February 6, 2013

Considering grad school?

Read this first.

My students mostly study the evolution of cooperation, in systems ranging from legume cover crops to test-tubes full of evolving yeast. For example, why do symbionts like rhizobia invest resources in costly activities that help their host (and competing symbionts sharing that host) rather than using those resources for their own reproduction? PhD students Toby Kiers and Ryoko Oono found that, when a soybean or clover root nodule fails to fix nitrogen, the plant often imposes "sanctions" on the rhizobia inside, reducing their reproduction. But does that translate into lower fitness for rhizobial "cheaters?" Or do density-dependent effects equalize the number of rhizobia released into the soil? And how do the relative numbers of rhizobial cooperators and cheaters change during the months or years between hosts? Is the starvation-resistant "persister" form, discovered by PhD student Will Ratcliff, key to long-term survival in soil?

I am interested in a variety of topics, but prefer to have students work on something related to a current grant, so they can be supported more by a Research Assistantship, rather than having to work as a Teaching Assistant every semester. Getting some teaching experience is highly recommended, though. I have two grant proposals submitted on legume-rhizobia cooperation.

October 29, 2010

Join my lab?

I am mainly interested in the evolution of microbial cooperation, particularly by the symbiotic rhizobia that provide some crops and wild legumes with nitrogen. I have money in a current grant that could be used to support a new student working on legume symbiosis with "eusocial" rhizobia. Other student research and collaborations (especially with Mike Travisano) have extended from microbial bet-hedging and the evolution of aging and multicellularity (submitted) to applying ecology and evolution to improving agricultural productivity and sustainability.

October 20, 2010

Grad school application deadlines in December

If you're thinking about grad school next year, it's time to get serious. Application deadlines for the two grad programs I'm associated with are both in December. You might want to read my thoughts on who should go to grad school first, though.

If that didn't scare you away, I still have some money left to support a student to work on the first of these two grants. Other topics are possible, but it's nice to work on something for which your major professor has a grant. You may be able to support yourself in grad school as a teaching assistant, but what about money for supplies?

Prospective grad students must apply to the grad program. In my case that would be:
Ecology Evolution and Behavior or else Plant Biology. If you want to be taken seriously by any grad program, you also need to identify specific professors you might want to work with and contact them individually -- after reading at least two of their recent papers. If the papers seem boring to you, you will probably hate working in that lab. Look elsewhere!

July 31, 2009


Just as I was starting to dip into retirement savings to keep my lab going, we got word that both of the grant proposals we sent to the NSF in the latest round were funded, one of them with money from Obama's stimulus funding. We won't be paying ourselves any billion-dollar bonuses, but I may be able to get two months salary this year after all. Both proposals are resubmissions, significantly improved based on suggestions and criticisms from past reviewers. Both projects will use rhizobia, bacteria best known for providing legume plants with nitrogen, but the second project may have eventual applications in medicine (e.g., curing persistent infections) rather than agriculture. The summaries below are intended for a nonscientific audience, such as members of Congress.

"Suppression of rhizobial reproduction by legumes:
implications for mutualism"

(with Prof. Michael Sadowsky, largely based on ideas and preliminary results from grad student Ryoko Oono -- see this recent review article we wrote with Toby Kiers)

Rhizobia are bacteria that can live in soil, but also symbiotically, inside root nodules on plants like soybean or alfalfa. Although many rhizobia provide their host plants with nitrogen, saving farmers billions in fertilizer costs, less beneficial strains cause problems in some areas. Some hosts, including alfalfa and pea, make rhizobia swell up as they start to provide nitrogen. Unlike the nonswollen rhizobia from soybean or cowpea nodules, swollen rhizobia apparently lose the ability to reproduce, but does rhizobial swelling somehow benefit the plant?

To find out, the investigators will map this trait on the family tree for crops and wild plants that host rhizobia, to see if causing swelling evolved more than once, suggesting a positive benefit to the plants. Three dual-host rhizobia (plus mutants that differ in their ability to hoard resources) will be used to measure effects of rhizobial swelling on costs and benefits to the plants. Plant defenses against rhizobia that provide little or no nitrogen, already demonstrated in soybean, will be tested in species that impose bacterial swelling.

This research will increase understanding of a symbiosis that supplies nitrogen to agricultural and natural ecosystems, with implications for other important symbioses. Results could guide the development of crops that selectively enrich soils with the best rhizobia, decreasing future fertilizer requirements. Educational opportunities will be provided for undergraduates, at least one graduate student, and a postdoctoral researcher. Two female high school students have already won trips to the International Science Fair for research done in the principal investigator's laboratory, where such mentoring will continue to be a priority.

Evolution of persistence in the model bacterium, Sinorhizobium
(with Prof. Michael Travisano, largely based on ideas, preliminary data, and writing by grad student Will Ratcliff, with some ideas from Andy Gardner and colleagues -- see the second paper discussed in this post -- and possible relevance to our work on evolution of aging.)

