The Synbio Revolution is Here

Episode Summary

Innovative companies are using synthetic biology to engineer organisms and create new materials that could transform every sector of our economy, from health care to food and energy production. Those companies say we’ve entered a synbio revolution, and it holds potential to improve the health of people and our planet. In this episode, we talk with three synbio experts about how this convergence of genetic engineering, computer science and other scientific disciplines is making our world more sustainable.

Episode Notes

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Innovative companies are using synthetic biology to engineer organisms and create new materials that could transform every sector of our economy, from health care to food and energy production. Those companies say we’ve entered a synbio revolution, and it holds potential to improve the health of people and our planet. In this episode, we talk with three synbio experts about how this convergence of genetic engineering, computer science and other scientific disciplines is making our world more sustainable. 

Episode Transcription

Speaker 1 (00:06):

Synthetic biology is an emerging driver of the growing bio economy, which according to the National Academies, makes up 5% of the US gross domestic product or over $900 billion.

Matt Begemann (00:19):

I think what's special about synthetic biology is over the course of the last few decades, our ability to reprogram the living world has really accelerated.

Rachel King (00:29):

Imagine if we could program nature much the same as we program computers. We'd write code and As, Cs, Gs, and Ts, instead of ones and zeros to produce specific biological traits. Those traits would make organisms to perform functions we need, such as microbes that help fertilize plants and recycle carbon from the atmosphere. We don't have to imagine it because it's happening now. Innovative companies are using synthetic biology or syn bio to engineer organisms and create new materials that promise to transform every sector of our economy.


Those companies say we have entered a syn bio revolution, and similar to previous industrial revolutions and the digital revolution, the syn bio revolution could change nearly every facet of our lives from medicine and pharmaceuticals to food and agriculture, climate mitigation and energy production. Today we talk with experts from three companies that are leveraging syn bio about what it is and the potential it holds to improve the health of people and our planet. I'm Rachel King, and you are listening to I Am Bio.


When people hear the term synthetic biology, they may have different ideas of what it means. That's not surprising because syn bio is a multidisciplinary technology involving genetic engineering, computer science, physics, and more. It brings those multiple branches of science together to design biological systems for specific purposes, and it does so with a precision and speed that scientists could only dream of a decade ago. Each of our guests works at a company that is applying the principles of synthetic biology to make better, more sustainable products. Our first guest was inspired by the potential of synthetic biology as a graduate student.

Matt Begemann (02:38):

Hi, my name is Matt Begemann. I lead gene editing and trait discovery at Benson Hill. Benson Hill is a plant technology company that's focused on using AI and machine learning tools to create the next generation of protein crops, specifically soybeans and yellow peas. Synthetic biology is really a catchall term for a lot of really new advancements in genetic engineering, molecular biology, metabolic engineering. Really what it enables us to do is be much more precise in how we assemble pieces of DNA. So in the past we used something called recombinant DNA technology, and really what that allowed you to do is take existing chunks of DNA and you could stitch them together and get them to do something, whether it was produce something like insulin in a microbial system that can then be used as a pharmaceutical, but it was really limited by the pieces and parts that you had at your disposal.


What synthetic biology allowed us to do is have complete freedom on the design front and synthesize those pieces using modern DNA synthesis technologies, which has gotten much cheaper, which enables us to dramatically increase the complexity and size and scale at which we were doing things like metabolic engineering or genetic engineering.

Rachel King (03:48):

Here's a breakdown of synthetic biology from our second guest who says, we're only beginning to see what's possible through synthetic biology.

Michael Koepke (03:55):

I'm Michael Koepke. I'm the chief Innovation Officer at LanzaTech. LanzaTech has developed a new technology for carbon capture and transformation using biotechnology, but synthetic biology is, is I think, the ability to make biology easier to engineer, which really is the convergence and advances in biology and genetic engineering, but also combining that with chemistry, with computer sciences and engineering principles. So it's really about how we can go from idea to product faster and cheaper and with greater precision.

