junk DNA

Is Big Science Worth It? Debating the Brain Activity Mappping Project

The bad boy columnist for the life sciences is at it again. Bill Frezza is an unabashed libertarian venture capitalist based in Boston who pens a regular column over at Bio-IT World called the Skeptical Outsider. Though he’s invested in our industry, he’s undeterred from disparaging things the industry holds sacred, such as the War on Cancer or the Human Genome Project. He is emboldened by two major influences. First, he had some success in the IT industry and sees important lessons there for the life sciences.

Debating ENCODE Part II: Ross Hardison, Penn St.

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Ross Hardison, PhD, Professor of Biochemistry and Molecular Biology, Penn State University Bio and Contact Info

Listen (3:39) ENCODE has provided valuable data

Listen (3:36) Lineage specific selection

Listen (6:50) Looking for specific biochemical activities that are important

Listen (9:28) It's not so simple as big science vs small science

Listen (4:08) Have the critisicms changed your mind at all?

Listen (4:11) The debate itself a great outcome

In an earlier show, we interviewed Dan Graur and Michael Eisen about the ENCODE project, a massive research undertaking to further characterize the human genome. It’s been done by over 400 researchers at a cost of over $400 million. Both of the guests were quite critical of the published findings of the project and of big projects like this in general.

To represent the ENCODE project we're joined by Ross Hardison, a professor of Biochemistry and Molecular Biology at Penn State University and a collaborator on the ENCODE project from the beginning. Ross says he is delighted with the debate about how much of the genome is functional that the Graur paper has excited. And he makes a strong argument that the ENCODE team was focused on specific biochemical activities, and that these are important. He says Graur's charge on our previous show that the project might have called 100% of the genome functional because all DNA replicates, "just silly." He also says that Graur's and Eisen's rants about Big Science don't mean much to him. He considers himself a researcher funded by RO1's just as they are. It's not as simple as Big Science vs. Small Science. What was the goal of ENCODE and are they reaching that goal, we ask Hardison in Part II of Debating Encode.

Debating ENCODE: Dan Graur, Michael Eisen

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Dan Graur, PhD, Professor, University of Houston Bio and Contact Info

Listen (4:45) Active does not equal functional

Listen (3:44) ENCODE claims play into the hands of creationists

Listen (2:24) Big Science never accomplished anything

Listen (3:01) ENCODE should have claimed that 100 percent of genome is funtional

Listen (2:19) Why the strong tone?

Michel Eisen, PhD, Associate Professor of Genetics, Genomics and Development at University of California, Berkeley Bio and Contact Info

Listen (3:54) 80% claim, silly and disingenuous

Listen (3:30) Scientists responsible not the press

Listen (2:23) Is there an appropriate tone for scientific publications?

Listen (9:02) Big Science is a fundamental shift to Soviet style

Listen (4:56) BONUS: Why are you not happy with the White House response to Open Access Petition?

Last week, Twitter went ablaze with the hashtag #ENCODE. ENCODE (the Encyclopedia of DNA Elements) is a massive, multi-phase research project costing over $400 million done by over 400 researchers. Project findings, published last September in more than 30 scientific papers, were centered around the claim that though 80% of the genome doesn’t contain genes, it still plays a role in health. The media was quick to pick up on such a claim. The headline "Death of junk DNA" went around the world. Even Science Magazine was quick to issue the Eulogy for Junk DNA.

Now, a group led by Dan Graur, a professor from Houston University, have just published a paper criticizing the ENCODE project and their findings. The Graur et al critique is the third major paper to do so, but went more forcefully after the ENCODE claim that the genome is 80% functional. There were lots of tweets supporting the scientific validity of the Graur paper, but expressing disappointment with it's tone.

We're joined first on today's program by Dan Graur. If you didn't pick it up from the title of his paper (On the Immortality of Television Sets), Dan is an hilarious speaker, and leaves nothing to guesswork as to his position. He is clear on what constitutes "functional" in his view and replies to the charge that his tone was over the top mean.

We're joined next by Michael Eisen, the co-founder of PLOS, for a third party take. Eisen is equally blunt in his answers. He is heavily critical, not only of the ENCODE publications (agreeing more with Graur's definition of "functional"), but also of the ENCODE project in general. When asked about the appropriate tone for a scientific publication, Eisen answers, "the truth." He further surmises that the strength of Graur's tone is more than venom for one claim, paper, or even project. It is a frustration with the NIH over their priorities. A biology professor himself at UC Berkeley, Eisen feels that Big Science projects such as ENCODE and the recently announced brain mapping project are a fundamental shift that threatens molecular biology research in America.

We reached out to some leaders of the ENCODE project but unfortunately were not able to schedule any of them in time for today’s show. We hope to have one of them on soon.