jeff smith

While putting my Myxo work together into a talk, and trying to present it all with some semblance of coherence, I had the opportunity to think about where the evolution of microbial cooperation is as a field and where I think it should go.  The way I see it, the most important open are these:

Is shared genes the primary evolutionary mechanism maintaining cooperation in microbes? By shared genes I mean that the benefits of cooperation are preferentialy experienced by individuals who also share the alleles for expressing the cooperative trait.  This process can be described as kin selection or group selection.  Shared genes is widely thought to be the primary mechanism for the evolution of cooperation in animals—is it true for microbes, too?  And what role do other mechanisms like enforcement, direct benefits, or pleiotropic constraint play?

What is the primary cause of genetic correlations among individuals? Limited dispersal, kin recognition, green-beard genes, infectious gene transfer, or something else?  Do cooperative traits themselves create genetic correlations through their effect on migration and motility?  The important part of these questions is getting at what IS happening, not just what CAN happen.

How does social evolution shape microbial traits? Many traits seem to involve interactions between individuals (quorum sensing, biofilms, and so on), but are these traits cooperative in the evolutionary sense of increasing the fitness of other individuals?  How does the magnitude, regulation, or form of these traits differ from that what they would evolve to be if they did not have social effects?  To what extent do microbes actively alter their behavior in response to social conditions?  Which traits are adaptations and which are only side-effects of some other function?

How do social traits change over evolutionary time? Are social traits under stabilizing selection or do they evolve in evolutionary arms races?  How often are they lost?  If cheaters occur in natural habitats, do they persist because of selection or recurrent mutation?

What are the origins of microbial cooperation? What traits were co-opted into becoming the building blocks of cooperation?  Worker behavior in social insects, for example, is a modified form of maternal behavior.  Are the benefits of cooperative traits the same now as they were originally?  How many times have similar cooperative traits originated?  Are cooperative traits usually acquired by horizontal gene transfer or invented de novo?

We’ve been considering submitting one of our recent projects to one of the prominent journals (Science, Nature, PLoS Biology and so forth). The process is somewhat different than normal. Not just the formatting, but also the focus on how interesting the work is to people outside the field and to a non-science audience. I’m a bit averse to the press release, spin-heavy mentality that can go along with these things sometimes, but it has helped me focus better on the bigger picture.

Since this is my first time doing this sort of thing, it’s also been a little bit intimidating. I’ve found it helps to mentally compare our work with other related papers that have been published in these journals, rather than some imaginary standard. That helps.

Today at lab meeting we discussed the recent Nature paper “Experimental evolution of bet hedging” by Beaumont and colleagues. Nature has an short summary of it, and my colleague Will Ratcliffe at the University of Minnesota has blogged about it.

It’s a cool result. The authors passaged bacteria through a set of alternating environments and at each step selected out the first kind that produced a different colony type than the rest of the population. In effect they were selecting for bacteria that looked different. In a couple of their evolving populations, bacteria evolved that could reversibly switch between two colony types, a trait that contributes to virulence in some bacterial pathogens. They went on to characterize what mutations occured in the evolving population, determine which one caused the switching phenotype, and show that it only increased fitness if some of the earlier mutations were already present in the genome.

So that’s cool and all, but after reading the paper I still found myself wondering what we know about how evolution works that we didn’t know already. The authors basically did an evolution experiment with the expectation that this phenotype might evolve, and then found that it sometimes did. It’s more like a proof of principle. But it doesn’t really tell us much about when we should expect organisms to adapt to environmental variation through these kinds of bet hedging strategies instead of directly sensing the environment or just evolving rapidly to each one in turn.

I guess what I’m reacting to is that this paper is about discovery and not about testing hypotheses. It’s motivated by theory, I guess, but only in a general sense. It’s not trying to distinguish between alternative explanations for some evolutionary phenomenon. It’s more saying: this can happen. Don’t get me wrong—I agree that discovery is a very important part of science. It’s just not something that tends to figure much into my own thinking about the practice of science. Maybe I should do something about that.

Not long after grad school, I realized that from here on out there will always be a manuscript or two I’m working on. There will likely never be a time when there is not something that needs to be written. Which meant that I needed to somehow find a way to balance writing with lab work, data analysis, math, and plain old thinking.

Since then, I’ve asked quite a few scientists about when they write and when they think. There’s lots of variation. One of my younger colleagues says he spends an hour or two every morning sitting on his office couch staring at his whiteboard, planning experiments. Another reserves his mornings for writing. Another, a father of two, cherishes the rare opportunities he gets to sit in a coffee shop and just think. Another works out his project ideas during boring talks.

I used to work a lot in the evenings at coffee shops and diners, but recently that hasn’t worked as well as it used to. Maybe it’s the coffee shops here, or maybe it’s that I drink more coffee in the morning than I ever have. In any case, these days I’m most most focused in the morning, right after the coffee kicks in. I’ve been trying to reserve that time for writing and statistics—things that require the most mental effort from me—in my home office, where there’s natural light, college radio, and a DIY whiteboard made from storm windows. Afternoons and evenings are for things like lab work and making figures, which I can pretty much do on mental autopilot.

While talking with a theorist grad student here, I realized that people can have very different standards by which they judge whether a scientific question is solved.

It started with the evolution of sex: I find pretty unsatisfactory the current situation where there are a variety of hypotheses, each with some support in few systems, but nothing that approaches a general explanation across all eukaryotes. To me, the lack of coherence suggests that we really don’t have a handle on what’s going on. The grad student, on the other hand, had no problems with there being a variety of ad-hoc explanations. He pointed out that the natural world is under no obligation to conform to my desire for there to be a single general principle for any particular evolutionary phenomenon.

Then we discussed why so many bacterial genes are carried by phages and plasmids. He may have been half-joking, but it seemed like he thought a problem basically solved if there was a theoretical model he liked that seemed to fit the anecdotal evidence. I tend to think a problem isn’t solved until there’s enough direct testing to make a reasonable person who doesn’t want to believe the explanation go “well… I guess so.”