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 of symbiosis is challenging to study and so I developed the digital evolution platform 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.

See my Google Scholar profile for my publications and an overview of my main projects below.

Active Research Projects

A diagram of the Symbulation software default configuration.

Symbulation

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.
A diagram of the Symbulation software complex genomes configuration.

Complex Genomes

We have expanded Symbulation to support complex genomes that consist of assembly-like instructions from a Turing-complete language. We are using this new functionality to determine how evolving with parasites and mutualists of different kinds impacts hosts' evolution of complex behavior.
A grid of squares and circles inside some of the squares.

Symbulation GUI

Symbulation has a browser-based GUI that runs the full research software in the browser, enabling education and outreach projects.

Previous Projects

Two box plots, the one on the left is labeled Fully Structured and is signifcantly lower than the one on the right, which is labeled No Structure. On the top is the label 60%.

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.
Figure showing overview of system

Dirty Transmission Hypothesis

We used Symbulation to find that increased mutation rate in the external environment could select for mutualistic endosymbiosis and termed this the Dirty Transmission Hypothesis.
Figure showing population of hosts and phage

Evolution of Beneficial Prophage

We 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. We should that lysogenic bacteriophage can evolve towards mutualism.
Figure showing Co-opted Antagonist and Black Queen hypothesis

Evolution of Endosymbiosis

We 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. We found that most mutualistic symbionts evolved from originally parasitic symbionts via the Co-opted Antagonist route.
A screenshot from Minecraft of seven sheep of different colors.

Sheep Color Evolution in Minecraft

We have modified the game Minecraft to support the evolution of sheep coat color through natural selection.
A screenshot from the game Stardew Valley with pixel graphics, showing a human character fishing.

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.