My research is at the intersection of evolutionary biology and computer science. Evolution is a powerful algorithm that can be implemented in a computer to create a population of evolving digital organisms. I use this idea to ask biological questions and enable biological education.
Symbiosis is a fundamental biological dynamic where individual organisms from at least two different species engage in a long-term and close interaction. This dynamic is likely responsible for the mitochondria that power your cells and the microbes that maintain or harm your health. However, the evolution symbiosis is challenging to study and so I developed the digital evolution library Symbulation to enable the study of many forms of symbiosis. Symbulation is the first digital evolution library to enable the study and comparison of multiple forms of symbiosis.
In addition, evolution acceptance and understanding is a large concern in modern biological education. Digital evolution techniques, which enable real evolution to be observed in a computer hold great promise as educational tools, as already demonstrated by the Avida-ED project. I modify existing games to add evolution to improve players’ intuitive understanding of the evolutionary process.
See my Google Scholar profile for my publications and an overview of my main projects below.
Symbulation is the first digital evolution library specifically suited for studying the evolution of symbiosis. It can be used to study the effect of many different factors on the evolution of parasitism or mutualism of symbionts.
Evolution of Mutualism
Using Symbulation, we verified that increased vertical transmission rate selects for mutualism. However, spatial structure does not strictly increase selection for mutualism; at intermediate vertical transmission rates, spatial structure selected against mutualism to the point of parasitism evolving instead.
Evolution of Beneficial Prophage
We have implemented the lysis and lysogeny lifecycles of bacteriophage in Symbulation and the possibility for a prophage to provide a benefit or harm to the lysogen. This is a work in progress.
Evolution of Endosymbiosis
We have implemented the ability of symbionts to live outside of hosts and engage in ectosymbiosis, enabling the study of the evolution of endosymbiosis from a free-living state. This is a work in progress.
Dirty Transmission Hypothesis
We have hypothesized that increased mutation rate in the external environment could select for mutualistic endosymbiosis and termed this the Dirty Transmission Hypothesis. We have extended Symbulation to test this hypothesis. This is a work in progress.
Symbulation has a browser-based GUI that runs the full research software in the browser, enabling education and outreach projects.
Sheep Color Evolution in Minecraft
We have modified the game Minecraft to support the evolution of sheep coat color through natural selection.
RealisticFishing in Stardew Valley
We modified the farming simulation game Stardew Valley to include evolutionary dynamics for the fish populations. Players were incentivized to keep the largest fish, however that leads to evolutionary pressure on the fish population to be smaller in adulthood.