Posted by: Kay at Suicyte | May 29, 2007

Weird research funding (I)

Obviously, research funding is run differently in different countries – not only with regard to the amount of money you will be able to get (or the chances that you get any), but also with regard to the scope of fundable projects. I guess that every major country has at least one funding agency responsible for various kinds of biomedical research. In addition, there are several funding opportunities with a more limited scope, e.g. restricted to projects in a particular disease area. As we all know, over a longer time period there is a good chance that research directions stray from the original path. It is interesting to observe what happens when there is the danger of leaving the area deemed acceptable by the funding body.

I have witnessed at least one major conflict of this type myself. Several years ago, I was working at a cancer research institute, which largely depended on money coming from cancer charities and from donations of cancer victims (or their relatives). At this time, there was a lot of high-level research going on at that place, in areas like genetics, cell biology, bioinformatics (I admit to being biased), virology, and others. Over the time, money started to run low, and at one point all PIs saw themselves confronted by a reviewing panel chaired by charity people, former cancer patients and wealthy relatives of cancer victims. Soon it became clear that the number of cancer cures made possible through research at this institute was extremely close to zero. The institute’s publication output, while quite good by national standards, tended to be in journals with words like ‘nature’, ‘science’ and ‘cell’ in the title, while ‘cancer’ titles were clearly underrepresented. Strangely, though, the researchers didn’t even feel bad about it. Finally, the research topics caused many raised eyebrows – several groups were working on yeast, which doesn’t even get cancer !

I should say that I am not taking sides here, the arguments from both groups made perfect sense. The money donors either had their own cancer experiences or at least represented people who had. They expected to get some ‘real’ cancer research for their money, not that basic research stuff that seemed to be going on in the institute. On the other hand, most groups had a quite good justification for what they were doing. The yeast groups were studying cell cycle and DNA damage pathways, which are obviously pertinent to cancer research. Obvious to me, this is, but not necessarily obvious to the charity people who expected to see tumor masses growing on petri dishes – possibly being magically shrunken by some wonder drug (the tumors, not the dishes). I am not totally sure how this discussion ended – I left the institute while the battle was still raging. But when I looked it up recently, I found that most of the yeast groups are still there, so I guess they must have found a solution.

At other places, things seem to be quite different. It happens quite frequently that I see papers acknowledging funds from sources that make me wonder: why the heck are those guys are giving money for this kind of project? It always has been a mystery to me why of all things the US Department of Energy runs its own genome sequencing center. A while ago, I think I read a statement by somebody saying that the DoE plans to exploit strange microorganisms for energy generation or such. However, when I look at their latest sequencing projects, I ask myself who suggested that Xenopus tropicalis or Nematostella vectensis could be useful for that purpose.

Today, I saw an even stranger example. DARPA, the research agency of the US Department of Defense (DoD) seems to be funding a program for identifying and studying the Fundamental Laws of Biology. To give you an impression of what this project is about, here is a quote from their web page:

The initial phase of the Program focuses on identifying key fundamental problems in biology and promising innovative mathematical techniques to approach these problems. Later phases will translate this new mathematical language into testable theories of biological phenomenon with the goal of establishing fundamental, predictive laws of biology.

It is probably hard to go more basic in the way of basic research. I cannot help it, but I find the thought of US defense researchers tackling the ‘fundamental laws of biology’ kind of scary. I also wonder how the scientists convinced the DoD to allocate money for this project from their tight budget, instead of doing useful things like defending homeland security or …. (I deleted several nasty comments here, because I vowed to not talk politics on this blog) . But wait, here is the rationale, right on their web page:

The Program will impact DoD and national security by developing a rational and predictive basis for doing biological research to combat bioterrorism, maintain healthy personnel, and discover new vaccines and medicines.

Ok, this explains everything. Combating bioterrorism and maintaining healthy soldiers through fundamental laws of biology. What a brilliant scheme. But again, there is no doubt about it: a dollar spent on fundamental biology is better than one spent on combating Iraq.

P.S. The project acronym “FunBio” also strikes me as strange in a DoD context.

Note added in proof: Tree of Life blogger and Open Access advocate Jonathan A. Eisen seems to be involved in FunBio, maybe I should ask him about the connection between fundamental laws of biology and national security.

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Responses

  1. Well, where to begin with this one. Here are a few comments:

    1. DOE sequencing center.

    The world of science funding is baffling if you actually stop to think about it. Why NIH does this or NSF does that or DOE does this is not always easy to figure out. DOE is perhaps the most enigmatic, as they were the ones who started the human genome project, at least on a big scale.