Rachel King (04:30):

And here's our third guest with her perspective on why the syn bio revolution is such an exciting advancement in science and industry.

Jennifer Wipf (04:38):

Hi, I am Jennifer Wipf, I am the SVP leading the commercial team at Ginkgo Bioworks. At Ginkgo Bioworks, we have built a platform to do synthetic biology at scale, and what that means is that we've taken the work that it used to take PhD scientists in a lab doing things by hand, and we've built out automated ways to do that work at really high scale so that we can increase the throughput of asking scientific questions. Biology has solutions to a lot of the problems we're looking for. It has spent billions of years with evolutionary pressure trying to solve those problems, right?


It's why muscles have an amazing adhesive, and if we could harness that elsewhere, do we need to use adhesives that are made from petrochemicals or fish don't need sunscreen, right? Like they have developed ways to block out UV. Microbes use a lot of interesting substrates if they're at the bottom of the sea or around a lot of sulfur. Plant create energy from sunlight, right? So biology has these solutions and it's about us trying to figure out how to use those or think about that as more of like an engineering discipline to create those products in a way that are usable for us in other formats.

Rachel King (05:55):

Matt was inspired to become a scientist and work in synthetic biology because of its potential to make life better for people.

Matt Begemann (06:01):

I was an undergraduate at the University of Missouri and I went to a guest lecture by a professor named Jay Keasling, and he had come from the University of California Berkeley, and he talked about, you know, this was the early days of synthetic biology, of taking a metabolic pathway that was in a very rare plant to create a chemical compound called Artem Medicine, which is used as an anti-malarial drug. But because it was grown in a fairly rare plant, it was hard to make enough of this drug to really apply as a pharmaceutical. And this was one of the first, you know, major applications of synthetic biology as they were able to move that entire metabolic pathway into a bacterial system so that they can use something like fermentation to create a lot of that compound. And that got me really excited about the applications of genetic engineering and synthetic biology, because it just wasn't an experiment in the lab where you got a result, but it was an outcome that has a real impact on people.

Rachel King (06:54):

Here's Michael again on why he thinks synthetic biology is so beneficial to our world, especially in meeting the challenge of reducing our environmental impact and becoming more sustainable.

Michael Koepke (07:05):

So why is this important? We're in a climate emergency and the world is literally on fire. So every day you look in the news, you see new climate disaster reports, or whether it's flooding or drought or extreme weather events, and all really is linked to our industrial activities and the rising levels of greenhouse gases in the atmosphere, for example, CO2. It turns out that biological systems are fixing CO2 since billions of years. In fact, life on earth might originated from CO2 as, as building block. So now by harnessing this capacity to partner with biology through biotechnology and synthetic biology, we can take advantage of this abundance of available CO2 and other based carbon streams and really transform the way the world creates and uses carbon and enabler circular carbon economy. At LanzaTech, we're using such ancient biology for modern need and applied it to an industrial setting.


We built the process around a carbon fixing microbe that's called Clostridium Autoethanogenum. You can imagine the process a little bit like a brewery, but instead of yeast that feeds on sugars, we use this clostridium microbe to feed on gases. The gases can be, for example, off gases from industrial plant like a steel plant. To do this, we have developed, uh, specialized bioreactors and highly trained and deficient microbes. Using this process, we can make ethanol, which is the basis for fuels, but also other key building blocks for various consumer goods like apparel, packaging, cleaners, detergents. And with synthetic biology, we further have the opportunity to make an array of other key building blocks with our process.

Rachel King (08:55):

You heard that right. Thanks to synthetic biology in concert with genetic engineering, microbes can be supercharged with carbon fixing abilities. We can use those super microbes to take a harmful greenhouse gas out of the atmosphere and turn it into clean green biofuel. Michael says, producing sustainable aviation fuel is one of the most exciting outcomes of his company's work with sym bio, and that's only the beginning of the exciting applications of this technology.

