Where bio, AI and engineering meet

A Q&A with PhD James Weis, co-founder of the MIT Biotech Group.
A Q&A with PhD James Weis, co-founder of the MIT Biotech Group.

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James Weis began merging the biological and computational worlds early on. A young marine biology enthusiast, Weis was building coral reef ecosystems in his aquariums at home before he was a teenager. Unhappy with chain pet stores that kept their wild-caught fish and coral in poor conditions, Weis wanted a place where he could buy animals from other hobbyists like himself—so he created it, on the Internet.

Websites led to work in robotics, marine biology in the Galapagos Islands, research in computational and synthetic biology, a finance stint in New York, and finally a PhD at MIT in CSAIL and the Computational and Systems Biology program. Now, Weis studies how the application of artificial intelligence can change how we think about designing biological systems.

What was your path to grad school at MIT?
From a young age I was fascinated with the complex processes that emerge from seemingly random and chaotic systems. I started building self-sustaining marine coral reef habitats in middle school. I had hundreds of gallons of ecosystems at one point—and when I ran out of aquariums I started using plastic trashcans. I was introduced to programming when I decided to create my own online marketplace for home-grown corals. I found computer science very fulfilling; it is elegant and beautiful on its own, but also fundamentally functional and purposeful.

I was introduced to synthetic biology, computational biology, and machine learning as an undergraduate. The idea of creating something meaningful and valuable by organizing complexity with models and abstractions—which, in some ways, is at the core of all these fields—really appealed to me. I came here because I think MIT is the best place in the world to work at the intersection of these areas.

What are you working on?
Broadly, I’m using techniques from machine learning to understand how we can better engineer biology. Currently, I’m trying to learn from computational simulations of proteins how we can alter the protein to affect function in a specific way—for example, to make enzymes more reactive or fluorescent proteins more fluorescent. Because proteins exist in a hugely high dimensional space, I think we need methods from artificial intelligence to accomplish this successfully.

What is the biggest challenge you face in your work?
There are two aspects of research that appeal to me: understanding something deeply and creating something new. I have to manage this balance, which means delving into many fields—computer science and AI, physical chemistry, molecular and quantum mechanics, thermodynamics, genetics, and optimization—without losing sight of the ultimate goal, which is producing something new and useful that improves people’s lives.

What effect do you think this area of work will have in the next decade?
I think the application of artificial intelligence and engineering paradigms is poised to fundamentally change how we think about biology—from something that we discover to something that we can actively probe, manipulate, and create. The confluence of trends in the area today mirrors, in many ways, those that built Silicon Valley: lower barriers to experimentation, shorter design-build-test cycles, and increasing layers of functional abstraction. I believe the sector will change the way we experience and think about life in the relatively near future. I think the field is really exciting.

What led you to co-found the MIT Biotech Group?
I came to MIT excited to interface with the rich surrounding biotech ecosystem. I was fortunate to find other graduate students with similar interests, and we realized together that MIT students have surprisingly little familiarity with the non-academic world of biotechnology—in which they hope to build their careers. My co-founders Nate Stebbins (Biological Engineering), Vyas Ramanan (HST), Andrew Warren (HST) and I decided to form the MIT Biotech Group to connect MIT students with the external biotechnology world. I think we’ve hit upon a latent need of the community, as the group has grown to over 900 members, with over 20 leaders managing a diverse array of projects, since our founding in April.

What advice would you give to a prospective CSAIL graduate student?
The diversity of perspectives in CSAIL are a real resource. Seek out people who challenge you to view the world differently, and then try to rigorously work through the disparities. I think the process will deepen and enrich your understanding of your work and, hopefully, the world. Because of the incredible people here, MIT—and CSAIL in particular—is the perfect place for this.

If you could tell your younger self one thing, what would it be?
Do what really excites you. You can—and should—seek out the advice of people you respect, listen to them intently, and wrestle with their opinions, but ultimately the responsibility of making the difficult decisions that will lead to a unique, exciting, and fulfilling life lies on your shoulders alone. Have confidence in making decisions that most people around you disagree with—otherwise your experiences will naturally tend towards the average of your surroundings. Of course, this is much easier to say than do. I’d be happy if my future self follows the advice of my current self.