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« Clustering: Art or Science? | Main | Challenges of building communities online – Part 1 »
Wednesday
Sep122012

ENCODE versus junk Science or Hype?

Elsewhere in the mighty web, the blogosphere is alight with point and counter-point following recent news involving the ENCODE project. Some of it is getting rather hot.

Fighting about ENCODE and junk

A favorite "Devil's Advocate" of mine has been fairly active. Larry Moran's Sandwalk blog has some rather harsh things to say about scientific reporting and the whole ENCODE project.

The Story of You: Encode and the human genome – video where Larry writes:

The average person watching this video will think that ENCODE is the best thing since sliced bread. The hype is astounding, and totally unjustified considering that we haven't learned anything of fundamental importance from the ENCODE project.

One of his recent posts addresses the response from the "Intelligent Design" community.

ENCODE/Junk DNA Fiasco: The IDiots Don't Like Me

Anybody have a passionate opinion they care to share?

Maybe you can also declare if you are a Gouldian or a Dawkinsonian.

Reader Comments (3)

I'm too intoxicated by the heady mix of evidence, belief and marketing to respond immediately. It sure is exciting to engage in public discussion of science these days though...

September 13, 2012 | Registered CommenterDavid Lovell

Even the ENCODE people here at University of Washington, Seattle, make fun of the whole media machine that sprung into action and the somewhat gimmicky tools (iPad-app, interactive graphs) that are provided to justify the millions of dollar spent to the general public.

But what is the justification to the science community? While there are good arguments against money-burning exercises like ENCODE, HapMap, HGP (e.g. from Eisen) I don't think we can judge the value of the whole undertaking by the final release only. ENCODE published throughout the different stages and anyone who kept up with the literature will hence find little new in the 40-odd papers published, but that does not mean we would have made the same progress without ENCODE.

In my mind the real value comes from the interactions between the different (even rivaling) labs that are encouraged (forced) to work together by a central committee with a good (not necessarily the best) plan of where the different groups and their strength can contribute. So seemingly simple things like having to make programs/data compatible, comparing approaches, and engaging in constructive discussions outside your group has accelerated research and produced valuable findings along the way.

Knowing how to collaborate, I think, is the real benefit ENCODE has delivered at least for the contributing US- and UK-based labs -- but where does that leave Australia ?

September 14, 2012 | Registered CommenterDenis Bauer

Excellent points. I personally have no issue with BIG SCIENCE as part of the overall mix, and have some good things to say about ENCODE. Valuable data and well run program, high QC standards etc.

At a different level, however, there's a problem. <rant on> Their definition of "function" is non-functional. We know many mechanism of how genomes grow and big genomes are littered with broken transposable elements, we see them (the ones that haven't degraded beyond recognition). Yes, transcription is sloppy and lots of "Junk" gets translated. We knew that. Redefining "functional" to include things that we know don't matter gets in the way. Some of that transcription may well matter but ti should do so because we see an effect, not because we change definitions. </rant off>

September 14, 2012 | Registered Commenterwade hines
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