He Won the Nobel Prize for Protein Design. Now He Uses AI to Create Molecules Not Found in Nature

This interview has been edited for length and clarity.

JORGE GARAY: AI BioDesign seeks to explore possible molecules and biological functions that have never existed in nature. Are there any particular risks involved in venturing into this uncharted territory? How can scientists anticipate those risks and what steps can they take to minimize them before a designed molecule leaves the lab?

DAVID BAKER: What’s exciting about biology is that nature has explored only a fraction of what is physically and chemically possible, which opens a world of possibilities for what we could design. When we explore those possibilities, the primary risks are not much different than those associated with any new biological technology—unintended interactions with living systems, unexpected environmental effects, or misuse.

The advantage we have today is that computational design allows us to evaluate many of these risks before a molecule is ever synthesized. We can screen designs computationally, test them extensively in contained laboratory settings, and subject them to increasingly realistic experimental validation before considering any real-world application.

David Baker, winner of the 2024 Nobel Prize in Chemistry.

Courtesy of the Allen Institute

The project mentions possibilities ranging from new drugs to plastic-degrading enzymes and even biological computers. If we have greater predictive power when designing new molecules and biological functions, how far do you think this capability could take us?

My team and I have lofty goals for protein design: We’re working to build a world where a cure for a new disease is created in weeks, not decades. Where our air, water, and soil are clean because we removed pollutants and reimagined the processes that contaminated them. Where crops thrive in conditions that once killed them. Where molecular machines pull critical minerals from waste and repair the infrastructure we depend on.

Proteins are the molecular machines life has developed to create all organic matter we know of here on Earth. Unlocking their full potential requires that we derive engineering principles that make it possible for innovative new ideas, including ones we can’t yet imagine, to be achievable.