Michael Koepke (09:24):

We actually spun this out into a separate company [inaudible 00:09:27] to really accelerate this development and really kind of build out capacity since I think this is something that I think critically needed. I think air travel is responsible for a significant amount of greenhouse gases, and there is a huge demand, I think for sustainable aviation fuel. So I think this is certainly one thing that we're very excited about, but the technology is really flexible. So I think we also had a lot of launches in the consumer good space. So I think we have, uh, apparel collections now out with, with Zara, with H&M, with Adidas, with Craghoppers. So it with a lot of, uh, global brands. And also I think we've looking at various kind of applications in the home care area with Unilever, we've worked on various cleaning, uh, agents and also like with [inaudible 00:10:14] and Gucci for example, we have a fragrance line out as well.


So I think we really kind of see this technology being broadly applicable across sectors, and we really very, very focused looking at where can we make the biggest impact. So I think if you look at sustainable aviation fuel is, is certainly linked to a lot of greenhouse gas emissions. If you look at the fashion industry, a lot of greenhouse gas emissions. So this is really where we, we see where we can make an impact. And in fact, to date, I think we've already mitigated over 300,000 tons of CO2 with the plants we have in operation. And now we have, by the end of this year, I think we have six commercial units that are operating. So I think these will each year debate half a million tons of CO2 and at the same time make 300,000 tons of product.

Rachel King (11:05):

Michael says, we're just getting started with transforming many other products we use, making them more sustainable through syn bio and biotech.

Michael Koepke (11:13):

Synthetic biology and biology in general, I think can do things that no other human made technology is able to do. So I think we can think about really advanced materials with advanced features, whether it's biodegradability or specific other features, for example, that, uh, cannot be achieved in a different way. It's also really critical stage now that we bring these products to market and bring these products to scale. I look at the room I'm sitting and everything is really coming from fossil resources, I think whether it's the, the computer or the chair I'm sitting on and everything really comes from petrochemical sources. It's really kind of thinking through how can we change that and biology can really be a big part of that. We also have a, a growing population that needs to get fed.

Rachel King (12:02):

Michael talked about the need to feed a growing population, and that's a good point to turn back to our first guest, Matt at Benson Hill, a food and feed ingredients company that specializes in breeding high protein crops.

Matt Begemann (12:15):

These crops have mostly been bred for yield over the years, but our mindset is really can we shift that to things like protein, protein quality, and nutritional quality of those crops. Something interesting that we've been working on recently is developing really high protein soybean meals that are low in anti-nutrients, like oligosaccharides that can irritate the guts of humans, but also animals that we feed. So our high protein, low anti-nutrient soybean meal can actually be used as a replacement for a more expensive, more energy intensive soy protein concentrate normally used in aquaculture.


When we think about real world impacts at Benson Hill, we can really think about soybean as our most efficient protein source in the world. It's a really incredible crop that's grown on over 80 million acres in the United States alone. If we could make that crop a little bit better in terms of higher protein content, what we've achieved is increased sustainability across that entire platform. If we can make that soybean variety have lower anti-nutrients that are gonna have a larger impact on animal health outcomes, animal welfare, that's a really broad impact that we can have as a company because soybean is used in so many diverse applications from human food to animal feed. So by making better varieties that are focused not just on yield, but yield and quality, yield and higher protein, we can have a really big impact on our agriculture system.

Rachel King (13:38):

Matt explains the unique role of synthetic biology in the company's research and development.

Matt Begemann (13:43):

At Benson Hill, we don't use synthetic biology to create a new product, but we do use synthetic biology in our discovery lab to speed up the rate of innovation. So if we wanna do an experiment on a plant, let's say we're trying to understand how a particular gene or piece of DNA affects protein content or protein quality in a plant. To do a specific experiment in a plant can take multiple plant generations, which means multiple years. And plants take up a lot of space. So we can use something like synthetic biology to recreate that chunk of DNA and synthesize it, design it, and test it in parallel and really small test tubes using automated equipment. And we can do thousands of experiments in a year versus just a couple over the course of a year using traditional plant biology. So this allows us to learn really quickly, look at multiple variations of a gene, and then give very specific instructions to our breeding team or our gene editing team on how we wanna precisely change a particular gene or look for a particular version of a gene within a population of plants.

