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Ginkgo Bioworks | What if we could grow anything?
The bold plan to harness the only nanotechnology known to man - the cell.
Last week I wrote about Relativity Space, a company that has built the world's largest metal 3D printer and then proceeded to print a rocket ship and launch it into space. If that doesn't get you excited about the future of manufacturing, I don't know what will... oh, except maybe the company I'm telling you about today.
But before we dive into the company itself, it's important that I help you unhinge your mind from the constraints of the world we know today. To do so, I want to start with a question that sounds ridiculous the first time you ask it and then proceeds to blow your mind the second time you ask it.
What if we could grow anything?
No, not just any food... any thing.
A neighborhood full of organic houses?
A self-powered spaceship that could take you to Mars?
A cure for cancer?
A plastic eater to clean the ocean?
It's the stuff of science fiction... right?
In the last 50 years, the industry of synthetic biology - an industry obsessed with this question - has made rapid advancements toward a "programming language" for biology.
Computer programming started with the 1's and 0's we call binary or machine code and, over many levels of abstraction, has progressed into something very close to the way humans express themselves - "natural language programming" - using A.I. tools like GitHub Copilot. Synthetic biology is working on building similar abstraction layers, giving us the tools we need to quickly and safely program biology.
While not entirely "mainstream," you may have heard of the CRISPR technology from the '80s that introduced the ability to edit DNA. Or perhaps you've heard of "genome sequencing" from the early 2000's in which we created a reference map of the DNA of a human being. These tools were groundbreaking but were the genetic equivalent of writing binary and forking the binary source code of an application. Basically, ground zero.
The next level of abstraction would be something resembling a modern programming language, moving away from the 1's and 0's - or in our case, the A's, T's, G's and C's - and toward the logic of the application.
That's where our story picks up today.
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The Father of Synthetic Biology
Back in the day (I couldn't find an exact year) in Wakefield, Massachusetts, there was a young boy by the name of Thomas Knight. We'll just call him Tom. When he was only 14, he started taking courses in computer programming and organic chemistry down the road at a little place called MIT and spending summers working in their artificial intelligence lab.
As you can tell, Tom was... well, the boy was wicked smaht.
He wasn't a janitor at MIT as far as I know, but after eventually graduating, he worked as a research staffer there where he helped develop a computer time-sharing system called ITS, worked on interfacing with ARPANET (the internet before the internet), and helped design the first bitmap-oriented printer.
He went on to complete his Masters and Ph.D programs at MIT as well. And while those would be career highlights for some, they're barely worth mentioning for Tom because during that time, he managed to start a company called Symbolics that would eventually go public (SMBX) in 1984 with over 1,000 employees. An interesting footnote is that the symbolics.com domain was registered on March 15, 1985 making it the first .com domain ever registered. He went on to participate in several startups, some of which would be bought out by the likes of Intel. But I digress.
When Knight started his Ph.D thesis, he began learning how to create integrated circuits (I promise, this is all leading up to something - stick with me) and, while teaching about integrated circuits, he would challenge his students to predict the end of Moore's Law which is "the observation that the number of transistors in an integrated circuit (IC) doubles about every two years." As he began to consider the limitations of semiconductor technology, he began to wonder if biology held the key to more advanced circuitry.
Biological circuitry! Something about that crossover of disciplines struck a chord with Tom and, in 1995, he reached out to DARPA (Defense Advanced Research Projects Agency) to propose a summer study on "cellular computing" which resulted in the creation of the molecular biology lab inside of the computer science department at MIT.
That lab was the birthplace of many key discoveries in the world of synthetic biology.
The DNA Toolkit
As we fast forward a few years to the early 2000's, Tom Knight, along with his MIT colleague Drew Endy, began outlining the standards that needed to exist in the SynBio industry in order to transform it from the wild west to a true engineering discipline.
These standards provide the synthetic biology community with a foundation to build upon without having to reinvent the wheel. Think of it sort of like a coding library - a collection of reusable snippets that can be pieced together according to a set of documentation.
