Tuesday, July 02, 2013

Will There Be a Junk DNA Debate in Chicago?

Quite a few people think that there's going to be a serious debate about junk DNA at the SMBE meeting in Chicago next week. One of the sessions has a provocative title, "WHERE DID 'JUNK' GO?", but if you look at actual session titles it doesn't look like there's going to be much of a debate.

It's true than the session organizer, Wojciech Makalowski, advertised the session as a dicussion about junk DNA ....
Late Susumu Ohno once said "So much junk DNA in our genome" and the phrase junk DNA was born. For a long time mainstream scientists avoided these parts of the genome. However, over the years the picture slowly started to appear suggesting that the junk DNA hides a genomic treasure. With the completion of the current ENCODE project, junk DNA effectively disappeared because there's no longer useless DNA in the genome. This symposium will discuss the current understanding of these not-so-long-ago obscure areas of the genome, with special attention to transposable elements' activities and their evolutionary consequences. The integral part of the symposium will be general discussion of Ohno’s idea and its place in today's biology.
Most of the talks are just going to address some little bits of new functional DNA that their labs have discovered. The abstracts go out of their way to avoid taking a stance on whether most of our genome is junk.

Dan Graur is giving a talk about defining junk DNA.
Functional DNA, Junk DNA, Garbage DNA, and Indifferent DNA: An Evolutionary Classification of Genomic Constituents with Special Reference to the Human Genome
Dan Graur
University of Houston

It is relatively easy to classify genomic sequences by biochemical activity, such as transcribed elements, protein-coding regions, and transcription-factor binding sites. It is also relatively simple to dissect the genome into compositionally homogenous and nonhomogenous regions, or to ascribe vertical or horizontal origins to different fractions of the genome. However, it is much more difficult to classify the various elements within the genome according to their evolutionary import. Such a classification is needed to put an end to the confusion related to amount of junk DNA in eukaryotic genome. In devising an evolutionary relevant genomic classification, one must determine for each element its selected (or unselected) functions, and that determination requires an evolutionary analysis of the genome (either interspecifically or intraspecifically). We suggest distinguishing among four major evolutionary compartments within eukaryotic genomes: functional DNA, junk DNA, garbage DNA, and indifferent DNA. “Functional DNA” refers any segment of the genome whose “selected effect” function is that for which it was selected or by which it is maintained. The tell tale sign of selected function is purifying selection and the ability of point mutation to destroy function. “Junk DNA” refers to a genomic segment on which selection does not operate and which, hence, evolves under selective neutrality. “Garbage DNA” refers to sequences that are actively selected against. “Indifferent DNA” refers to sequences that are functional, but show no evidence of selection against point mutations. Segmental mutations at these sites, however, are deleterious, and are subject to purifying selection. They serve as spacers, fillers, and protectors against frameshifts. The evolutionary affiliation of a segment belonging to one evolutionary compartment may change into another. For instance, some junk DNA may be coopted into functionality (zombie DNA) and, similarly, functional DNA may become junk or even garbage DNA. However, the classification of any such a segment within the genome must only rely on past and present evidence and cannot presuppose teleological knowledge and potentiality.
I fear that this is going to get us bogged down in terminology rather than addressing the real issue; namely, is most of our genome junk?

I deliberately prepared a talk that will address the issue raised by Wojciech Makalowski in his summary of the symposium's purpose.
Evidence for Junk DNA
Laurence A. Moran
Department of Biochemistry, University of Toronto

Scientists have been debating the rationale and evidence for junk DNA since the early 1970s. Several powerful arguments in favor of junk DNA have emerged in those four decades. We now have considerable evidence to support those arguments and the controversy is close to a resolution. I will summarize the evidence for junk DNA leading to the almost inescapable conclusion that most of the DNA in our genome is non-functional by any reasonable definition of function.
Unfortunately, I only have ten minutes at the end of the session: 6:20-6:30 pm on the last day of the meeting.

There isn't going to be a debate.


1 comment :

  1. I suspect there will also be no debate about whether the world is round or about the atomic number of carbon. Do we really need a debate? What percentage of biologists, or even molecular biologists, or even members of the ENCODE consortium, actually believe the hype about the demise of junk DNA? (Serious question: I'm curious about numbers.)

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