Nick has engineered these petunias to include an inducible gene. When he lightly touches their buds with a clear molecule called dexamethasone, the molecules seep into cells, switch on the gene, and cause them to make a pigment. The result is a paintable flower, where molecules literally control which colors show up in particular places. Nick’s plan is ultimately to engineer these petunias to express three separate inducible genes, or biosynthetic pathways, for cyan, magenta, and yellow. For a prior project, Nick turned Arabidopsis, a small (and quite ugly) plant that researchers commonly use in research, into little pink “micro-roses.”

We filmed this episode surrounded by flowers. Nick patiently explained to me how each one gets its shape and pigmentation; how he combines breeding and genetic engineering to make new flowers; and how he searches scientific papers for mutations to figure out which plant crosses to make next. His ultimate dream is to build a botanical garden full of weird and wonderful flowers that exist nowhere else.

Watch on YouTube. Listen on Apple Podcasts or Spotify.

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Timestamps

1:28 Paintunia
7:46 Tools for flower design
18:47 Petunia patterns
33:16 Engineering new traits
40:38 Turning Arabidopsis into pink micro-roses
54:26 Getting genes into plants
1:06:02 Mutant botanical gardens
1:14:24 Beauty is sufficient
1:20:30 Flower design studio

Transcript

Desnoyer: I would like to create a botanical garden that you walk into and you don’t just appreciate the flowers, but you actually understand them a bit deeper through a scientific lens. I want these flowers to only exist there. I want them to be weird and wonderful. When you walk through this garden, you get that feeling of magic in that when you walk through the garden, you’ll be forced to take a closer look at what’s going on. That once you leave this garden, you want to take a closer look at nature.

McCarty: I’m extremely excited for today’s interview, which is with Nick Desnoyer. He’s a plant biologist in the United Kingdom; a postdoctoral fellow at the Sainsbury Laboratory in Norwich, England, which is where we’re filming today. But more famously online, he’s known as a flower designer in that he designs and then creates his own types of flowers using breeding, mutations, and genetic engineering. If you can watch this interview on YouTube, that’s probably the best option because we have a lot of props. There’s a lot of flowers that we’re going to talk about. And let’s just get into it. Welcome, Nick.

Desnoyer: Thanks for having me. Very excited to be here.

McCarty: Let’s just start with the announcement. You’re working on a new project. You haven’t revealed it yet. Tell me about that.

Desnoyer: I haven’t actually talked about this project that I’ve been working on for a bit. It’s my next big project after the micro-rose. It’s called the Paintunia. The whole vision of the Paintunia is that it’s a living canvas. In contrast to a normal canvas that you would paint onto that’s made of dead plants, fiber and cotton, this is a living canvas that you actually direct it to paint itself. And I think there’s a lot of magic in that, which we can maybe get into.

McCarty: How does it actually work? It’s an engineered line of petunia, and tell me about it. We have it on camera.

Desnoyer: We have it here. This is the first version. There’s going to be many iterations. The final concept is that you would add three different inducer molecules. These are small molecules that you can treat to the floral bud at different stages and different concentrations. And based on those treatments, you direct transcription factors that lead to the expression of pigment biosynthesis genes that become turned on after about 16 hours. And so in a way, you’re orchestrating the gene expression of the flower and you get some feedback from the flower after you’ve treated it to see how the molecules diffuse through the flower. How is it responding to different pigments being produced in the same place? Things like that.

McCarty: This is one of the flowers here. And so this is not actually a flower that you made, right? It’s from a 20-year-old science paper, research paper.

Desnoyer: Yeah.

McCarty: But they basically made an engineered line of petunia that when you paint it with this small molecule called dexamethasone, it turns those regions pink as the flower opens. And so you get this. This flower has actually been painted.

Desnoyer: We have a few more of them as well. You can see that you can make different patterns based on how you treat it. And so I want this flower to really become a medium for art, where the flower really becomes the canvas. I’m calling it Paintunia because it’s based on Petunia hybrida, which is probably the second most studied flower in the world just after Arabidopsis. But there’s a lot more known about the colors in Petunia versus Arabidopsis. It’s the most studied in that realm. And what’s really nice about it is you see you have these five fused petals that are papery thin. They’re like three cell layers thick. And so it really seems like a perfect canvas.

