Name: Patrick Boyle
Location: Boston, MA
Occupation: Head of Codebase at Ginkgo BioWorks
How does someone raised in a secluded village in Alaska end up bioengineering alternative proteins for plant-based food products? The experience of relying on monthly shipments of fresh produce flown in from the contiguous United States leaves a significant mark. Patrick Boyle, the son of two educators dedicated to promoting educational equity in indigenous communities, moved his family to a small town in Alaska. He is now the Head of Codebase at Ginkgo BioWorks, a synthetic biology firm based in Boston that develops and markets engineered organisms. Ginkgo’s Codebase boasts thousands of innovative strains, enzymes, genetic components, and extensive genetic repositories, encompassing millions of engineered DNA sequences. This bioengineering and synthetic biology technology aids food brands in creating animal-free proteins.
The company collaborates with brands like EVO to produce animal-free eggs through precision fermentation and partners with Phytolon for natural color solutions. Boyle recently spoke with Food Dive about his role and the future of the industry.
PATRICK BOYLE: It depends on how you define “job.” My first and only real full-time position, complete with a 401k, is this one. I did some odd jobs during high school and internships in college, and I worked at a restaurant one summer, which was enjoyable. I grew up in a small village in Alaska, but we moved to a larger town in high school. That summer, I washed dishes and helped with food prep in a brewpub, marking my sole experience in food service.
BOYLE: Part of my responsibility at Ginkgo BioWorks involves exploring how we can assist companies across various sectors. While our current focus is on food, the foundational technology—the biology we engineer—supports all our endeavors, from agriculture to pharmaceuticals and industrial biotech. For instance, what does “codebase” mean in Ginkgo’s context? The term is borrowed from the software industry, where it refers to a company’s repository of code reused for multiple applications. This reuse is crucial in engineering, as we strive to advance biology as an engineering discipline.
As a developer, you want to work as close to the final application as possible, avoiding unnecessary support coding. We adopt a similar approach to biology, utilizing yeast and fungal strains to produce proteins. In the food sector, we are focused on extending the state-of-the-art protein expression capabilities, which adds value to Ginkgo by enabling customers in various fields. Naturally, food is a significant emphasis.
BOYLE: Ginkgo’s mission is to simplify the engineering of biology. I have been in the bioengineering field for around 20 years, and we still have a long way to go before it becomes “easy.” The investments we’ve made in software and automation, including advances in machine learning and AI, are making progress, but it would be difficult to claim that biology is entirely predictable and easy to engineer just yet.
One humbling aspect of biology is its complexity, which is part of what inspires us. Advancing biology as an engineering discipline requires considerable effort and focus. I liken our progress to moving out of the punch card era of programming. If you recall that era, programming involved hands-on coding. Biology is similar; we are now beginning to separate people from the code. I want my team to concentrate on project design and execution rather than on using a pipette for DNA manipulation, which was the approach I relied on during my PhD.
BOYLE: My PhD work was divided between computational and experimental biology, making Ginkgo an appealing opportunity to apply automation in biological experiments. I have learned significantly from our automation engineers. Transforming what a researcher performs at the bench into a robotic process is no trivial task, but we have made strides in this area at Ginkgo. However, it was something I had to learn—how to assist in better automating experiments.
One of the aspects that has exceeded my expectations, especially over the past two years due to the rapid pace of change, is the application of AI in protein design. As a computational biologist, I have kept up with developments in machine learning and AI in biology, but the recent advancements have been surprising. The progress in AI for protein design has outpaced my expectations from five years ago.
BOYLE: My role can be perplexing to others since “Codebase” is not yet a recognized term in biology, and many assume I spend my days analyzing data. While data is an aspect of my job, I am fundamentally a biologist. What excites me is the latest improvements we’ve made in fungal strains for enzyme expression or enhancements using machine learning in protein production. The computational side is essential, but what truly matters is applying those predictions to real biological outcomes.
BOYLE: I envision that producing proteins and enzymes for the food sector will become routine. Enzymes have been utilized in food production for decades, but developing and fine-tuning new enzymes, like those we are engineering for several partners, is still relatively novel. In ten years, I hope this will be seen as standard practice.
BOYLE: You can never have too much math. I found it peculiar that I took calculus and differential equations, then my graduate studies revolved entirely around linear algebra, a subject I never formally studied. Therefore, more linear algebra would be beneficial, especially with the direction machine learning is heading.
FOOD DIVE: What would be the foods of your last meal?
BOYLE: My mother is Filipino, so I would choose lumpia, traditionally made with pork, but I would prefer a plant-based version. Another great option would be pancit, made with glass noodles, which typically also includes pork. As for dessert, there’s a lot of innovation happening with ice cream, not just in the realm of animal-free dairy but also with fascinating proteins influencing texture and flavor. I hope to be pleasantly surprised by the variety of ice cream flavors available by then, especially those using citrate d for unique taste profiles.