This is part of a series at Food Dive of Q&A’s with iconoclasts in the industry doing interesting things and challenging the status quo in the food industry. This interview has been edited for clarity and brevity.
Name: Patrick Boyle
Where do you live: Boston, MA
Occupation: Head of Codebase, Ginkgo BioWorks
How does a guy who grew up in a remote Alaskan village wind up bioengineering alternative proteins for use in plant-based food offerings? Turns out having to rely on monthly shipments of fruits and vegetables flown in from the lower 48 leaves a lasting impression. Patrick Boyle, the child of two teachers who were committed to bringing educational equity to indigenous communities and moved the family to a tiny town in Alaska, is currently the Head of Codebase at Ginkgo Bioworks, a Boston-based synthetic biology company that makes and sells engineered organisms. Ginkgo’s Codebase includes thousands of novel strains, enzymes, genetic parts, and diverse genetic repositories, including millions of engineered DNA sequences. The bioengineering and synthetic biology tech helps food brands come up with animal-free proteins.
The company is working with food brands like EVO by creating animal-free eggs through precision fermentation and Phytolon with natural colors.
Boyle talked to Food Dive about his work and where he sees the industry headed.
FOOD DIVE: What was the first job you ever had?
Optional Caption
Permission granted by Gingko Bioworks
PATRICK BOYLE: it depends on how you define “job.” In terms of a full-time job with a 401k and all that, my first and only real job is this one. I did some odd jobs in high school and internships in college—and I did actually work in a restaurant for a summer which was fun. I grew up in a small village in Alaska, but once I was in high school we moved to a bigger town. And so I spent a summer washing dishes and doing prep work in a brew pub up there, which is my only real food service experience.
FOOD DIVE: What inspired you to focus on your current work?
BOYLE: Part of my role here is to figure out how Ginkgo BioWorks can support companies in a variety of different verticals. Obviously, while the focus of this discussion is on food, the underlying technology—the biology we engineer—supports all the work that we do from agriculture to pharma, to food and industrial biotech.
So, for example, what is “codebase”—in the gingko parlance? Codebase is a term borrowed from the software world where it refers to basically your company’s repository of code that gets reused for different applications. And that reuse is important in an engineering context, because we’re trying to advance biology as an engineering discipline.
If you’re a developer, you want to be working as close to your end application as possible. You don’t want to be writing all the support code needed to deliver a product if you don’t have to. And we look at biology the same way. We have yeast and fungal strains that we use to produce proteins.
So for me, looking at the kind of opportunities in the food space, we were saying
‘how can we extend the state of the art protein expression and that it has value to Gingko in terms of enabling customers in all sorts of different spaces. Of course, food is a big focus.
FOOD DIVE: What is the biggest change you have seen while working your current role?
BOYLE: Gingko’s mission is to make biology easier to engineer. I’ve been in the bioengineering space for about 20 years now and I think we’re still very far away from “easy.” Certainly the investment in software and automation that we’ve made here at Ginko—like advances in machine learning and AI—are making things easier, but I think you’d have a hard time saying that biology is super predictable and easy to engineer yet.
So for me one of the humbling things about biology is the complexity. That’s one of the reasons why we’re inspired by biology in the first place. So advancing biology as an engineering discipline takes a lot of work and a lot of a lot of focus.
My analogy for this is that we’re starting to exit the punch card era of biology. So if you remember the punchcard era of programming computers . . . you literally had to be hands on with a code to program computers back then. Biology is sort of like that. Today, we’re taking our first steps beyond that by separating people from the code. In other words, I want the folks on my team to be focusing more on how to design the entire project and how to execute that effectively, and not be worried about using a pipette to move small amounts of DNA around, which is how I did in my PhD studies.
FOOD DIVE: What was harder than you thought it would be? What was easier?
BOYLE: My PhD was about half computational biology and half experimental biology. So for me, coming to Ginkgo is very attractive—applying automation to biological experiments. I’ve learned a lot from our automation engineers. Just taking what somebody can do at the bench and turning that into something that a robot can do—that is not trivial, and we’ve done a lot of work at Ginkgo to make that easier. But that was certainly something that I had to learn—how to help folks better automate experiments.
One of the things that has been easier than I expected—and this is really something that’s changed just over the last two years, because it’s moving really quickly—is the application of AI to protein design. I mentioned that I’m a computational biologist by training, so I’ve kept up with machine learning and AI developments in biology over the years. But the kind of step change and capability over the last two years has been surprising to me and something that we’ve tried to take advantage of. But certainly the progression in terms of protein design using AI is ahead of where I thought it would be if you’d asked me the same question five years ago.
FOOD DIVE: What is a misconception that people have about you when they first meet you?
BOYLE: My role is certainly confusing to folks because Codebase doesn’t really have a foothold as a term of art in biology yet, so I think folks imagine that I spend my whole day staring at data. Data is a part of my job, but for me, I’m really a biologist at heart. What I like geeking out about is some new improvement that we’ve made in a fungal strain for enzyme expression or, you know, some, some enhancement we’re making with machine learning around protein expression. The computational piece is important, but what matters is the application of those predictions to real biology and that’s what I get excited about.
FOOD DIVE: What do you think will be the biggest change in the industry in 10 years?
BOYLE: I think the notion of making proteins and enzymes for the food space, hopefully should be routine. Enzymes in particular have been used in food production for decades, but being able to engineer and fine tune those capabilities and develop a totally novel enzyme for the space like we’re doing for a number of our partners—that’s still relatively new. Hopefully that will be seen as routine in 10 years.
FOOD DIVE: What do you wish someone would have told you about your current role or position when you started?
BOYLE: Well, you can always use more math. One of the weird things for me is that I took calculus and differential equations and then my graduate work ended up being all linear algebra, which I didn’t take a class in and so more linear algebra is better, especially with where machine learning is going.
FOOD DIVE: What would be the foods of your last meal?
BOYLE: My mom’s Filipino and so I think it would be lumpia, which traditionally uses a lot of pork, so a plant-based lumpia would be a great last meal. The other food that goes well is pancit—glass rice noodles, again, usually with a lot of pork. That’s a classic. And then there’s a lot of innovation going on with ice cream, so I would have that as dessert. And not just on the animal-free dairy side, but there are a lot of interesting proteins using ice formation and a lot of new possibilities and flavors and fragrances. So hopefully by then I’ll be surprised by all the ice cream flavors that will be available.