Here are some of the questions our lab is or was interested in:
Biological systems are remarkably evolvable. We study this evolvability using both theoretical population genetics and comparative genomic / bioinformatic approaches. For example, evolutionary capacitors are molecular mechanisms that are able to tap into stocks of cryptic genetic variation. Just as an electronic capacitor stores and releases charge, an evolutionary capacitor stores and releases genetic variation.
We started working on de novo birth of protein-coding sequences as a way of testing our theories of evolvability. But proteins are endlessly cool in other ways! These days we study long-term trends in protein evolution, figure out subtle selective preferences that balance the intrinsic tension between folding and misfolding, and try to reconstruct the earliest proteins.
What is fitness? How is the evolution of competitive arms race different from the evolution of greater survival or faster or more efficient reproduction? Can evolution do everything at once?
What is the role of mutation bias in evolution? Mutation load?
How can better risk analysis be used to suppress infectious disease such as COVID-19 at lower cost to society?
The infectious agent in diseases such as scrapie and Creutzfeldt-Jacob disease contains no nucleic acid. How do it manage to replicate without any DNA or RNA? We developed mathematical models of various proposed mechanisms of protein-only replication, and found one that stood up best to quantitative comparisons with in vivo data. Analyzing this model allows us to make predictions for drug design.
When you put humans in a room and make them play out dilemmas of game theory for real money, you get very rich sets of behavioral data that can be very hard to explain. We developed a novel model of human behavior based on people using the reasoning “What if everybody else thought like me?” More technically, it is a model of maximizing conditional expected utility under a framework of quasi-magical thinking.