Rachel King (14:42):

A primary driver of global hunger is the cost or lack of availability of fertilizer. Jennifer shares a real world impact that Ginkgo Bioworks is developing to strengthen food security around the world.

Jennifer Wipf (14:55):

The fertilizer problem is really about nitrogen fixation for plants, and some plants have developed ways to fix nitrogen on their own, but not all, and importantly, not any of the crops that we rely on quite a bit, right? Like corn and things like that. And so we are working on a solution with, it was a company called Join that was a joint venture from Ginkgo and Bayer to work on solutions in the agricultural space. One example of that is teaching microbes to live on the surface of plants to do that nitrogen fixation for them in the way that other plants have already learned how to do.

Rachel King (15:38):

I've always been hopeful about the potential for scientific innovation to make our world more sustainable and healthier. When we come back from the break, we'll look at how these companies are combining multiple scientific disciplines to power up their success in tackling some of our toughest challenges.


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In the first part of this episode, we talked with our three guests about some exciting outcomes and applications of synthetic biology. Now let's take a closer look at the process and how their companies are combining subfields of science, including artificial intelligence to engineer organisms as precisely and efficiently as possible. Jennifer Wipf of Ginkgo Bioworks explains the role of AI.

Jennifer Wipf (17:15):

People ask us what kind of company we really are, and in a way, we're a synthetic biology company, right? We're trying to harness what biology can do. We also view ourselves in many ways as a tech company and sort of take a lot of lessons from tech companies like Google or like Amazon. We also think of ourselves as a biotech company, right? Because we're creating solutions in the biotech space. So we're really this kind of intersection of a lot of disciplines. What we're really excited about is the application of AI in the work that we're doing. We've all become acquainted with AI in our vernacular because of things like ChatGPT and GPT 4. And what's really interesting about that is that those were created off of the English language. So we trained GPT 4 off of the Library of Congress and everything that's in the internet and Reddit and all of these things.


But if you think about using AI in biology, we have a different set of challenges, right? We invented, humans invented the English language. We did not invent biology, it invented us. And so when you go to train something like GPT 4, we're doing that by basically giving it, let's say a sentence, a 10 word sentence, and leaving off the 10th word. And we ask the AI to say, "What's the 10th word?" And then we read it. You can read the sentence and say, "GPT 4 got it right." I can read the sentence and say what the word should be, but we can't answer the rest of that sentence In biology. I can't put a string of DNA together and say, fill in the next GCAT or fill in the next amino acid. I can't tell it that answer, you can't tell it that answer. And so what we have to be able to do is actually test that each and every one.


And we can do that with the foundry that we built in Ginkgo. We can basically systematically go through and say, "What does the rest of the sentence look like? What's the answer?" And then use that to continue to program and hone that AI. And so what that allows us to do is get closer and closer to understanding the way biology works. We, we really have a limited understanding of that at this point in time. And the more we can do that, the faster we can develop these solutions, the faster we can understand not just what will work, but what won't work, and the faster we can rethink kind of what we can use biology to do. And so I think the combination of AI and synthetic biology, like that's the killer app, that's the most exciting thing that's happening right now.

Rachel King (19:48):

Matt Begemann at Benson Hill says his company is also pairing AI tools with synthetic biology to enhance the speed and performance of their new crop varieties.

Matt Begemann (19:57):

At Benson Hill, we have an AI machine learning system called Crop OS. And what Crop OS is, is it's a platform that allows us to design, build, and test new varieties of, of plants like soybeans. Many of the listeners are probably familiar with more consumer driven, um, AI machine learning tools like Netflix and Spotify, where these tools will provide you with a new playlist for that day or it'll give you your next recommendation on a movie to watch. And how these tools work is they absorb what I call strategic data layers. So decades of viewer data on what movies you watch, what did you watch next? What did your friends watch or what songs did you listen to? What categories of song, what type of news do you like to listen to? At Benson Hill, our strategic data layers are genome sequences of soybean varieties, and all of the data we have on those varieties in terms of their performance, like protein yield, anti-nutritional compounds, flavor, whatever type of data that we collect, and we can feed that into our machine learning tool.


