google genomics?

August 5, 2006 at 7:36 pm | Posted in research | 8 Comments

I went to a talk this week by Leroy Hood of the Institute for Systems Biology.  He talked about his group’s work on identifying genes that were involved in the pathogenesis of prion diseases (eg mad cow disease), but also about systems biology and Big Science in general.  The results he showed were pretty exciting, but I was most interested in the general discussion of different ways of approaching scientific problems.

Unsurprisingly, Dr Hood is a strong advocate for systems biology.  He talked about the need for sophisticated methods for measuring large numbers of outputs simultaneously, and about some very cool nanoscale systems that are currently being developed to do this.  His vision of the future of medicine is one where the optimal state of each protein and gene regulatory network is known, and any perturbation can be detected from a small blood sample and corrected with appropriate drugs.  This all sounds very exciting, but as someone working at the smaller end of big biology, and struggling to figure out how to deal with my (only a few) thousands of data points, my first thoughts were of the data management issues.
He mentioned that he’d met with Sergey Brin and Larry Page at Google, to discuss ways of handling such large amounts of data.  I’m sure Google is a good place to find the right kind of expertise, but I already have issues with letting Google have access to information about my internet usage, let alone trusting them with medical records…  There were understandably a number of concerned questions about the ethical issues that arise when such detailed information becomes available.  Dr Hood mentioned that physicists he’s spoken to have stressed the importance of thinking about the ethical implications of research, given their experience with research that led to the development of nuclear weapons.  Hopefully, biologists will learn from previous mistakes.

As I was listening, I thought of the other science bloggers who would probably have enjoyed the talk a lot.  Particularly, Dr Free-Ride for the ethical questions.  Alex Palazzo at The Daily Transcript also had a post a little while ago about the impact of “Big Biology” on science, especially for young investigators.  I commented then that I could see the value of funding large consortiums in order to accomplish projects that were larger than the scope of an average lab, but not as something that would produce the most innovative results (at least, that was what I was aiming to express).

I’ve been trying to reconcile that opinion, which I still believe in, with the fact that my project could easily be considered “big biology”, although I’m lucky to be getting in at the stage where the initiative is small enough that nobody is in danger of feeling like a cog.  Perhaps it depends on the definition of “big biology”.  Large consortiums that just allow PIs to expand their research empires without using dramatically different techniques definitely don’t seem like the best use of funding to me.  I do believe that individual labs offer great opportunities for innovation, but at the same time, systems biology approaches that allow you to get a sense of how a whole network fits together can also result in important discoveries and speed up the process of identifying key genes.  In this way, such systems approaches also create fodder for many smaller projects.  I think ideally, big biology and small biology would complement each other to build up knowledge of how organisms work on different scales, just as eg structural, biochemical and cell biological approaches can work together.  The challenge is obviously to find the right balance.

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8 Comments »

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  1. Dr. Hood is not the first to turn to Google with the problem that modern Genomics is a formidable challenge to “Information Technology”. It was reported (see in the news column of http://www.junkdna.com/new_citations.html) that Dr. Craig Venter has been negotiating with Google for well over a year by now.  The problem is not how to strike a deal, and certainly “money is not an object”. The problem is, how to find a business model that resolves the colossal problem of privacy. For one particular solution, see http://www.safedna.com

    Regards,
    Dr. Pellionisz
    pellionisz@junkdna.com

  2. Thanks for the links. I hadn’t heard about Google being involved in this kind of thing before, but I’ll be interested in following the story.

  3. To facilitate finding the “Google/Venter” and “Genomics and Big IT” articles, pls. use links:

    http://www.junkdna.com/new_citations.html#google_venter

    http://www.junkdna.com/new_citations.html#google_the_big_one

    In addition, the “Junk DNA news column” at http://www.junkdna.com/new_citations.html has a number of further articles on the cardinal issue of “Genomics and big IT”

    Regards,
    Dr. Pellionisz
    pellionisz@junkdna.com

  4. As a grad student in a lab that is increasingly a part of a Big Bio consortium, I certainly have mixed feelings. Sure the results possible for those involved could be great…but I need to have a thesis project, dammit! Which is necessarily something I conceive of and largely do myself–not a great fit in a Big Bio context.

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  7. This sounds good. Would like to discuss few ideas about novel algorithms and approaches. Looking for right people who can think out of the box.

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