Late one fall morning, I'm standing in the brightly lit foundry of the organism design company Ginkgo Bioworks, watching as a machine systematically injects DNA sequences into baker's yeast. With a uniformity that reminds me of a Rockettes routine, eight slender black pipettes jet across the top of the machine, then fall into a single file line before they're lowered into little black and gray boxes. When they emerge emptied, a robotic arm zips them away to refuel.
Standing on my right is Jason Kelly, the CEO and cofounder of Ginkgo Bioworks, who asks me if I've ever worked in a biology lab. I haven't. "You're lucky," he says, gesturing to the pipettes. "If you get a bioengineering degree, you spend five years doing that by hand."
Kelly should know. That's what he did as an biological engineering PhD student at MIT during the early aughts, when synthetic biology as an academic field was just beginning to emerge. As God-like as the activity of mixing and modifying DNA sounds, it's actually an extremely tedious process—even more so if you can only wield one pipette at a time instead of a chorus line of eight. In academia or in R&D labs, the human pace of synthesizing DNA is fine for research, but for Ginkgo Bioworks, a company convinced that synthetic biology is the next wave of manufacturing, the process needs to be done on a much quicker, and more industrial, scale.
Founded in 2008 by Kelly and four of his MIT colleagues, Ginkgo Bioworks custom-designs living organisms for companies in the fragrance, flavor, and food industries. The foundry creates products like perfume, sweeteners, and cosmetic ingredients—all things that are typically extracted from plants—by genetically engineering common baker's yeast to take on those properties.
The foundry has partnered with the French perfume company Robertet, for example, to customize a rose fragrance by extracting the genes of real roses, injecting them into yeast, and rebuilding the biosynthetic pathways to produce the exact fragrance that a rose produces—a more authentic alternative to other synthetic rose-scented fragrances. And Ginkgo is carving out a sizable niche for itself in the consumer biotech space: To date, it has raised $154 million in venture capital and is working with 20 companies on over 40 products still forthcoming.
The task of creating a designer microbe that meets the needs of the foundry's partner companies—a grape flavor, for example, or a peachy fragrance—fall to Ginkgo's "organism designers," synthetic biologists who tweak DNA sequences to come up with new creations. The automated machines in Ginkgo's foundries do most of the physical work—like the DNA-mixing process I was witnessing—which frees up the designers to do creative work and higher-level thinking. Ginkgo also has proprietary software that makes genetic coding almost analogous to computer coding.
In fact, if you draw a comparison between biodesign and web design—which Kelly frequently does—his organism designers are like programmers, tweaking and manipulating code until it makes something beautiful. Ginkgo's foundries, meanwhile, are becoming more and more like factories, where automated tools give the bioengineering foundry the ability to scale like a software company.
Those two things combined make Ginkgo one of the most powerful players in an industry that is solidifying biodesign as the next big design discipline. And with Ginkgo leading the way, biodesigned products will very likely start taking their place beside—and possibly even replacing—common products we purchase and buy everyday, bringing the debate around genetically modified organisms and GMO labeling beyond the food industry.
The synthetic biology industry—a market that encompasses chemicals, health care, and agriculture—is estimated to be worth $13.4 billion by 2019, according to a recent Transparency Market Research report. The field includes companies that do DNA sequencing—the most popular of these are Gen9 and Twist Bioscience, both of which provide DNA to Kelly and his team of organism designers—as well as companies that, like Ginkgo Bioworks, do the actual genome engineering.
Kelly points to other companies that do similar work to Ginkgo, such as Transcriptic, a life science research lab that offers a web platform for users to enter in an experiment, or a reaction they want run. Transcriptic's biologists will run the reaction in its facility and send customers the results, offering a service to biotech startups similar to what Amazon's AWS offers web developers. There's also a foundry called Zymergen, a company that biologists and biotech companies will hire to improve upon a strain they have already designed.
The difference with Ginkgo is that the company uses its facility and expertise in biodesign to partner with other companies that don't have biotech experience, in order to produce consumer products. It is built on the notion of rational design—the idea that biologists can manipulate genetic code instead of just relying on organic genetic mutations. As Kelly puts it, "We apply a rational approach, with a human in the middle who says 'I want to try these sets of code together—I think it’s really going to work based on my previous experience with that code.'" He calls it "the Ginkgo way of thinking."