And rather than making the next playlist, what it can actually do is it can predict the performance of a plant based on its DNA sequence. So what we can do is we can go into our Crop OS system and say, "Hey, we're looking for a plant with these properties." What Crop OS can do is it can select parents of specific plant varieties that we wanna cross. It can predict what the progeny or children of that cross will be. It'll tell us what those DNA sequences are potentially gonna be, and based on those DNA sequences, it can tell us the performance of those new varieties. So then we can go into build mode, which is we go into our crop accelerator, we can make these crosses.


The crop accelerator is an indoor agriculture facility that allows us to do multiple seasons in a year versus working outside where you get basically one season, maybe two seasons if you're working really efficiently. And we go through and we identify those plant varieties with the DNA sequence that we're looking for. We can ramp up those varieties in our crop accelerator, and we take the very best out to the field where we measure their performance and generate new data on them.

Rachel King (21:52):

There are barriers to adopting the technology. Michael says cost is one of the biggest challenges.

Michael Koepke (21:58):

I think the key gap, especially if we look at using biology for, for manufacturing and using scale up, scale up is certainly something that's costly, that's expensive, that's difficult. For LanzaTech, it took over a decade to scale the process, and it's been a first of its kind process, of course, from the lab bench to this commercial scale, which is bioreactors that are greater than 500,000 liters. So we went through multiple pilot and demonstration units to get to this stage. And I think that that's where a lot of the technologies really kind of fail or really kind of, uh, need to go through often refer to this valley of deaths. So I think these are things that I think are really important.


There's also tools like techno economic analysis to get a sense of the process economics, uh, as well. These are things that can be used to de-risk the scale up stage. But right now I think there's a lack in infrastructure and, and scale up compared to the number of synthetic biology companies that are outside that are starting. This is really an area where I think we need to see further development. It's been also recognized, there's also in the US now, I think a lot of focus around the bio economy and I think addressing that. So I'm, I'm very, very positive about that.

Rachel King (23:17):

Jennifer also says the cost of scaling up syn bio can be a barrier.

Jennifer Wipf (23:21):

It has been, and to some extent still continues to be manual work, expensive, time-consuming. The cost to make those new compounds maybe is outweighed by the future revenue or applications that they could have. And so as you reduce the cost of entry to try something with biology, I think you open up a lot of new possibilities. And so I think the barrier is really just the ability to do the work at scale and really cheaply and, and quickly.

Rachel King (23:55):

Jennifer says another barrier, consumer understanding and acceptance can be addressed by explaining the technology, its safety and its benefits.

Jennifer Wipf (24:04):

Certainly we welcome those kinds of discussions and we think a lot about how to approach this industry and the work that we do with care and thoughtfulness. With any new technology, it's really important to think about the positive benefits, but also the challenges and the changes, the societal changes, the environmental changes that are gonna come with that. And we think a lot about that at Ginkgo and welcome those conversations.

Rachel King (24:41):

The synthetic biology revolution is the next big thing that will transform our world and the things we use every day. It's truly a testament to the boundless potential of scientific innovation to address societal challenges and improve our wellbeing. I wanna thank our guests, Jennifer, Matt, and Michael for their help to uncomplicate this complex topic and for sharing their perspectives on the exciting progress and promise of sym bio. And thank you all for listening.


Make sure to subscribe, rate, and or review this podcast and follow us on Twitter, Facebook, and Instagram @Iambiotech. And subscribe to Good Day Bio at bio.org/goodday. This episode was developed by executive producer Theresa Brady and producers Lynne Finnerty and Kourtney Gastinell. It was engineered and mixed by Jay Goodman with theme music created by Luke Smith and Sam Brady.