    Much of what is done at the DOE sequencing center (JGI, or the Joint Genome Insitute) is DOE mission related these days (more so than the human genome was). You can question the mission itself, but most of their sequencing now is of organisms that can serve as biofuel sources, or may be used in bioremediation, or may have some connection to energy production (e.g., hydrogen producing bacteria). So for DOE to have its own sequencing center is not surprising given that sequencing is central to much biology research and DOE funds a lot of biology research.

    2. DARPA FUNBIO.

    This one is hard to answer/address without getting into political discussions which you wisely try to avoid. I personally would rather see all agencies funding more basic science and when DARPA does this, if it takes any money away from other types of research (e.g., bomb development), who knows. What I do know is this FUNBIO project is the most interesting scientific program in which I have ever been involved. Basically, we have been charged with finding areas of biology where they may be unexplored “laws” (you know, like F=MA for physics … we told them there would not be laws like this in biology but they wanted us to go ahead and look for laws anyway). And then we are supposed to get biologists together with mathematicians and see whether we can formulate the laws more precisely and if (as they hope) some new math and new biology will come from trying. While I woudl not say if any completely new laws have been discovered as part of this program, there has been some interesting biology and math to come out of it. The key to me is that through a bit of a self- selection process the program identified biologists and mathematicians who were interested in working on each others problems.

    As for myself, I am working on one small project in this on metagenomics – basically how can you identify an organims from a small fragment of its genome. There are obvious dark and nefarious potential uses for such methods but such methods will also be of great use in metagenomics in general. And these could in fact be of use in some of those things they list on their website as goals of the program. For example, metagenomics is in essence being used as a component of some of the “biodetectors” that screen for nasty bugs in various locales. A better theoretical underpinning for metagenomic analysis would make this work better.

    It is late now – I will try to write more about FUNBIO later. As for the acronym, I do not know when they came up with it – I just know between what was I think our first and second workshop in the planning stages of this – the acronym appeared.

  2. Jonathan, thanks for this comprehensive explanation! I am not sure if it became clear from my original post: I am quite happy that the DoE runs this sequencing center, as many of the data the generate and make available through the internet has been extremely useful for me (and probably for lots of others, too). I also think that they have a quite interesting selection of organisms, e.g. I think it is a excellent idea to sequence a choanoflagellate like monosiga. I was just thinking that if I were in charge of US energy, I probably wouldn’t run a sequencing lab.

    With regard to the FunBio: project: I could think of much worse bioscience programs that might be run by places like the DoD. The main reason for mentioning this was the stark discrepancy between the immediate goals of the project (finding fundamental laws of biology) and the envisaged application areas (fighting bioterrorism and keeping personnel healthy). This goes to illustrate the “bending over backwards’ that has to be done to justify a research project. The thought that the DoD sponsors something called “Fun Bio” also struck me as, eh, funny.

    In the case of metagenomics, I can see a potential link to national security and health. If I try hard, I can also think of potential connections to fundamental laws of biology. However, it appears that the security aspects of metagenomics are quite different from the fundamental aspects, and it is hard to imagine working on both aspects at the same time. In any case, I agree with you that I rather see the DoD spending money on fundamental science than on building new bombs.

  3. Yes, certainly, connecting the fundamental aspects of “FUNBIO” and the security aspects is not straightforward. But DARPA is charged with doing this exact type of thing – risky research that no other agency will work on in essence. And my impression is, that, as long as their is some potential major reward, they might be interested. In terms of metagenomics, it is remarkable to me how closely connected the fundamental and applied are. In this case, we have a few issues that set up the project well:

    (1) many people view metagenomics as a powerful tool in microbial forensics studies as well as in human health studies (both things DOD is interested in),

    (2) metagenomic analysis is very very very hard to do well,

    (3) one of the biggest difficulties in metagenomics is taking the fragmentary data one gets (basically, in most cases you get shotgun sequence data from environmental samples) and assigning fragments to “bins” that correspond to organisms (for more see my paper in PLoS Biology )

    (4) better math will unquestionably help us do this better

    (5) if we figure out how to do this binning, we should learn something about the intrinsic information content of DNA, and about how organisms shape their genomes, which I view as ‘fundamental” things

  4. The Department of Energy’s role in sequencing stems from it’s interest in radiation (like from A- and H-bombs), and the effect on DNA. Ever since the bomb, DOE has had an interest in defining what “normal” DNA is, in order to better understand what isn’t.

    But beyond that, the first inklings for the concept ultimately known as the Human Genome Project came from DOE scientists (around 1984), and a DOE conference in 1986 really kicked things off. [NIH established it’s National Center for Human Genome Research in 1989.]

    Technological and sociological arguments also were at work. DOE had big “mission oriented” labs, and in particular, had instruments that could sort chromosomes, which made them easier to study. NIH, on the other hand, was traditionally the place where independent investigators running small university-based labs went for funding. But I guess the genome has been big enough for the both of them …


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