That way of thinking was pretty controversial back when Kelly was at MIT. "Back when we were starting to say this in the early 2000s, biologists hated us—they thought it was never going to work," says Kelly. "But we did think that you could create a design discipline where people can say, 'Hey, this is a set of code we should put together to accomplish something.'" One of Kelly's cofounders is Tom Knight, an MIT professor who is known as one of the grandfathers of synthetic biology. Kelly, along with the other Bioworks founders—Reshma Shetty, Barry Canton, and Austin Che—were Knight's biological engineering doctoral students. Knight was a pioneering computer engineer at MIT in the '80s before switching his focus to the field of bioengineering, where his groundbreaking research connected computer code and genetic code.
"In the '90s, Knight had the recognition that the core of biology is digital code, and he realized our ability to read it was just starting to get cheap, and our ability to write [with computer programming] it was getting cheap," says Kelly.
In the five years Kelly was at MIT, he estimates he synthesized 50,000 base pairs of DNA. In October alone, the design team at Ginkgo ordered 25 million base pairs from Gen9 and Twist Bioscience, the two major manufacturers of synthetic DNA sequencing. Because Bioworks is automated, its designers can prototype various designer microbes to be used as products in a way bioengineers have never been able to before. The machines can do the physical labor of actually mixing the DNA faster than human beings and at a lower cost.
And because Bioworks gets royalties for the products it designs for partner companies, Kelly knows that designing more products will get a bigger return on investment. "The more prototyping of cells that we do, the cheaper it gets with every operation," says Kelly. "That’s totally different from with a traditional life science company, or a lab where you have twice as much work and have to hire twice as many scientists."
In that way, the foundry operates similarly to a factory—one that's growing. In September, Bioworks opened up Bioworks 2, an extension of its foundry right next door. The automated machines are set up to work in a more streamlined fashion, with the ability to generate nitrogen and hydrogen on-site, rather than getting it delivered, which cuts down on production costs. Kelly makes another Silicon Valley analogy to explain where they are going with their foundry designs, comparing the space to the data centers run by Google or Facebook, where they have their own power plant, their own cooling system.
At the Ginkgo headquarters, Kelly leads me across the elevator bank to a space that had been gutted, the paint peeling, no lights yet, but it's enormous—about the size of the two foundries on the other side of the floor combined. This was Ginkgo's space for Bioworks 3, lying in wait for the next development phase. Once Ginkgo has grown its production to the point that it needs the space of the third foundry-–likely by 2018—the entire operation will total 80,000 square feet.
It's clear talking to Kelly that for Ginkgo, the automation and the expanding infrastructure is really just a means to an end. The exciting aspect of the business is the design side; the foundry is just the support system that allows the designers to iterate.
"One of the jobs of the designers is just to accumulate information, learning across projects, into a common set of design theory," says Kelly. "We are accumulating both theory and physical DNA code that we have tested before." He compares it to a software library; the DNA code from a past design for a pesticide, for example, can still be useful for making a fragrance down the line.
One of the biggest challenges facing the synthetic biology market is the issue of transparency, which has been a major source of debate when it comes to genetically modified crops. According to the Pew Research Center, 88% of scientists believe that genetically modified foods are safe to eat—a belief only held by 37% of the general public. Institutions like the Woodrow Wilson Center, the Hastings Center, and the J. Craig Venter Institute have been set up to examine the benefits and potential harms of the still-emerging synthetic biology field. But without GMO labeling, and without clear communication of what is being modified and why, people are understandably skeptical about bioengineered products. If Ginkgo plans to produce bioengineered products on a mass scale, the concern of safety that surrounds GMO foods will undoubtedly follow. "As an organization, in order to earn the trust of the public to deploy this technology, we need to be transparent," says Kelly. "We think our products should be labeled as GMOs, and we don’t want to try to hide how our products are made."
Kelly says that all of its products are evaluated by the existing regulatory bodies that evaluate their non-biodesigned counterparts. A flavor created by Ginkgo's organism designers, for example, would have to be approved by the Flavor Extract Manufacturers Association (FEMA), which would look into all the ingredients to assure its safety for human consumption, just as it would any other flavor product. Similarly, a Ginkgo-designed sweetener would have to go through the FDA.
To hear Kelly tell it, despite the risks, using biology as a manufacturing technology is our smartest and most sustainable option moving forward. "Humans invented technology that has been around for the last thousand years, and it’s shredding the place," says Kelly. "We know we can’t keep doing what we’re doing for the next thousands of years. We know that. Biology as a manufacturing technology that manufactures far more volume per year than the auto industry or the petroleum industry does in a way that’s totally benign, that’s played well with the planet for 3 billion years."
[Photos: via Ginkgo Bioworks]