McCarty: You want to take this line essentially that somebody had already developed and you want to add more colors so that there’s different small molecule inducers that would turn on a cyan, a yellow. How hard do you think that’s actually going to be?

Desnoyer: This might actually be the first time that you have a flower producing all of these different classes of pigments. For example, flowers that make betalains don’t typically make anthocyanins. And so we don’t necessarily know how those blends of colors are going to look.

McCarty: But what color is a betalain? What color is an anthocyanin?

Desnoyer: Right. Because this will be a living canvas for painting, it needs three major colors, cyan, magenta, and yellow. And with this, you can make blends to reach the entire color spectrum. Right now I have magenta, which is anthocyanins, but I’m going to eventually make this to be the cyan, or at least try and get close to cyan. For cyan, I’m going to now cross this to ornamental varieties that are a bit more blue. A mauve. Actually, I think we have one here. Yeah. In this background, this is also anthocyanins, but it’s a bit more blue. Ideally, it would be a perfect cyan. I’m going to try and introgress some of the anthocyanin biosynthesis genes in this background into that flower. When you add the dexamethasone, it turns a bit more blue. And then for the magenta, I’m looking for betacyanins, which are betalains.

And then for the yellow, I’m going for either betaxanthines or carotenoids.

McCarty: Do we have a yellow one?

Desnoyer: Oh yeah, down here. This is a more newer line. I think this one popped up about five years ago. And this one was exciting because they didn’t have a true yellow petunia before this. This one’s called Bees Knees and it’s a completely different class of pigments. It’s called carotenoids. This is probably accumulation of beta carotene within the chromoplasts. But what’s cool is that once you now have this true yellow, you can cross this to all the anthocyanin lines and then see how does this pigment blend with the others.

McCarty: Is that what you’re doing? To get your second color for the pentunia?

Desnoyer: Totally. For example, if you were to cross this yellow with this dark purple line, you get a flower called Black Mamba. And this is... I wouldn’t say true black. It’s almost a philosophical question about what true black is. But because you have all these anthocyanins that are absorbing a certain spectrum of light and the yellow doesn’t overlap with that spectrum, it’s just absorbing a lot of the light. And so you get kind of a black flower. The reason I’m going for CMYK and not RGB is these are two classes of colors. What RGB is, is additive. So it’s like a screen. A screen starts as black and then you add red color or you add blue color and you see how those blend. Whereas in real life when you’re not illuminating something, but it’s rather the absorption of the light, it’s subtractive. And so that’s why printing in physical paper is CMYK.

McCarty: When you actually think about designing a flower, what are the dimensions that you can control? What are the sorts of parameters that you think about? And how much can you actually deviate from natural designs?

Desnoyer: I break it down into two major principles of flower design that helps me organize all the thoughts. And this is a simplification. It’s just based on the visual of the flower. There’s other dimensions like smell and taste, maybe even hearing that we can get into. But this is just based on the visual. I think of sculpting the flower and painting the flower.

In terms of sculpting, you can think about rearranging the architecture of the flower. That’s where and what organs are placed and how many. And then once those organs are placed, how are they shaped? Their size and shape, that’s more organogenesis. And then on the painting side, I think of changing its color or pigmentation and then where those pigments are placed. The patterning with those four major principles, you can think about designing any flower you’d want.

McCarty: For example, this flower here, this is just a wild type flower, right? This is a plant that people bred probably to look like this. People have basically been creating flowers that have certain forms for thousands of years, right?

Desnoyer: Yeah.

McCarty: In terms of construction or the first part of this, the sculpting: is there really any additional benefit you get from genetic engineering? Or is it basically all breeding?