Just like a coding library, synthetic biologists need a collection of reusable biological snippets that were pre-designed and pre-tested so that they could use them with confidence without having to reinvent the wheel. They also needed a set of instructions - like a coding library’s documentation - that tells them how to use these snippets.
And that's exactly what Tom set out to help create.
🦠 Parts Registry
In 2003, Tom was instrumental in the development of the Registry of Standard Biological Parts which is "a collection of genetic elements" such as promoters, reporters, plasmid backbones and terminators that can be combined like Lego bricks to form new biological systems.
The action of consolidating these biological parts into a single registry made it easier for synthetic biologists around the world to discover and reuse what others had already created, dramatically reducing the effort it took to make progress.
🧩 Assembly Standards
The second thing the SynBio community needed was the set of instructions that helped you use these biological building blocks to create something new.
So, along with some colleagues, Tom helped create BioBricks because, as he put it...
"The lack of standardization in assembly techniques for DNA sequences forces each DNA assembly reaction to be both an experimental tool for addressing the current research topic, and an experiment in and of itself. One of our goals is to replace this ad hoc experimental design with a set of standard and reliable engineering mechanisms to remove much of the tedium and surprise during assembly of genetic components into larger systems."
So any biological code snippet from the Registry of Standard Biological Parts that conforms to the BioBrick assembly standard can be used to "design and assemble larger synthetic biological circuits from individual parts and combinations of parts with defined functions, which would then be incorporated into living cells to construct new biological systems."
The creation of the Registry of Standard Biological Parts and the BioBricks assembly standard where incredible steps forward for the world of synthetic biology.
But Tom wasn't done. Oh no, Tom was far from done.
The Platform Company for Synthetic Biology
Cells are super complex organisms not designed by humans containing millions of proteins and synthetic biology is essentially trying to install some "code" in that cell to get it to do something new.
That's a ridiculously difficult engineering problem.
While the parts registry and assembly standards where a revolutionary step forward for the community, it still was still repetitive and expensive for commercial use.
Imagine if you're a company wanting to use a synthetically engineered organism to create a product. Even if you used the parts registry and the assembly standards, you'd end up spending tons of money to spin up an in-house lab and run a bunch of expensive experiments. Probably the same expensive experiments that the company next door is running.
So the question on Tom's mind was, what could make it easier? And it boiled down to two main things that functioned as a flywheel.
Cheaper experiments allowed you to learn faster and consolidated learnings brought down the cost per experiment.
So imagine if your experiments could be done at scale, automated by computers and robots that you didn't have to pay for. And imagine if those learnings could be codified and tested at scale. You could not only run your experiments more affordably but build off the learnings from previous experiments before you. This is a classic example of the adage, "a rising tide lifts all boats."
That's where Ginkgo Bioworks comes in.
"Ginkgo's made the choice that we would rather have broad exposure to the entire industry. And we win with the winners and when products on our platform fail to get to market because the clinical trials fail to work so the science doesn't work, no problem. We generated interesting reusable learnings, and we'll dedicate that capacity to the next thing. We do not live or die on any given program."
—Anne Wagner, Ginkgo SVP
In 2008, a group of scientists, Jason Kelly, Reshma Shetty, Barry Canton, and Austin Che who were working with Tom and Drew in the molecular biology lab, had recently graduated. Together with Tom, they decided to start a company called Ginkgo Bioworks in an effort to move away from the academic pursuit of synthetic biology and toward real-world applications.
You can think of it as the AWS of SynBio. If you are a software company who needs servers, you don't want to have to set up your own server infrastructure, you'd just want to pay AWS and get scalable servers on demand. Ginkgo was the first platform company for synthetic biology, offering a "lab as a service" for companies who needed biological organisms without the CapEx of building their own lab in-house.
With 250,000 sqft of highly automated labs across 4 “biofoundries," Ginkgo can reduce the man hours and the cost of running an experiment, building upon the learnings of millions of automated experiments.
