It's really sad that much of the public get their scientific beliefs from misleading press releases that lead to utterly incorrect headlines and articles like this, and the ENCODE consortium should be ashamed of themselves. They've done lots of damage that many other scientists will have to spend time and effort to correct.<p>splatterdash posted a link to an excellent summary of the problems in this thread, and I'd add a couple more links: <a href="http://www.michaeleisen.org/blog/?p=1172" rel="nofollow">http://www.michaeleisen.org/blog/?p=1172</a> and <a href="http://www.forbes.com/sites/johnfarrell/2012/09/07/reports-of-junk-dnas-demise-have-been-greatly-exaggerated/" rel="nofollow">http://www.forbes.com/sites/johnfarrell/2012/09/07/reports-o...</a>
There has been a lot of buzz in the (scientific) twitter/blogo-sphere regarding this. The main point of contention is essentialy the % of functional element ENCODE annotates. As it turns out, their criteria of denoting a DNA element as 'functional' is debatable (i.e. a DNA sequence with biochemical activity). These elements when deleted from the genome often has no visible phenotypic change to the organism (us), which is why the % they put is believed to be way too much.<p>Here's a recent excellent blog post on the issue, in readable form to the layman: <a href="http://selab.janelia.org/people/eddys/blog/?p=683" rel="nofollow">http://selab.janelia.org/people/eddys/blog/?p=683</a>
Sorry, but it was obvious to me for years.<p>DNA is a program. Programs contain data and code. They also contain all sorts of control sections. This stuff is there for a reason and we should think by default that genetic code will have those too.<p>(For those who think DNA is not a program because it is environment and state dependent - sorry, computer programs are very adaptable beasts too)<p>Another frequent misunderstanding - any running program looks like it has most of its code never used. This is false, because code falls under 90%/10% law. 90% of code is needed 10% of time. The time for those "dead" genes will come more often than not, and they will fire.
This is far from a revelation, and this article is just popularizing what has been known for [at least] the past 2 decades. Several scientists have built their careers on studying so-called "junk DNA" since the 1990s. See Jurka 2007:<p>"Eukaryotic genomes contain vast amounts of repetitive DNA derived from transposable elements (TEs). Large-scale sequencing of these genomes has produced an unprecedented wealth of information about the origin, diversity, and genomic impact of what was once thought to be 'junk DNA.'"<p><a href="http://www.ncbi.nlm.nih.gov/pubmed/17506661" rel="nofollow">http://www.ncbi.nlm.nih.gov/pubmed/17506661</a>
Reminded me of something I read in an article "The Insanity Virus" a few years back.<p>><i>If our DNA were an airplane carry-on bag (and essentially it is), it would be bursting at the seams. We lug around 100,000 retrovirus sequences inside us; all told, genetic parasites related to viruses account for more than 40 percent of all human DNA. Our body works hard to silence its viral stowaways by tying up those stretches of DNA in tight stacks of proteins, but sometimes they slip out.</i><p>HN discussion: <a href="http://news.ycombinator.com/item?id=1938618" rel="nofollow">http://news.ycombinator.com/item?id=1938618</a>