My last thoughts on the media coverage of ENCODE

I’m interested in moving on to the science of ENCODE, and to put the media coverage behind us. My final thoughts on the subject are up at the Huffington Post: “A Genome-sized Media Failure:”

This was a fantastic opportunity for scientists and science journalists to explain to the public some of the exciting and important research findings in genome biology that are changing how we think about health, disease, and our evolutionary past. But we blew it, in a big way…

[The media] stories failed us all in three major ways: they distorted the science done before ENCODE, they obscured the real significance of the ENCODE project, and most crucially, they mislead the public on how science really works.

A few supplemental points:

1) You’ve got to read John Timmer’s excellent discussion of the media coverage, filled with more details.

2) The ENCODE consortium was well-run, produced high-quality data, and measured the right biochemical activities; and I’m very interested in seeing the results.

3) However, I’m not convinced that big science was the way to go here, nor am I convinced that this will become the one dataset to rule them all as the technology rapidly changes… which means you can justify an open-ended project that has no concrete end point.

4) My opinion in point #3 could of course be wrong, but it will take time to for that to become clear.

Keeping genomes small

We read this paper in my Eukaryotic Genomes class (more than 10 years ago…sigh). The paper suggests that you need to be proactive about getting rid of pseudogenes and transposable elements if you want to keep your genome small:

High intrinsic rate of DNA loss in Drosophila

DMITRI A. PETROV, ELENA R. LOZOVSKAYA & DANIEL L. HARTL

Nature 384, 346 – 349 (28 November 1996)

Differences in deletion rate may also contribute to the divergence in genome size among taxa, the so-called ‘C-value paradox’. Two reports find a positive correlation between genome size and intron size in a variety of taxa. In addition, the reduction in the intron size in birds, whose genome size is smaller than that of other tetrapods, has been inferred to be due to multiple separate deletions scattered along the introns. It is noteworthy that pseudogenes are much rarer in birds than in mammals. These results argue that differences in genome size among related organisms may be determined primarily by the variation in the genome-wide deletion rate, and not, for instance, by different rates of insertion of transposable elements.

The Art of Science: Courage Unmasked

Courage Unmasked, an art exhibit at the Katzen Art Center in Washington, DC, consists of 59 sculptures incorporating radiation masks previously worn by head and neck cancer patients.  Each radiation mask, made of plastic mesh, is heated and fitted individually to the patient prior to treatment so the head and neck can remain perfectly still, allowing the radiation to be precisely directed and avoid damage to healthy tissue.  Not surprisingly, many patients who have used these masks never want to see them again. “Some people run over them with cars,” noted artist Jessica Beels, one of the organizers of the exhibit.  But some donated theirs to be turned into works of art, which in turn will be auctioned off to support other cancer patients. Continue reading “The Art of Science: Courage Unmasked”

Do as we say, not as we did

In the recent Federation of American Societies for Experimental Biology (FASEB) Washington Update, there is a letter to NIH director Francis Collins that supports recommendations from the Biomedical work force working group’s recent report. The report recommends, among other things, shortening the average Ph.D. training time to five years, while increasing training in skills targeting scientific careers outside of academia. How practical would it be to implement these recommendations? Continue reading “Do as we say, not as we did”

Genome PR is OK

There was some criticism of this video out there, but I liked it. Given how little attention the average news reader/online browser is going to devote to genomics, I think this kind of thing is just right (except for the misleading throwaway line about junk DNA).

Sure, the video hypes ENCODE as biology’s latest, greatest, development, but nobody outside the scientific community is going to know the difference between ENCODE and all of the rest of us genome biologists anyway. So basically, the video us hyping all of us.