of polynucleotide for certain types of regulatory proteins. Through the building up or abolishing of high-order structures, these proteins either sequester sites for the control of, e.g., transcription or make the sites available to local molecular signals. If this is to take place, the existence of a 'c-value paradox' becomes a requirement. Multiple binding sites for a given protein may recur in the form of a sequence 'motif' that is variable within certain limits. Noncoding sequences of the chickens ovalbumin gene furnish an appropriate example of a sequence motif. GAAAATT. Its improbably high frequency and significant periodicity are both absent from the coding sequences of the same gene and from the noncoding sequences of a differently controlled gene in the same organisms, the preproinsulin gene. This distribution of a sequence motif is in keeping with the concepts outlined. Low specificity of sequences that bind protein is likely to be compatible with highly specific conformational changes.
But sure, creationists 'predicted' it.
And regarding the '
As more study & testing continues, junk DNA is not junk' assertion, I suppose you are still clinging to that early ENCODE paper, the one in which many co-authors distanced themselves and/or complained that Birney had dreamed up the 80% figure for no good reason...
This is from Ewen Birney's blog. He pretends to interview himself, in a sneaky attempt to admit that they were wrong in their claims by not totally admitting it.
ENCODE: My own thoughts - Ewan's Blog: Bioinformatician at large
Q. Hmmm. Let’s move onto the science. I don’t buy that 80% of the genome is functional.
A. It’s clear that 80% of the genome has a specific biochemical activity – whatever that might be. This question hinges on the word “functional” so let’s try to tackle this first. Like many English language words, “functional” is a very useful but context-dependent word. Does a “functional element” in the genome mean something that changes a biochemical property of the cell (i.e, if the sequence was not here, the biochemistry would be different) or is it something that changes a phenotypically observable trait that affects the whole organism? At their limits (considering all the biochemical activities being a phenotype), these two definitions merge. Having spent a long time thinking about and discussing this, not a single definition of “functional” works for all conversations. We have to be precise about the context. Pragmatically, in ENCODE we define our criteria as “specific biochemical activity” – for example, an assay that identifies a series of bases. This is not the entire genome (so, for example, things like “having a phosphodiester bond” would not qualify). We then subset this into different classes of assay; in decreasing order of coverage these are: RNA, “broad” histone modifications, “narrow” histone modifications, DNaseI hypersensitive sites, Transcription Factor ChIP-seq peaks, DNaseI Footprints, Transcription Factor bound motifs, and finally Exons.
Q. So remind me which one do you think is “functional”?
A. Back to that word “functional”: There is no easy answer to this. In ENCODE we present this hierarchy of assays with cumulative coverage percentages, ending up with 80%. As I’ve pointed out in presentations, you shouldn’t be surprised by the 80% figure. After all, 60% of the genome with the new detailed manually reviewed (GenCode) annotation is either exonic or intronic, and a number of our assays (such as PolyA- RNA, and H3K36me3/H3K79me2) are expected to mark all active transcription. So seeing an additional 20% over this expected 60% is not so surprising.
However, on the other end of the scale – using very strict, classical definitions of “functional” like bound motifs and DNaseI footprints; places where we are very confident that there is a specific DNA-protein contact, such as a transcription factor binding site to the actual bases – we see a cumulative occupation of 8% of the genome. With the exons (which most people would always classify as “functional” by intuition) that number goes up to 9%. Given what most people thought earlier this decade, that the regulatory elements might account for perhaps a similar amount of bases as exons, this is surprisingly high for many people – certainly it was to me!
In addition, in this phase of ENCODE we did sample broadly but nowhere near completely in terms of cell types or transcription factors. We estimated how well we have sampled, and our most generous view of our sampling is that we’ve seen around 50% of the elements. There are lots of reasons to think we have sampled less than this (e.g., the inability to sample developmental cell types; classes of transcription factors which we have not seen). A conservative estimate of our expected coverage of exons + specific DNA-protein contacts gives us 18%, easily further justified (given our sampling) to 20%
Wow - 20% is totally most of the genome! 20% = 80% via magic (to justify the billion-dollar price tag of the ENCODE project!).
But sure Hockey, you go on spouting about junkDNA function.... what with your amazing genetics background and all...