Thursday, May 17, 2007

Calling all microbiologists - please help save the world

I read with dismay today news reports of the discovery that much of the Southern Oceans are saturated with CO2. This has happened much sooner than anyone anticipated and bodes very poorly for limiting the damaging effects of global warming. So I am starting a new call in my blog here

To all you microbiologists out there. Are you bored with what you are doing? Looking for something important and challenging to do? Sick of working on yet another human pathogen? Switch to working on a topic relating to limiting global warming and climate change (note if you want to learn more about global climate change check out the recent New Scientists article here which I found out about from the Davis Egghead Blog). Among the topics you could work on:
Any other suggestions for topics welcome.


  1. Good idea. Admirable even. But flippant...any thoughts on how a junior scientist working on those naughty human pathogens could switch careers with no published experience or record of funding in those fields? Seriously. How can this be done without career damage?

    All of these areas are heavily populated by scientists who have worked for years on these topics. I would be rightly massacred at any review panel for daring to engage in such dilettantism.

    It's like open source publishing - it's a lovely idea for those with established reputations who can afford to dabble wherever their restless tenured minds may lead them (and those tenured reputations are typically founded upon "evil" non-open-source journals I might add). But not realistic for the rest of us mere plebs...

    I need more coffee...

  2. OK, I did not think about how hard any of this would be to do in practice.

    I think the only way to really switch fields is to start slowly through collaborations or small projects. For example, I really wanted to get involved in doing symbiont genomics when I was at TIGR since I had worked on symbionts previously as an undergrad. So I kept badgering symbiont researchers that I would be their genome-slave if they would submit proposals with me. And eventually we got some funded. But in the mean time I had to work on whatever genomes were being done at TIGR, including some of those mind-numbing pathogen projects.

    Now that I have done 4-5 symbiont genome projects I think I could hold my own in a proposal. Although I must say, I prefer to do all things through collaborations anyway. I like the big scale collaborative projects.

    Right now I am using my start up money for my new job to explore an area I would really like to move into. If this fails I guess I could always move and burn another start up package trying (just kidding all you Davis people reading this).

    The exact details for how one would switch fields depend on areas of expertise. But if you work on pathogens, I would be willing to bet that just about anything you do could be switched subtly to working on saving the world. For example, protecting algae and plants from pathogens may be critical for C02 capture. Give me more detail on what you do and I will suggest more.

    As for open source publishing, I understand your plight and accept that it is much much harder for junior people to take what they view as a risk. Which is why we need to change the system - by creating quality OA journals (e.g., PLoS journals) and by rewarding people for publishing in OA journals (e.g., making it a part of tenure review, making it favorable for grant funding, etc).

  3. I will back that up by supporting the seeking out of collaborations as a way to make a switch. One's specialty can help or hinder cross-disciplinary is more the attitude of the individual wanting to do so (backed up by an idea that is good science). I am a theoretical physical scientist with some life sciences training, but first and foremost, most of my work is on the (biogeo)physics/climate side. Through emails, conferences and some downright badgering, I have forged some relationships with genomics folks, and now work and publish with this community, with numerous potential projects on the horizon. **hint: I am still waiting for an invite to Davis ;)**

  4. And I thought I was grumpy without coffee! :)

  5. OK OK - Michael I would like to invite you to give a talk at the Davis Genome Center --- and to meet with people at Davis and JGI to discuss environmental genomics. But hey - I did just have a baby (or well, my wife did) so you know - building these collaborations is not ALWAYS smooth sailing.

  6. Actually - want to comment on the first commenter's comment (heh) re: open access publishing.

    I sympathize but it's unfair to criticize folks who advocate open access publication on the basis that they built their reputations on closed journals. Before open access (B.O.?), there was no choice! It was the journal's way or the least there is a viable choice now. The important thing is that the viable open access choices retain credibility...

  7. ok, I will cut you some slack (but only because my kids are in school baby memories are still somewhat recent)

  8. It is indeed a bit unfair, but alas it is true also. There is no way around this. However, it is important to point out that there are a bunch of young scientists publishing in OA journals and I do not think their careers are harmed by this. I think they are helped.

    Nevertheless, some people are still afraid and rather than trying only to calm their fears (which I try to do), I also think we should accept that the fears do reflect some real problems and try and fix those. Now as for those established researchers who still refuse to try OA ... these people baffle me.

  9. So here's a question...does anyone maitain a current list of open access journals? There is a spectrum from the PLoS journals to the totally closed journals. Many are transitioning in some form to some flavor of open access...

    Maybe a rating system like a Best or Worst Dressed list?

  10. Jessica Green suggests I post a link to the recent AMNH symposium . As one of the co-advisors, I wish I could have gone to it, but was unable to due to other conflicts. If anyone out there went, I would love to hear more.

  11. Garry - the DOAJ link you post is very useful but it does not cover the intermediate OA journals. So it would be good to have that list somewhere. Maybe I will try to compile for a future blog.

  12. Yeah - a tabular list of all biology-relevant OA journals with a ranking that reflects the degree of "OA-ness" would be very useful...should also include some of the non-OA ones as well as a contrast...

  13. This site has a rating system based on publishers' copyright agreements. It has information on pre- and post-print archiving as well as OA compliance. It seems reasonably up to date.

  14. Did you submit your site at

    You can reach blogsearch by just typing in your browser window or click here

    This is a service by bizleadsnet directory of web logs.



Irresponsible reporting on "poop doping" from the Washington Post

UPDATE - see below - the author updated her article including some of my critiques. Went on a bit of a Twitter tirade last night. See mor...