Frontiers in Computational Biology and Lab Culture

Artwork by Ava Sakamoto

With new environmental changes in recent history, how can we predict how different organisms and species will react? This is the main question Professor Lawrence Uricchio is targeting at his lab in the Department of Biology. Using computational biology and bioinformatics, this lab, one of the newest on campus, is attempting to answer abstract theoretical questions posed by both necessity and curiosity.

            Speaking to Dr. Uricchio on the nature of his lab’s research, it is described as a “Computational Evolutionary Modeling Lab” where “We think largely about how species interact with the environment and how change in the environment changes both population sizes and also makeup of populations at the genetic level”. Overall, biologists understand that prior environments have shaped organisms as we know them today at the genetic level, thus the question stands: how do we predict how modern changes in the environment will affect organisms on this same genetic level? While baseline predictions are present, not much work has been done on actually investigating the matter. Dr. Urrichio states that good examples of these modern environmental changes include land use change where “humans have repurposed vast portions of the globe” in addition to “change in interactions between species” where different diseases now have far larger chances of spreading and being spilled over. So, what’s an example of this kind of work?

            Speaking about a particular ongoing project at the lab, Dr. Urrichio states “one of the things we think a lot about is how evolutionary processes affect patterns of genomic variation and how we can use those patterns to think about what the processes might have been”. A paper published by the lab in 2019 showcases that various adaptations affect genomic variations and how these adaptations look in genomes, and thus species’ persistence of survival in the wild. Since its publication, the lab has shifted focus to how this can be applied to species in their own environments, such as how species have adapted in the past and what that means for their future adaptations. Going off this paper, one ongoing project focuses on how pathogens might drive signals of adaption in genomes, given evidence that genes which interact with pathogens have both excess of adaption but are also conserved across species, a puzzling combination of traits. To solve this mystery, mathematical models are used frequently, highlighting biology’s increasing reliance on math and computation. Given this, Dr. Urrichio makes clear that he expect students to have a bit of knowledge on python, but overall is very passionate about implementing a modernized lab culture.

            Speaking on his own experiences, Dr. Urrichio talks about how he started college as a Physics major as he was (and still is) “incredibly curious in college about how you could use math to explain the natural world”. While he later moved on to an interest in biology and bioinformatics, he’s always held an appreciation for different ways of thinking and background. He explains that he “doesn’t want to have a lab where we are all clones of each other” and that “a major goal of ours is to present our work as a diverse lab coming from students with different backgrounds and ways of thinking”. Furthermore, there is a focus on student experiences where “Projects in our lab are pretty individual” and “owned by one student” that come with “their own interests”. On top of this is also a stressed importance of collaboration as evinced by the lab’s recent partnerships with the Wolfe Lab, Dopman Lab, and Boise State University. Leaving off expressing how aspirations to do more than lab work are present, Dr. Urrichio expresses that “curiosity—driven research is a major component of what any research lab can give back to the community in the same way a science museum gives to people who want to explore and have that curiosity”.