Just because it's value is not understood, doesn't mean it will never be understood.
There are all things that ARE understood:
Transposable Elements: (44% junk)
DNA transposons:
active (functional): <0.1%
defective (nonfunctional): 3%
retrotransposons:
active (functional): <0.1%
defective transposons
(full-length, nonfunctional): 8%
L1 LINES (fragments, nonfunctional): 16%
other LINES: 4%
SINES (small pseudogene fragments): 13%
co-opted transposons/fragments: <0.1% a
a
Co-opted transposons and transposon fragments are those that have secondarily acquired a new function.Viruses (9% junk)
DNA viruses
active (functional): <0.1%
defective DNA viruses: ~1%
RNA viruses
active (functional): <0.1%
defective (nonfunctional): 8%
co-opted RNA viruses: <0.1% b
b
Co-opted RNA viruses are defective integrated virus genomes that have secondarily acquired a new function.Pseudogenes (1.2% junk)
(from protein-encoding genes): 1.2% junk
co-opted pseudogenes: <0.1% c
c
Co-opted pseudogenes are formerly defective pseudogenes those that have secondarily acquired a new function.Ribosomal RNA genes:
essential 0.22%
junk 0.19%
Other RNA encoding genes
tRNA genes: <0.1% (essential)
known small RNA genes: <0.1% (essential)
putative regulatory RNAs: ~2% (essential)
Protein-encoding genes: (9.6% junk)
transcribed region:
essential 1.8%
intron junk (not included above) 9.6% d
d
Introns sequences account for about 30% of the genome. Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA.Regulatory sequences:
essential 0.6%
Origins of DNA replication
<0.1% (essential)
Scaffold attachment regions (SARS)
<0.1% (essential)
Highly Repetitive DNA (1% junk)
α-satellite DNA (centromeres)
essential 2.0%
non-essential 1.0%%
telomeres
essential (less than 1000 kb, insignificant)
Intergenic DNA (not included above)
conserved 2% (essential)
non-conserved 26.3% (unknown but probably junk)
Total Essential/Functional (so far) =
8.7%
Total Junk (so far) =
65%
Unknown (probably mostly junk) =
26.3%
For references and further information click on the "Genomes & Junk DNA" link in the box
LAST UPDATE: May 10, 2011 (fixed totals, and ribosomal RNA calculations)
What made you think that all of that is not understood?
And the trend is moving in the direction of 100% every day.
Not really.
Ewan Birney?
Did you not see this - on his own blog, wherein he pretends to
discuss the 80% claim with himself:
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. ... 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. ...
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
rotein 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%....A conservative estimate of our expected coverage of exons + specific DNA
rotein contacts gives us 18%, easily further justified (given our sampling) to 20%
So using their actual data, and employing definitions of "functional" that means that the DNA does something that produces an effect (as opposed to just being able to be bound to), they could, under favorable assumptions, extrapolate the ACTUAL number to maybe 20%. And the best part:
Q. Ok, fair enough. But are you most comfortable with the 10% to 20% figure for the hard-core functional bases? Why emphasize the 80% figure in the abstract and press release?
A. (Sigh.) Indeed. Originally I pushed for using an “80% overall” figure and a “20% conservative floor” figure, since the 20% was extrapolated from the sampling. But putting two percentage-based numbers in the same breath/paragraph is asking a lot of your listener/reader – they need to understand why there is such a big difference between the two numbers, and that takes perhaps more explaining than most people have the patience for. 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.
IOW - it was basically marketing.
Oh, and you support an interview with Birnery with a .... story about the ENCODE releases that Birney played a part in...
Yeah, so, you have nothing.