Desnoyer: Right. Just for some context, there’s about 300,000 flowering plant species. And then when you think about all the varieties that we’ve made, it’s tens of millions, even the varieties of the wild type and the ones that we’ve bred. What’s really beautiful about breeding is anyone can do it. It’s extremely accessible. All you need to do is just cross two flowers, collect the seeds and then start selecting the traits that you like. This goes back like 10,000 years. For example, modern corn comes from tiosinte, also a flower. And this has actually been fundamental to the success of humanity. It’s probably the biggest driver of human success is flower breeding. And so there’s breeding for purely aesthetic purposes, but also obviously breeding for food. It’s very powerful. Almost every flower you find in the grocery store has been bred, and you can make so many different forms and funky colors, everything under the sun.

Bioengineering, in contrast, it’s a bit more modern and new, and you have, I would say, less control. I would compare it to kind of like levers that you have that you can introduce to create new traits. And what I’m really interested in is creating traits that you wouldn’t be able to make with breeding. And so with breeding, you’re stuck within the plant family that you’re able to cross these flowers with. And so if you try and cross this rose with another species of rose, maybe they’re incompatible. All you have is the natural genetic variation, which still there’s a lot. Every single one of these petunias comes from an original cross of Petunia axilaris from like 200 years ago. But what really makes me excited is with bioengineering, you break out of that natural variation and that plant species and you can access the entire tree of life.

And so then you can think of all the molecular inventions that evolution has created. And so some of these flowers are taking molecular inventions or genes from bacteria, fungi, humans, you name it.

McCarty: The thing I’ve been most impressed by, hanging out with you the last two weeks, is that you have this somewhat encyclopedic knowledge of papers and mutations and phenotypes. You can recall things such as, “Oh, in 2002, this lab made this cross. They found this mutant and the flower had these traits.”

Desnoyer: Yeah.

McCarty: So basically, a big part of your design process is just knowing which mutations people have already found and what that led to in the flower. And then crossing those in interesting ways. There’s actually not a lot of genetic engineering involved, right? There is in the designs and we’ll talk about other projects later where you’re adding pigments and these things. But the sculpting process seems to be finding the right mutants and then breeding them.

Desnoyer: Right, exactly. It’s not like a typical design process where you would start with a customer and think about what’s the ideal product for them and then go back and this year limited to the code. It’s like, what can the code make? And do we know the code that makes that? And so for example, in Arabidopsis, it’s the most studied flower in the world. It’s got 34,000 genes and we know the function of most of the important ones. And so that is like a whole sandbox for genetic engineering and all the tools that are made for Arabidopsis. That’s probably the most powerful medium for genetically engineering a flower in terms of sculpting.

McCarty: There is a database of Arabidopsis mutations. Basically, there’s so many people who study that. But you started working in Petunia and there are much fewer known mutants, right? Why do you not spend the first part of your project just making mutants? How difficult would it be to just make a ton of Petunia mutants and discover your own phenotypes?

Desnoyer: Well, I would love to do that. But at the moment, it’s just me and a colleague, Juan Pablo. And I still have a postdoc project, actually, that consumes most of my time. But the ideal scenario would be that I have a garden, I have every possible mutant, I can do mutagenesis and pick up ones that aren’t even found yet. And so most of the diversity that I’m actually working with, they’re commercial cultivars or they’re from the Amsterdam Petunia germplasm collection, which is maintained by Francesca Quattrocchio and Ronald Koes, who have totally helped me get into this.

McCarty: If you wanted to make a huge library of mutants, how would you actually do that? How do people mutagenize flowers and then screen for phenotypes? I would imagine it’s just a lot of waiting. Are they using chemicals? Are they using x-rays? Does it matter what you use?

Desnoyer: There’s a lot of ways you can mutate plants. A famous one, especially in Arabidopsis, is called EMS, which is a chemical that induces—causes the polymerase to make more mistakes and you get all of these mutations. You soak the seeds in this chemical mutagen. Another way is fast neutrons. I don’t know too much about this, but I guess you blast it with neutrons. And this is—breaks the DNA and then repairs, possibly. Another way is actually just putting them in full sun. UV radiation induces more mutations. Well, that all falls under breeding. One of the coolest ones is transposon-mediated mutagenesis, and this is a really cool flower here. This is actually why petunia was a major model organism for so long, is because they found this mutant. This flower, it’s now called W138. It originates from a commercial line called Roter Vogel, which means red bird in German.

