Originally posted by Arbitrageur
From what I've read so far, the authors indirectly assert that the 80% figure is "not conservative" which is a sentiment echoed by various blogs by people that seem to know more about this than I do. In other words, a more conservative number would be lower than that at this point. This alone would seem to he reason to downplay the 80% number if even the authors themselves can't fully support it. But I'll know more after I read some of the papers, though that will take some time and I haven't done that yet.
Interestingly, even using the most conservative estimates, the fraction of bases likely to be involved in direct gene regulation, even though incomplete, is significantly higher than that ascribed to protein coding exons (1.2%), raising the possibility that more information in the human genome may be important for gene regulation than for biochemical function.
"We had to decide on a percentage, because that is easier to visualize, and we choose 80% because (a) it is inclusive of all the ENCODE experiments (and we did not want to leave any of the sub-projects out) and (b) 80% best coveys the difference between a genome made mostly of dead wood and one that is alive with activity. We refer also to “4 million switches”, and that represents the bound motifs and footprints.
We use the bigger number because it brings home the impact of this work to a much wider audience. But we are in fact using an accurate, well-defined figure when we say that 80% of the genome has specific biological activity."
Accounting for all these elements, a surprisingly large amount of the human genome, 80.4%, is covered by at least one ENCODE-identified element. The broadest element class represents the different RNA types, covering 62% of the genome (although the majority is inside of introns or near genes). Regions highly enriched for histone modifications form the next largest class (56.1%). Excluding RNA elements and broad histone elements, 44.2% of the genome is covered. Smaller proportions of the genome are occupied by regions of open chromatin (15.2%) or sites of transcription factor binding (8.1%), with 19.4% covered by at least one DHS or transcription factor ChIP-seq peak across all cell lines.
Birney himself admits the various definitions of "functional" and discusses some of the issues here along with different percentages:
Originally posted by squiz
You'll find the objections get down to splitting hairs over the word functional. ENCODE defines it as “specific biochemical activity”. Whatever that activity might be. You'll also find many of the objectors having a prior investment in Junk DNA.
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%
Originally posted by jiggerj
Originally posted by kennyb72
Why wouldn't the OP present the fact that this little nugget of information strengthens the case for creationism.
It does? All I see is that it strengthens the claim that there is no junk DNA. Plus, do creationists really want to lay the blame for the cancer gene on a competent creator? How about the faulty genes that cause mental retardation, deformities, and all the other genetic diseases. No, you guys don't want to go there.
edit on 9/9/2012 by jiggerj because: (no reason given)
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.
Originally posted by de_Genova
YO Pinke - Am I invited toooooooo?
FYI - Clear headed thinkers have always said that God doesn't make junk.......the criminal scientific atheistic community invented the term "junk DNA" to further their evolutionary nonsense - DNA and the human genome is the language of God - "THE WORD" - people like Dawkins and Hawking et al., in comparison produce "Gangsta Rap" - atheistic fools.........in denial of God's wonder of creation.
edit on 10-9-2012 by de_Genova because: pre-