Science Caturday: Teh ENCAT Project

encat

Ubber 20% = 5% snuggles, 5% noms, 5% ebil and 5% catnip.  Moar interested in hoomin DNA? See Josh Witten’s latest post on the ENCODE project here.

LOL via Cheezburger.com

So I take it you aren’t happy with ENCODE…

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 “So I take it you aren’t happy with ENCODE…”

ENCODE, Astronomy, & the Future of Genomics

The ENCODE media fail was epic enough that it totally dominated the discussion when the results were released to the public. Now our collective fury has abated1, I’d like to talk about, not what ENCODE did, but what it might mean for how we conduct genomic research in the future.

ENCODE produced an unprecedented amount of data with unprecedented levels of reproducibility between labs. This data will be useful to researchers around the world for year to come. To do so, however, it commanded tremendous resources and marginalized the concerns of independent researchers. Can we harness the data collection power of these collective projects without destroying the creativity and risk-taking of individual scientists in the crucible of collaborative compromise? Continue reading “ENCODE, Astronomy, & the Future of Genomics”

Skeptically Speaking about ENCODE

The latest episode of Skeptically Speaking is out, where you can listen to host Desiree Schell talk to WIRED writer David Dobbs about Naomi Wolf’s latest book, and to your truly about the disastrous media coverage of ENCODE. Listen online, grab it in podcast form, or find on one of the many radio stations that carry the show.

A big thanks to Desiree and producer K.O. Myers for having me on the show, and helping me sound less incoherent than I might have.

I’ve got two clarifications on some dates I tossed out during the interview:

I said ENCODE has been going for at least five years. I was thinking of the post-pilot phase, which began in 2007, after the pilot phase publications. ENCODE itself began in 2003.

I said people have been studying transposable elements for at least 30 years. I had in mind the 1980 papers on selfish DNA by Orgel and Crick and Doolittle and Sapienza. But of course don’t forget that Barbara McClintock discovered transposable elements in the 40’s and 50’s, and won her Nobel Prize on the subject almost 30 years ago.

Has ENCODE redefined the meaning of ‘gene’?

While I’ve been criticizing how ENCODE has been hyped and spun, it’s useful to take a look at the situation from the perspective of someone within the consortium. Why are the ENCODE findings supposed to be so revolutionary?

John Stamatoyannopoulos, who has made some of what I see as the most unjustified statements to the press on the topic of ENCODE, lays out his views on the significance of ENCODE in this piece. (Genome Res. 2012. 22: 1602-1611)

He argues that the view of the genome emerging from ENCODE (and, I must emphasize, from the work of other scientists who have used and developed similar technologies, but are not part of the consortium), thanks to its unprecedented detail and global perspective, has radically changed our understanding of just what a gene is. (But have we ever settled on what is a gene?) Continue reading “Has ENCODE redefined the meaning of ‘gene’?”