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Friday, June 28, 2013

John Mattick on the Importance of Non-coding RNA

John Mattick is a Professor and research scientist at the Garvan Institute of Medical Research at the University of New South Wales (Australia). He received an award from the Human Genome Organization for ....
The Award Reviewing Committee commented that Professor Mattick’s “work on long non-coding RNA has dramatically changed our concept of 95% of our genome”, and that he has been a “true visionary in his field; he has demonstrated an extraordinary degree of perseverance and ingenuity in gradually proving his hypothesis over the course of 18 years.”
I wrote an lengthy post explaining why this award was not justified [John Mattick Wins Chen Award for Distinguished Academic Achievement in Human Genetic and Genomic Research]. I don't think Mattick is correct. Here's are some of the reasons why: [How Much Junk in the Human Genome?] [Genome Size, Complexity, and the C-Value Paradox] [Basic Concepts: The Central Dogma of Molecular Biology].

Mattick is interested in the evolution of complexity. For example, he wants to know why humans are much more complex than nematodes. Mattick was one of those scientists who expected that the human genome would contain many more genes than the nematode genome in spite of all evidence to the contrary [see Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome]. When the human genome sequence was published he was shocked to learn that humans had the same number of genes as most other multicellular organisms. I refer to this as: The Deflated Ego Problem.

& Junk DNA
Scientists have come up with many ways of explaining the apparent discrepancy between complexity and the number of genes. The correct explanation is, of course, that the differences between nematodes and humans are more apparent than real. Only a small number of extra genes are required to make a human and the rest is mostly due to regulation by transcription factors at the level of transcription initiation.

Mattick doesn't think this is correct. He believes that the secret lies in "junk" DNA. His preferred explanation is that most non-coding DNA is transcribed to produce thousands of small regulatory RNAs involved in controlling the expression of the protein-coding genes.

John Mattick achieved a certain level of notoriety when he published a paper in Scientific American back in 2004. He claimed that complexity correlates with the amount of non-coding DNA in the genome and he illustrated this idea with the famous figure shown on the left.

This is the figure that Ryan Gregory labeled Dog's Ass Plot. Read his post to find out how many ways it is wrong.

Mattick is one of the most vocal opponents of junk DNA. He explains his point of view in the video (below). There's a transcript on the BMC Biology website at Non-coding RNAs and eukaryotic evolution - a personal view. Do you find his arguments compelling?

Mattick, J.S. (2004) The hidden genetic program of complex organisms. Sci Am. 291:60-67.


Pedro A B Pereira said...

He forgot to put the Amoeba genome there to the right of the human, and make it 100 times bigger than the human bar.

Mikkel Rumraket Rasmussen said...

My head is exploding by the amount of ad-hoc reasoning these people engage in. People just can't seem to let go of an idea once it sets in.
Time and again the evidence runs contrary to their expectations, and so they hypothesize and they speculate. Now, in and of itself that's fine, it's part of science. But how many failed predictions are you prepared to go through and still uphold this constantly wrong belief you came to decades ago? Hypothesizing is one thing, recurrent ad-hoc reasoning in the face of the facts is another.

Somebody needs to formalize a "recurrent loop" counter that halts the process once sufficient amounts of failed rationalizations have accumulated and get it worked into the scientific method.

Diogenes said...

Wow. Fake a plot, win an award.

Are people-- not just creationists-- so damn insecure that they'll believe any old hooey that makes them feel superior to critters? Is it so damn important that we have to keep inventing hoaxes like "functional alternate splicing", "translation regulation by super-low abundance RNA transcripts" and 3 hundred million regulatory elements in the human genome, just to make us feel superior to the damn dog?

Can we be manipulated by FLATTERY that easily?

John Harshman said...

What I find most interesting is that the range for chordates is apparently very small and doesn't include vertebrates, and that the range for vertebrates doesn't include humans. Looks like special creation.

chemicalscum said...

Wow! Those onions must be the the pinnacle of creation/evolution!. Yup it's the old Great Chain of Being idea.

John Harshman said...

By the way, I'm thinking that the slanted tops of some of the bars are an attempt to characterize the range of genome sizes in the taxon, the left edge being the small extreme and the right edge bing the large extreme. Of course under any interpretation the numbers are absurd.

Ron Maimon said...

John Mattick is the most maddening hero in biology. I wish that he didn't exist, only so that I could say what he was saying. The author of this article is obviously incompetent to do science.

Ron Maimon said...

I read your comment, and I can't figure out who you are criticizing, Mattick or his mentally deranged opponents?