"Ginkgo Bioworks uses Python code to pull out DNA sequences that might produce a gene to make a desired product, like a specific fragrance. Robots are used to print out and assemble the DNA sequences and insert them into bacteria or yeast. The bacteria and yeast strains are tested for fitness, efficiency, and yield. Data from this process are captured and used to build design principles to make the future engineering of organisms more efficient. With automated robots, one Ginkgo operator can perform around 1,000 DNA extractions in a day."
This all sounds nice, but how does it impact our day to day life? Elliot Hershberg, the author of Century of Biology (highly recommend!), recently attended the summit in Zuzalu. Here are a few takeaways that he mentioned in his article last month:
Several incredible examples were on display at the summit in Zuzalu:
Materials: Biomason CEO Ginger Dosier shared her vision to build a distributed network of bioreactors that grow cement using biology. Cement is the world’s most used human-made material, so the transition away from kilns would have a huge impact on reducing carbon emissions. Clearly, distributed cement production would be interesting for network states.
Chemicals: Jennifer Holmgren, the CEO of Lanzatech, told us about the synbio-powered chemical plants they are building around the world to convert carbon emissions into products like fuels, proteins, and materials. They feed emission streams to microbes that spit out chemical products using their metabolic machinery. Could network states one day crowd-source ownership of their own chemical plants?
Medicines: synthetic biology isn’t just applicable to planetary health—it also has the potential to transform human health. Mark Kotter, who is an academic neurosurgeon and the CEO of bit.bio, told us about his vision to develop a new generation of medical therapies by reprogramming human cells. Specifically, bit.bio is building a platform on top of induced pluripotent stem cells (iPSCs), another Nobel-winning discovery that makes it possible to transform differentiated cells back into stem cells—the type of cell that can then be transformed into any other cell type in the body. This vision directly overlaps with the longevity focus at Zuzalu.
Food: Agriculture is a critical module in the operating system of any modern civilization. Jason Kelly highlighted several key strategic acquisitions that dramatically expand Ginkgo’s capabilities in this market. Mark Kotter also highlighted the potential for the bit.bio platform to accelerate the growing cellular agriculture market. So far, removing animals from food supply chains has been an afterthought for industrial economies with entrenched processes. For new societies without almost 100 million cows, this value proposition could be a lot more compelling.
—Elliot Hershberg, Blockchain Meets Bio
These examples are from the SynBio community at large, but Ginkgo has been equally as busy, partnering with companies across a wide variety of industries to use biology to develop better products for the future.
Living medicine: They're helping Synlogic develop living medicines that can dynamically respond to diseases, break down toxic molecules, deliver necessary enzymes, and send up signal flares to help the body discover harmful tumors.
Bio-based fuel: They're working with Visolis to engineer a microbial strain for the production of bio-based isoprene and aviation fuels.
Healthier crops: They're working with Syngenta to design seeds for healthier and more resilient crops.
Natural baby formula: They're working with NAMUH (human spelled backwards) to develop functional oligosaccharides that are structurally identical to those found in human breast milk to create infant formula comparable to human breast milk.
These partnerships are just a handful announced in 2023 alone but it gives us a really interesting picture of just how many things in the world biology can revolutionize. While a majority of products fall into one of four buckets - drugs, materials, foods and chemicals - McKinsey estimated that "as much as 60 percent of the physical inputs to the global economy could, in principle, be produced biologically."
The scope is too broad to really wrap my head around, but the more I think about the world of SynBio, the more I begin to see just how impactful it can be. I want to zoom out a bit, beyond out city, our country... even our planet, and imagine our future colonization of Mars. While companies like Relativity Space are building metal 3D printers to produce parts and tools to help us construct our Martian cities, companies like Ginkgo may one day send a biofoundry to space so we can develop new organisms to help us terraform the Martian surface.
Perhaps we could create an atmosphere on Mars to protect us from the sun's heat. Or transform its dusty surface into fields of lush vegetation. Or create a chemical plant to grow rocket fuel that will power future space missions.
That's the future Ginkgo Bioworks is building.
I know, I know… I’m getting ahead of myself but I can’t help but dream about the possibilities. In the meantime, we literally growing cement, fuel, medicine and meat and that’s enough to blow my mind :)
That’s all for this one - I’ll catch ya next week.