ENCODE has its defenders!

You know I was really pissed off at the crap ENCODE was promoting, that the genome was at least 80% functional and that there was no such thing as junk DNA. And there have been a number of better qualified scientists (like W. Ford Doolittle and Dan Graur and many others) who have stood up and registered their vehement disagreement with that nonsense. But there are some who agree that the genome must be largely functional, like John Mattick. Larry Moran reminds me that Mattick is the author of this infamous chart, however, which is best known as the original Dog's Ass Plot.

baddiagram

That is so misleadingly dishonest it takes my breath away -- Mattick cherry-picked genome sizes to fit his curve. One of my cell biology labs involves teaching students how to properly construct a simple graph, and I think I'm going to include this figure as a bad example.

Well, Mattick has done it again. He has published a paper (how do these things get through peer review?) disputing the existence of large quantities of non-functional DNA, which is largely an attempted rebuttal of Graur's paper. It's a short paper, but painful in its contortions and extraordinarily poor arguments. Larry Moran has done an excellent job of tearing it apart — I think he needs to polish it up and get that published.

The worst part of the paper, though, is the concluding paragraph — you know, where most of us try to put the most important message of the work.

There may also be another factor motivating the Graur et al. and related articles (van Bakel et al. 2010; Scanlan 2012), which is suggested by the sources and selection of quotations used at the beginning of the article, as well as in the use of the phrase “evolution-free gospel” in its title (Graur et al. 2013): the argument of a largely non-functional genome is invoked by some evolutionary theorists in the debate against the proposition of intelligent design of life on earth, particularly with respect to the origin of humanity. In essence, the argument posits that the presence of non-protein-coding or so-called ‘junk DNA’ that comprises >90% of the human genome is evidence for the accumulation of evolutionary debris by blind Darwinian evolution, and argues against intelligent design, as an intelligent designer would presumably not fill the human genetic instruction set with meaningless information (Dawkins 1986; Collins 2006). This argument is threatened in the face of growing functional indices of noncoding regions of the genome, with the latter reciprocally used in support of the notion of intelligent design and to challenge the conception that natural selection accounts for the existence of complex organisms (Behe 2003; Wells 2011).

I'm sure the Discovery Institute staff are dancing in pirouettes of joy at getting a neutral or possibly favorable mention in a legitimate journal. It's not clear exactly what Mattick is trying to do here (lack of clarity is also a sin in science writing, let me remind you): either he's trying to pre-emptively slander his critics by impugning them with an ideological motive, or he's granting credence to Intelligent Design creationism. I'm inclined to think it's both; he's clearly trying to argue with the motives of Graur and others, but also, he's claiming, as the creationists do, that evidence of function for the highly variable component of our genome is a de facto argument for a purpose for that variation, and that evolutionary theory does not support the idea of a functional purpose for variation in the sequence of most satellite DNA, for instance.

But I would not argue that ubiquitious functionality is unlikely because it has consequences for our theories; it's wrong because of all the evidence that has been marshaled that most DNA is not there to serve a specific, selectable purpose for us humans.

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My little screed on junk DNA elicited some good feedback, including a comment from Dan Graur. In a somewhat ill-thought out rant, I implied that anyone who uses the term 'junk DNA' should be ostracized from the scientific community (or something along those lines). I restated my opinion in a far…
Last month, I wrote about the terrible botch journalists had made of an interesting paper in which tweaking regulatory sequences called enhancers transgenically caused subtle shifts in the facial morphology of mice. The problem in the reporting was that the journalists insisted on calling this a…
Some bio-bloggers are atwitter over an article by Wojciech Makalowski on Scientific American's website about Junk DNA. I'm a little late to the game because, well, I've been really busy looking at sequences to determine if they are junk DNA. Is it irony? Is it coincidence? Who cares? It's an…

In particular I don't think that if every last base-pair was occasionally transcribed (from both strands) that it proves much except that it's allot more like drunken sailors in there than most people seem to think. I mention it cause some people seem very impressed by the extent of the (once in awhile) transcription.

"Cells awash in useless RNA"

Transcription isn't dependent on the presence of a functional gene. It's a mess. It's not intelligently designed!

By David Marjanović (not verified) on 08 Aug 2013 #permalink

http://www.genengnews.com/keywordsandtools/print/3/32115/

That's a press release that doesn't cite any sources. It also acts as if regulatory DNA had been completely unknown – WTF?

There is almost daily news of important regulatory function in long non-coding RNAs posted here:

Yes, and more and more and more of these will be discovered. And all of them together will amount for at most a few % of the genome.

Over half of your genome consists of retrovirus corpses in all stages of decay, and much of the rest is just runaway slippage of the replication apparatus. Get over it.

By David Marjanović (not verified) on 09 Aug 2013 #permalink

The Discotute are on the case already: an article by one Jonathan M (maybe this is Jonathan McLatchie?) on the paper (http://www.evolutionnews.org/2013/08/john_mattick_on075241.html) concludes
"It is not every day that we encounter such a humble attitude from a scientist who is prepared to candidly acknowledge the substantial incompleteness in our understanding of the mechanics of evolution. Mattick's scholarly attitude is one that up-and-coming scientists would do well to emulate."

By Grumpy Bob (not verified) on 09 Aug 2013 #permalink

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If you take the time to watch this video, you will realize that evolutionary biologist have set back medical research into human diseases by probably 10+ years by dismissing the non-coding DNA as junk. Now that ENCODE has opened the door, we are finding that the dysregulation of lncRNA and other non-coding RNA is behind many major diseases.

http://www.youtube.com/watch?v=vg3qOuyfP9U

By whatjunk? (not verified) on 19 Aug 2013 #permalink

...what? The existence of regulatory RNA has never been denied, as far as I know. The question is how much of it there is, and the answer is: not much.

To repeat myself: Over half of your genome consists of retrovirus corpses in all stages of decay, and much of the rest is just runaway slippage of the replication apparatus. Get over it.

By David Marjanović (not verified) on 20 Aug 2013 #permalink

dismissing the non-coding DNA as junk

The last sentences from Larry Moran's post linked in the OP are seem strangely appropriate here:

You should also note that it's mostly IDiots who get confused about the difference between junk DNA and "non-protein-coding" DNA.

I find that very troubling.

Indeed!

are seem

Well, I blame the absence of a preview button.