The rebuttal to the ENCODE project’s claim to have vanquished junk DNA by Graur et al. got a lot of attention for its scathing rhetoric. If you already have enough troubles in your life, W Ford Doolittle penned a cogent, but polite rebuttal of the claim in PNAS.
…what would we expect for the number of functional elements (as ENCODE defines them) in genomes much larger than our own genome? If the number were to stay more or less constant, it would seem sensible to consider the rest of the DNA of larger genomes to be junk or, at least, assign it a different sort of role (structural rather than informational)…A larger theoretical framework, embracing informational and structural roles for DNA, neutral as well as adaptive causes of complexity, and selection as a multilevel phenomenon, is needed.
Unfortunately, you need a subscription to read the full length article, which I do not. Therefore, I’m not endorsing all of Doolittle’s arguments, but I do like that he seems to agree with my assertion from “Decoding ENCODE” that evolutionary theory expects junk DNA in species with the population and genomic characteristics of humans.
*Hat tip to Leonid Kruglyak.
Image of labeled (red) DNA breaks in a single cell courtesy of the Journal of Cell Biology
Do you ever think about how every time you encounter something new your brain adjusts and rewires and makes molecular changes so you can remember this new object in the context of what you already know? I know I do, though that may be a by-product of my neuroscience upbringing. Even if you don’t think about it, it’s happening. Complex changes in the numbers and amounts of gene expression are critical to developing and maintaining memories. And as it turns out, breaking the DNA in your brain cells into pieces is also part of the process.
Mike is very busy being an awesome scientist. So, I have the duty of reacting to the latest “ENCODE takedown” published by Graur et al in Genome Biology and Evolution: “On the immortality of television sets: ‘function’ in the human genome according to the evolution-free gospel of ENCODE”. The title kind of tells you that the ENCODE consortium has a snowball’s chance in Hell of coming out of this one looking good – not that the paper was written by unbiased critics. Continue reading
It is an unfortunate circumstance that ENCODE publicity decided to declare “junk DNA” dead, again. It’s not a totally unique position. Creationists and John Mattick have argued that there is no useless DNA for ages.
The demise of “junk DNA” is a fait accompli of the way “functional” is defined. It is not a definition of “functional” most of us would recognize. Ewan Birney, who should know, explains that when ENCODE says “functional” they mean “not biochemically inert in at least one of our many assays*”. As Mike has noted from his own research experience, many totally random DNA sequences synthesized in a tube are “not biochemically inert” nor are they biologically “functional”.
The fact is, if you only think of “junk DNA” as a problem, you aren’t seeing the forest for the trees – and you certainly are lacking a touch of poetry in your bleak soul. Continue reading
…where everybody knows their genomics. Bum bum bum.
Which is as far as I’m taking that, because I have the bad feeling that y’all would suggest that I’m the Cliff Clavin around here (I’m so the Carla).
Technology willing (let’s all take a long, suggestive look at Mike for a moment), we will be doing a live Google Hangout to talk about the ENCODE project tonight (Tuesday, 11 September) at 9PM Eastern. We’ll chat about what it means for science, “junk DNA”, and who (if anyone) actually knows what they are talking about.
Oh yeah, it is BYOB until we get that whole virtual liquor license thing sorted out.
*Leave a comment here or tweet @joshwitten or @finchandpea if you are interested and need a hangout invite.