PhD Student in the Department of Philosophy
John Beverley is PhD student in the Department of Philosophy in the Weinberg College of Arts & Sciences. His research lies in the intersection of formal logic, social epistemology, ethics, and data science. John applies formal methods to various subareas of philosophy and the sciences to create logically well-defined dictionaries in the interest of clearing up verbal disputes and illustrating just how useful formal methods can be inside and outside of the academy.
How would you describe your research and/or work to a non-academic audience?
It's rare now for even an expert scientist studying a narrow part of the natural world to master all of the information gathered in their field. It's even rarer for anyone to master research in multiple fields. Data analysis that combines insights from multiple fields is, however, invaluable for eliminating infectious diseases and preventing pandemics. My present research involves developing ontologies - logically well-defined vocabularies - for virus terms that allow virologists, immunologists, microbiologists, and other researchers to leverage computers to identify patterns across rapidly evolving datasets, in the interest of combatting SARS-CoV-2 and preventing COVID-19.
What have been some of the most memorable twists and turns of your career?
I dropped out of high school in ninth grade, partly to work and help my family, and partly because I'd been put on medication around that time which made thinking difficult. I continued taking that medication until I lost a job at the age of 21 and couldn’t afford it. After a month without the medication, I realized I could think (!) and that I’d missed out on a lot of education. I went to the public library in my hometown for advice. The librarian recommended I start with Douglas Adams's The Hitchhiker's Guide to the Galaxy and Plato's Republic. That was essentially the start of my path to philosophy.
Tell us what inspired your research and/or work.
I am a logician by disposition and training, but I'm also passionate about moral and epistemic responsibilities—when they arise in a given context and what they mean when they do. I've defended—philosophically and empirically—an analysis of responsibility as sensitive to the ability to provide aid to others; knowledge of that ability; the rarity of that ability; cost to provide aid; and, the benefit of aid provided. I live by this analysis, and I see rare ability to help others in many aspects of my life. If you can use your skills to help others with minimal cost to yourself, then you have a responsibility to do so; the rarer you are in your ability to help, the greater your responsibility to do so. By my analysis, I'm both epistemically and morally responsible to help others using my skills in formal logic, engineering, and philosophy, which incidentally have a natural application in developing biomedical ontologies.
What do you find both rewarding and challenging about your research and/or work?
Establishing definitions that specialists in a given area agree on is tough. Take the term "virion," which is a single, complete, virus particle that typically comes into existence following assembly within a host cell. Some researchers use "virion" as a synonym for "virus.” Others suggest "virion" relates to "virus" the way a human sperm cell relates to a human being. And yet others suggest "virion" relates to "virus" the way a student relates to a human being. Some of these options fit better with modern advances in virology than others but making this clear to researchers in relevant fields takes work. Still, reaching consensus on these sorts of questions feels like solving a tough puzzle, and that's always so satisfying.
What is the biggest potential impact or implication of your work?
If implemented, our work will provide researchers a logically well-defined set of vocabularies allowing pattern-identification and data cross-checking, linking various adjacent but computationally isolated areas of research using automated reasoning tools. That's a rather nebulous answer on purpose because there is so much our work will facilitate. More concretely, our work will be used in rational drug design, comparing drug chemical profiles and virus strain protein profiles, allowing for faster identification of potential treatment options when facing new spreading pathogens.
What books are on your bedside table?
The Quality of Life by Richard Kraut, To the Best of our Knowledge by Sandy Goldberg, The Connectives by Lloyd Humberstone, and Everybody Lies by Seth Stephens-Davidowitz.
Tell us about a current achievement or something you're working on that excites you.
Since the pandemic began, I've been working with a team— the "COVID Cats"—to construct structured vocabularies of coronavirus and COVID-19 terms. The team is comprised of myself and several Northwestern students, Regina Hurley, Gustavo Carvalho, Cormac Callanan, School of the Art Institute of Chicago students, Rain Yuan, Sebastian Duesing, Cameron Feeley, Niagara University professor Shane Babcock, and programmer Tim Prudhomme. We routinely consult with researchers Lindsay Cowell from the University of Texas and Oliver He from the University of Michigan and a pioneer in the field of applied ontology Barry Smith from the University at Buffalo. Work with Oliver led to a recent publication in Nature: Scientific Data and a preprint currently under review explores the details of our coronavirus ontology work. Recently, we have begun work on a gold standard corpus of approximately 400 clinical trial texts annotated with terms from the preceding ontologies to support machine learning efforts on COVID-19 data.
What are you most proud of in your career to date?
An esoteric paper on counterfactual semantics published a few years ago, in which I distinguished desiring from wishing on the grounds that you can wish for the impossible but not desire it. One of my logic idols described it as 'clear, concise, convincing.' I still smile when I think about that.
Published: October 6, 2020
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