Monday, September 10, 2012

Was ENCODE Worth It?

Michael Eisen is in a good position to ask whether the $200,000,000 spent on the ENCODE project was worth the money: Blinded by Big Science: The lesson I learned from ENCODE is that projects like ENCODE are not a good idea.

Here's part of what he says.
As I and many others have discussed, the media campaign around the recent ENCODE publications was, at best, unseemly. The empty and often misleading press releases and quotes from scientists were clearly masking the fact that, despite publishing 30 papers, they actually had very little of grand import to say, today, about what they found. The most pensive of them realized this, and went out of their way to emphasize that other people were already using the data, and that the true test was how much the data would be used over the coming years.
I'm not in a good position to judge whether the American investment was worthwhile but I can echo Michael Eisen's point about the importance of the data. We didn't learn anything new about the functional organization of the human genome. The conclusion that was most often attributed to the ENCODE result; namely, that almost all the genome is functional, is wrong.

I think this is a case where the misleading publicity campaign, aided and abetted by Nature and science journalists, has backfired. It has caused many people like Michael Eisen to question the value of ENCODE. Such questions might not have arisen if the consortium hadn't tried to put an improper spin on their results.

I feel sorry for the hundreds of graduate students, postdocs, and PI's involved in the consortium. The importance of their work, and the years of effort it took, are being overshadowed by the decision of a few leaders to make claims about it that don't hold up to scientific scrutiny.

1 comment:

  1. Larry, they claim that %80 of our genome is functional. But I don't think that most of them are under selection. I still feel that most mutations are neutral. If %80 of our genome were functionally important we would have extinct. How much of percent of all mutations are neutral? You know, slightly deleterious mutations are more dangereous than lethal ones. Lethal ones are being eliminated quickly from the gene pool. Slightly deleterious mutations are more dangereous because in small populations, genetic drift may accumulate some very slightly deleterious mutations as if they are netral alleles. Accumulation of very slightly deleterious mutations over time can cause extinctions, mutational meltdowns and genome decaying. Every individual gets at least 50 mutations from parents, if most of the genome were functional, all of us would be genetically ill.