Some bacteria can enter a nongrowing "persister" state that allows them to survive antibiotics and other treatments that normally kill them. By suspending growth, they may also free resources for their genetically identical clonemates.

Most species form only a few persisters. This makes persisters hard to study, despite their importance in long-term infections. However, certain harmless bacteria from plant roots can form up to 40% persisters. These will be used to determine whether persisters benefit mainly from enhanced stress resistance or by increasing the growth of their clonemates.

Successful completion of this research will provide two main benefits: First, this research will determine the conditions that favor the spread of persister-forming bacterial strains over nonpersister strains, and the genetic basis of persistence. This can provide direct medical benefits by aiding the development of novel management strategies, drug targets, and eventually treatments for patients infected with persister-forming bacteria. Second, some conclusions may apply to other species that are difficult to eradicate because they, too, form dormant, stress-resistant stages. These include many agricultural weeds and some species of mosquito. One key advantage of the proposed approach is speed: experiments that would take decades with weeds or mosquitoes can be conducted in months with bacteria. This research will provide training opportunities and jobs for undergraduates, high school students, and a post doctoral researcher.

I am planning to accept another grad student for autumn 2010.

July 20, 2009

Join my lab?

I hope to welcome one or possibly two new graduate students in autumn 2010.

As I noted on the Ecology, Evolution and Behavior web page, much of my research can be seen as following up on ideas first discussed by W.D. Hamilton. This includes our work on the evolution of cooperation (Nature 425:78-81) and on longevity-versus-reproduction tradeoffs as a possible explanation for the health benefits of eating low doses of plant toxins (PLoS One 4:e6055). Often, my grad students use crop plants and/or noncharismatic microfauna (bacteria, yeast, etc.), so if aesthetics is more important to you than science, choose a different major professor. I am also interested in agricultural implications of past and ongoing natural selection (Q. Rev. Biol. 2003 and forthcoming book), although I don't currently have any grant funding for this work.

I also accept students in the Plant Biology grad program, which has been unusually generous in financial support for grad students, providing first-year and summer stipends, paying for meeting travel, etc. (Budget cuts could change this.) Also, unlike most Plant Biology programs, their vision extends beyond molecular biology of Arabidopsis, with significant strength in evolution and in legume (especially Medicago) symbiosis. So students interested in plants should consider both programs.

June 21, 2007

Opportunity cost of grad school, etc.

Rob Knop liked my previous post. The comments on his post are well worth reading. For example, someone pointed out that, even if you don't go into debt to finance grad school, there's still usually an economic opportunity cost. During the years you spent in grad school and as a postdoc, you might otherwise be paying down a home mortgage, saving for retirement, etc., not to mention nonfinancial opportunities, like starting a family.

Terence Tao also has some good career advice,. It's aimed mainly at mathematicians, but much of it is relevant to science in general.

Continue reading "Opportunity cost of grad school, etc." »

June 20, 2007

Choosing a major professor

Advice sent to an aspiring grad student, without identifying particulars.

1) Don't use a generic subject line when contacting a prospective major professor. I almost didn't open your email, thinking it was probably spam. Snail mail with a stamp and handwritten address really stands out, but email with "reprint request" will probably be opened. Ask for a PDF of a paper or two whose abstract looks interesting, but you don't have full-text access.
2) Read the papers, plus others you can find on-line or in your nearest university library. You might also consider going to a relevant scientific meeting in addition to, but not instead of, reading scientific papers. The nice thing about a meeting is that you can ask questions and talk to people from lots of different labs all in one place. The problem with talks is that if something isn't clear, it's gone, whereas with a paper you can read it twice, think about it, look up relevant definitions, etc.
3) Do the papers (including the part about weighing 5000 seeds or chasing lizards in the rain) make you think "I wish I'd done that?" If not, look for another lab, that does make you react that way.

Continue reading "Choosing a major professor" »

June 19, 2007

Who should consider grad school in science?

This entry is inspired by "Why I got out of research" at and Rob Knop's blog entry Get out; you're not good enough , and is addressed to readers considering grad school in science.

There are more people qualified for faculty positions at research universities than there are openings. By "qualified" I mean having earned a PhD, done a postdoc, and published at least one senior-authored peer-reviewed journal article from each. By this definition, one can be qualified without necessarily being competitive in today's academic job market.

Those of us lucky enough to get such a research university position find that (as vwxynot put it):

"Even if you do make it big and get your own lab, you're suddenly responsible for your whole team's job security as well as your own. Grants depend on the quality of the researcher and their work, yes, but also on trends, fads, luck, nepotism, reputation, political interference and geography."

The importance of nepotism, politics, and geography probably varies among countries, but there's no doubt that only a fraction of good proposals get funded. And yet, getting grants is often an expectation for tenure.

So, if most PhD's won't get a research university faculty position (RUFP), then who should consider going to grad school in science?

Continue reading "Who should consider grad school in science?" »