Dark Matter Is Real, Not Just Noise or Junk

UPDATE: The title is facetious. I don't believe for one second that most so-called "dark matter" has a function. In fact, there's no such thing as "dark matter." Most of our genome is junk. I mention this because one of the well-known junk DNA kooks is severely irony-impaired and thought that I had changed my mind.

A few hours ago I asked you to evaluate the conclusion of a paper by Venters and Pugh (2013) [Transcription Initiation Sites: Do You Think This Is Reasonable?].

Now I want you to look at the Press Release and tell me what you think [see Scientists Discover the Origins of Genomic "Dark Matter"].

It seems pretty clear to me that Pugh (and probably Venters) actually think they are on to something. Here's part of the press release quoting Franklin "Frank" Pugh, a Professor in the Department of Molecular Biology at Penn State.

The remaining 150,000 initiation machines -- those Pugh and Venters did not find right at genes -- remained somewhat mysterious. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant since they did not code for proteins." Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylation -- a long string of genetic material, adenosine bases -- that protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.

"These non-coding RNAs have been called the 'dark matter' of the genome because, just like the dark matter of the universe, they are massive in terms of coverage -- making up over 95 percent of the human genome. However, they are difficult to detect and no one knows exactly what they all are doing or why they are there," Pugh said. "Now at least we know that they are real, and not just 'noise' or 'junk.' Of course, the next step is to answer the question, 'what, in fact, do they do?'"

Pugh added that the implications of this research could represent one step towards solving the problem of "missing heritability" -- a concept that describes how most traits, including many diseases, cannot be accounted for by individual genes and seem to have their origins in regions of the genome that do not code for proteins. "It is difficult to pin down the source of a disease when the mutation maps to a region of the genome with no known function," Pugh said. "However, if such regions produce RNA then we are one step closer to understanding that disease."

I'm puzzled by such statements. It's been one year since the ENCODE publicity fiasco and there have been all kinds of blogs and published papers pointing out the importance of junk DNA and the distinct possibility that most pervasive transcription is, in fact, noise.

It's possible that Pugh and his postdoc are not aware of the controversy. That would be shocking. It's also possible that they are aware of the controversy but decided to ignore it and not reference any of the papers that discuss alternate explanations of their data. That would be even more shocking (and unethical).

Are there any other possibilities that you can think of?

And while we're at it. What excuse can you imagine that lets the editors of Nature off the hook?

P.S. The IDiots at Evolution News & Views (sic) just love this stuff: As We Keep Saying, There's Treasure in "Junk DNA".

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Venters, B.J. and Pugh, B.F. (2013) Genomic organization of human transcription initiation complexes. Nature Published online 18 September 2013 [doi: 10.1038/nature12535] [PubMed] [Nature]

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