US presidential cancer forum

27 08 2007

Hillary Clinton is currently speaking at the Livestrong US Presidential candidate forum. The democrats are up today, while the republicans are up-to-bat tomorrow. Her thoughts are very inspiring, and one can only hope that if she is elected she holds true to her words. One interesting point, she said the Bush administration has declared a “War on Science”. More to come later …

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Structural genomics vs … the others

9 08 2007

There’s been some … communication … back and forth recently between those who support the Structural Genomics Initiative (i.e., received funding from the NIH for the protein structure initiative, or PSI), and those who, in so many words, think the PSI is a waste of resources.

For your reading pleasure:

a background article
Montelione GT. Structural genomics: an approach to the protein folding problem. Proc Natl Acad Sci U S A. (2001) 98(24):13488-9. [abstract/article]

an argument
Petsko GA. An idea whose time has gone. Genome Biol. (2007) 8(6):107. [abstract/article]

an indirect reply?
Liu J, Montelione GT, Rost B. Novel leverage of structural genomics. Nat Biotechnol. (2007) 25(8):849-851. [article]

I have to admit, I was excited to hear of the PSI when it was established in 2000, coincidentally the same year I began my graduate studies. Surely this would open up many research opportunities, in particular for structrual biologists!

Perhaps I was blinded by an intense blast of light, namely the “potential impact” hype, as I did not follow the PSI’s progress closely … that is, until I noticed this comment/article by Petsko.

Ouch!

Some scientists have argued that the PSI-1, which was funded between 2000-2005, produced structures of low-hanging fruit — structures that were easy to obtain, but did not significantly increase 3D structure/fold space. The PSI-2 (2005-2010) was a reformulation of the original PSI, designed to focus on more biologically relevant problems (taken from Petsko’s “article”):

  • to increase the number of sequence families with structural representatives, including families with high biological impact;
  • to continue methodology and technology development, especially for challenging classes of proteins such as membrane proteins;
  • and to facilitate the use of structures by the broad scientific community.
  • Petsko comments that

    “these goals are so squishy, it would almost be impossible not to meet them. Or for it to matter much if they were.”

    I think the blip of Petsko’s article sums it up quite well:

    “The $60 million a year in public money that is being spent on the Protein Structure Initiative is enough to fund approximately 100-200 individual investigator-initiated research grants.”

    It seems to me the PSI funding would be best appropriated to 100-200 individual scientists, rather than a handful of “PSI labs”. Why give funding for methodology and technology development to a small group of researchers, when there could be 100-200 individual labs working on solutions to hard structural biology problems?

    I wonder what the real biologists think about the PSI.