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Junk Worth Keeping

Is it time to retire provocative descriptors such as "junk DNA"?

By | July 1, 2007

June 30, 1972, was a high point for the lexicon of biology. That day, Susumu Ohno coined (or at least publicly introduced) the term "junk DNA." In a talk titled "So Much 'Junk DNA' in our Genome," Ohno argued that the frequency of deleterious mutations restricts the number of serviceable genes to around 105 and that the great bulk of our DNA is merely the debris of failed duplication. "The earth is full of extinct species," he said. "Is it a wonder that our genome, too, is filled with the remains of extinct genes?"1

The phenomenon of junk DNA has unsettled the research community over the years, and it isn't a surprise that it originated with Ohno. He was a mischievous and brilliant thinker who made numerous contributions to genetics and evolutionary biology, and he was a wonderful writer.2

Still, not everyone agrees with that term's importance. Andras J. Pellionisz, to whom I am grateful for bringing this notable 35th anniversary to my attention, suggested that The Scientist publish an obituary to "formally abandon this misnomer." Pellionisz's objection is that scientific progress is being inhibited, and declaring junk DNA dead would align us with his own organization, the International PostGenetics Society (postgenetics.org), which disavowed the term on the 12th of October last year.

Pellionisz is not alone. No less a genetic eminence than Francis Collins writes in his 2006 book, The Language of God: A Scientist Presents Evidence for Belief: "A certain amount of hubris was required for anyone to call any part of the genome 'junk.'"

Gentlemen, I respectfully disagree. While I did start this editorial off with a working title of "The Life and Death of Junk DNA," a few hours of browsing convinced me that we've benefited from a classic "framing" of science. Framing is a recent proposal from Mat Nisbet and Chris Mooney3: When scientists engage the public they deliberately select, or frame, the information for the desired audience. Reaction from the research community, some of it rather negative, is tracked on Nisbet's blog.4

Those decades have been filled with fights over genome junkiness. In the late 1980's, opponents of sequencing the genome cited the preponderance of junk as one reason not to waste resources on the project. And when Celera joined the fray in 1997, it was claimed that they would quickly locate the diamonds in the rough (i.e., genes), bypassing the endless strings of junk that were being pored over by the poor old Human Genome Project. Postsequencing, with the horrifying realization of just how few genes we posses, the craze of "junk DNA" reached its zenith in the mass media.

It's been all downhill. Since, undermined by discoveries of the complexity of gene structure, the sophisticated nature of translational controls (which includes a role for Alu repeats, on the face of it the most meaningless junk of all), and the reach and scope of transposons. Recently, and damningly to the concept of junk, we've had the revelation of regulatory RNA networks.

The latest iniquity to befall junk DNA is the attempted hijack by proponents of Intelligent Design. Some of them would have us believe that their movement has provided the tools to find function in junk DNA. A withering critique by Pim van Meurs can be found on the Web site, The Panda's Thumb, along with an entertaining and educational thread of 150 or so comments.5

So should we call time on junk DNA? Perhaps we should use a more precise alternative: "DNA of yet-to-be-determined function?" Please, no. A huge amount of the action in terms of evolution and function is taking place in what was once considered junk. Bear in mind though, there is still a heck of a lot of the genome that has no apparent function.

More importantly, junk DNA works as a catchy moniker that helps frame the debate for the general public while evoking passionate debate among scientists. That's worth cherishing. The occasional burst of presumptuousness, raciness, and arrogance in our subject does us no harm. Let's keep things interesting.

rgallagher@the-scientist.com

References

1. B. Kuska, "Should scientists scrap the notion of junk DNA?" J Nat Cancer Inst, 90:1032?3, 1998. 2. http://content.karger.com/ProdukteDB/produkte.asp?Aktion=Ausgabe&Ausgabe=225343&ProduktNr=224037 3. M.C. Nisbet, C. Mooney, "Framing science," Science, 316:56, 2007. 4. http://scienceblogs.com/framing-science/2007/04/dont_be_a_dodo_bloggers_weigh.php 5. www.pandasthumb.org/archives/2007/04/uncommon_despai.html
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