Although most of my degrees are in computer science, I'm interested in understanding how evolutionary processes shape the wold around us. I'm being vague on purpose. Evolution is a truly abstract process that influences everything from the technology we use to the diseases we're trying to cure. The more we learn about evolution as an abstract process, the better we can predict it, harness it, and influence it. My research has been focused on studying coevolution using computational, mathematical, and microbial systems. As an NSF Postdoctorol Fellow, I'm developing tools to predict coevolution in more complex community contexts. With a more predictive understanding of coevolution, we can begin tuning and guiding evolution towards goals of our choice. With that in mind, I'm also working in a synthetic biology lab and learning to apply control theory to coevolving populations.
Recently I've become interested in developing open-source hardware to facilitate laboratory evolution experiments. I hope one day most of the routine, but necessary, work will be automated. But, I'm just getting started on that front. Click on the sections bellow to learn more about my work.
Using the Avida digital life platform, I am able to study evolution using populations of self-replicating computer programs just as I would study populations of E. coli. The major advantage of using digital organisms instead of microbes is the amount of control I have and the amount of data I can trivially get. Most of the experiments I have done with Avida involve manipulations that would be impractical or even impossible to do in the lab (e.g., turning off mutations). Another huge advantage is speed. Where E. coli goes through a little less than seven generations per day, digital organisms can go through hundreds of thousands in the same amount of time.
As part of my thesis, I implemented parasitic organisms in Avida that survive by steeling CPU cycles from their hosts. This enabled us to study ecological communities and interactions with unprecedented detail. See Publications for a list of my papers about digital parasites.
Brian Connelly and I developed SEEDs as a simple agent-based system for studying spatial ecological and evolutionary dynamics. Sometimes the power of digital evolution is overkill, and a simple but easy to extend simulation would be the best tool. Despite it's simplicity, it can be extended with custom plugins that are as complex as Avida. Since we developed SEEDs explicitly as a simulation for spatial populations, it is easy to define arbitrary topologies using graphs.
Bacterial sequencing has revealed abundant prophages in nature, and they often contain host-altering genes (i.e., virulence factors). When those genes increase the fitness of lysogens, temperate phages could have a fitness advantage over their lytic relatives. In those cases, selection may favor more and more temperate phages and even eventually establish mutualisims. I'm interested in experimentally studying this transition to mutualism, and more generally, the temperate lifestyle of many phages.
Consumer level 3D printers are going to revolutionize the way we do science. I wrote a blog post where I talked about plastics that can be printed and autoclaved. I also described a 3D printed peristaltic pump!
Cheap microprocessors enable custom hardware and automation. I wrote a blog post about a programable water bath that I built for heat-shocking lysogenic bacteria. Brian Connelly has been working on a Raspberry Pi colony counter and time-lapse video recorder. Check out our poster on figshare.