Mike the Mad Biologist

I’m loath to call Scienceblogling Josh of Thoughts from Kansas out since he was one of my earliest linkers and readers, back when I was but a wee Mad Biologist; I probably wouldn’t have the readership that I have, in part, were it not for Josh. But Josh wrote something about Eric Lander that really pissed me off:

Lander’s work is very important, but the development of large-scale genome sequencing is largely a technical challenge, which scientists often distinguish from the challenges in testing our broad conceptual understanding of the laws of nature. While “test tube jockeys” often produce important results, there tends to be a certain skepticism of their work. Similarly, medical research is so focused on the practical application that scientists in other fields are dubious about regarding medical researchers as being engaged in the same sort of enterprise as a theoretical physicist or a landscape ecologist.

I call bullshit.

And it’s not because I’m some kind of ‘Lander groupie’–I believe I’ve talked with Lander once for about a minute. It’s the statements about genomics and the relationship between medically-oriented research and science. Onto genomics, then.

Is “the development of large-scale genome sequencing” a technical challenge? Of course it is. But science requires people who understand that to fundamentally change any field, you need to dramatically change the means and the scale by which data are collected and analyzed. Having been trained originally as a marine biologist, I find Josh’s description of Lubchenco (who is a “pure scientist” apparently) both odd and selling her short. In historical context, one of Lubchenco’s seminal contributions-perhaps her most important contribution to her field-was her recognition that experimental laboratory rigor-methodological rigor, in particular-could and must be used ‘out there’, outside of the lab. The only way we could begin to get a handle on ecological processes was if we had the methodologies (that is, technologies) to then apply to theoretical questions. And it goes without saying (or should anyway) that new methods transform fields by destroying old theoretical frameworks and requiring new ones.

Some of the genomics work I do (with many others) illustrates this. As I’ve mentioned before, I work on the human microbiome project. Because of the technical rigor that we and other major sequencing centers have brought to 16S rRNA characterization of microbial communities (really for the first time in the field’s relatively short history), we are now generating large datasets that will change how we analyze and understand microbial communities. Many of the assumptions made by microbial community ecologists in dealing with these data are inadequate, and were only found to be so because of the technical rigor and scale of the resources brought to bear.

That leads me to my next peeve, which is the claim that “scientists in other fields are dubious about regarding medical researchers as being engaged in the same sort of enterprise as a theoretical physicist or a landscape ecologist.” To use the above example, we can’t even do quality control (i.e., are we doing a good job of sequencing?) without doing rigorous community ecology (which is how we stumbled across the realization that many of the methods are bunk). Anyone who is doing ‘applied science’ without thinking about his or her problem just as a ‘pure scientist’ would isn’t doing good applied science. And the gains we make in medical microbiology (boo! hiss!) will change how ‘pure’ microbial ecologists will use the same methods and analytical tools to assess ‘real’ microbial communities.

But what I find truly disconcerting is that Josh, who works for the leading organization that combats creationism is willing to heap disdain on medical science. As I and others have argued before, the intersection between evolution and medical progress is one of the strongest arguments to the unconvinced about the utility of evolution (without repeating a whole bunch of posts, we already have many of the intellectually curious; it’s the rest that are the hard sell). In the field of microbial population genetics, the hundreds, if not thousands of bacterial genomes, many of which will deal with medically related organisms, will-not have ‘the potential’, but will revolutionize how we understand bacterial evolution ‘out there.’ The medical benefits are a bonus (and a life-saving one at that). Likewise, many of the gains in population genetics (and genomics) tools are a result of high-throughput medically-oriented research.

Trust me, Lander will be a very good friend to ‘pure science.’

Comments

  1. #1 Matt Hussein Platte
    December 22, 2008

    Plz change 2nd word to “loath” then delete this comment. KTHXBAI

  2. #2 Sigmund
    December 22, 2008

    Well I’ve talked to Lander for two minutes :p
    I think there’s a lot of research envy aimed at the genomics field due to the amount of cash its soaked up over the years. What some people don’t realize is that the Genome projects, while originally designed for a single specific goal, have resulted in huge spin-off benefits. New imaging and analysis technologies, new computing innovations, bioinformatics, disease analysis and prognostications. How about the discovery of whole new transcriptional regulatory pathways? And that’s even before we get to the evolutionary side of things where genomics has finally provided our own Rosetta Stone to follow the paths of descent from the smallest microbe to the tallest tree. Did the Manhattan Project or the Apollo missions come even close to the level of benefits to humanity that modern genomics is showing?

  3. #3 garance
    December 23, 2008

    Josh just got self-absorbed for a minute: it is not really him. In the 1950s, I knew a chemist who said that he despised people who worked “on big molecules” (I never forgot that), and then there was the long battle between “pure” and “applied” math, despite papers proving that there is no such distinction, as each feeds on the other. The head of the research institution where I worked once said that it was time for us to be “less selfish” and more involved in applied science. I wrote to him to ask if he would have cut funding to Galileo, and never got an answer. Long live genomics and don’t let any of this get to you: it amounts to territorial piss. Enjoy the holidays!

  4. #4 Ford
    December 24, 2008

    “More benefits to humanity than the Manhattan Project!” I’ll have to put that in my next grant proposal.

  5. #5 Greg Laden
    December 27, 2008

    He has a point. Researchers in the medical area are often disengaged with the theoretical core of biology, in a way that I think hinders their research. There are actually researchers in some areas who believe that evolutionary theory is not relevant to what they do, or can not inform or guide their work.

    I call THIS bullshit.

    It is possible that what I’m talking about is not what Josh is talking about, but I suspect it is at least related.

  6. #6 bizimlesohbet
    December 29, 2008

    nice site

  7. #7 Eleanore
    December 29, 2008

    I almost want to print out copies of this blog post to hand out whenever somebody starts trying to paint medical research and basic research as dichotomous and/or opposing entities.

    I think one of the most exciting things for me as a biologist was the realization that evolution is important, like really important, for just about everything. (Uh yes I’m an evolutionary biologist, why do you ask?)

  8. #8 dedektif
    July 25, 2009

    thanks admin

  9. #9 dış cephe
    July 25, 2009

    Great site.Thanks a lot.

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