And some scientists brought this into the lab and they made it inbred or they tried to homozygose it so that all the progeny are more or less the same and you can have reproducible results. But something cool popped up, which is that this transposon had jumped into one of those transcription factors that regulates anthocyanins, AN1. And it popped in just at the border of an intron in this gene. And so the transposon, it’s about 230 base pairs and it’s extremely unstable. But essentially the scientists saw this. They saw all these streaking patterns. They could tell that a transposon is moving. And then they just propagate this plant knowing that this transposon is going to excise and jump into other places of the genome. And so most of the mutants that we have for Petunia derive from this line and you can figure out what the causal mutation is quickly because they know the sequence of the transposon, so you do flanking PCR.

And they maintain all of those mutants actually in Lyon, in France. I’ve heard that they lost actually all of them due to a flood, which is really sad. And so when I was at the Petunia Community Conference, they were talking about how do we reestablish all of these mutations? What I think would be a really beautiful project actually is because these are wild type, but they don’t have any transgene, these you can grow in your garden. And so I would love to have a community breeding project where you give this out to like 10,000 gardeners. They can cross it to their own petunias or just have these grow and document these transposition events and the weird things that pop out. And this could come along with a guidebook of all the mutants that we know in petunia. They could figure out what the causal mutation is.

McCarty: And so these patterns of red, right? These are basically cells where the flower is naturally white. The flower is naturally white, but when you see the red, that means that the transposon has jumped.

Desnoyer: Right. This is in an AN1 mutant background. And so the flower is typically white because it has no anthocyanins. And the mutation is this DTPH1 transposon that sits within the gene. And so it can’t be fully translated because it has an early stop codon, but when it jumps out early during the petal primordium development, then it restores its function and all the function of all its daughter cells. And so you get these sectors where you can essentially trace the lineage of that cell. And depending on when that transposon jumps, you’ll have a different size of the sector. These really large sectors that happened really early. Whereas if it jumped really late in development, you can have it even in a single cell.

McCarty: There’s other petunias here too, right? Let’s talk about more petunias.

Desnoyer: Sure.

McCarty: That’s the transposon petunia. What are these ones?

Desnoyer: Let’s see.

McCarty: This is called Night Sky, right?

Desnoyer: Yeah.

McCarty: What’s going on with Night Sky?

Desnoyer: You can tell this one’s Night Sky because it has all of these white spots, but the spots can actually be much different than this. This is an example of post-transcriptional gene silencing. I think this one’s even cooler. It’s like an inversion.

You almost have this Rorschach looking pattern and you can see it’s quite diffuse. If you see this diffuse white and not a dark purple background and you especially see this gradient of color going white to red, you can be almost certain that that’s post-transcriptional gene silencing. Because these are actually—the silencing is mediated by small RNAs and these diffuse through the plasmodesmata. And so you get these gradients along the border. Whereas the transposon that I showed before, this is a genetic event. And so there’s none of that diffusion. This is actually where post-transcriptional gene silencing was discovered.

McCarty: Tell me that story.

Desnoyer: This comes from another petunia background called V26. It’s a really purple line. It’s this one right here. And I think it was back in the 70s, maybe 80s, some scientists wanted to make this flower even darker purple. And so they overexpressed one of the early genes in anthocyanin biosynthesis called chalconsynthase. And when they transformed this plant and overexpressed it, it actually didn’t get darker purple, but it reverted back to white in many cases. And so I think like 40% of the transformants, it went back to white or had these weird blotchy patterns or circles or even star patterns along the Corolla fusion sites. And there was a WTF moment when that happened. Apparently the first author of this paper was bringing it around showing people, coming up with crazy explanations about how this could be because back then they didn’t know about gene silencing.

McCarty: And there’s some other petunias here too, right? This is the original transposon line?

Desnoyer: Roter Vogel, I believe. This is a nice coral red. This is just another flavor of anthocyanins called peligronin.

McCarty: Why do some anthocyanins look red and some look purple?

Desnoyer: It’s just they have different enzymes that shift the pathway. Anthocyanins are a pretty complicated biosynthesis pathway where the compound is being hydroxylated or glycosylated. And so depending on the presence or absence or expression levels with these different enzymes, you shift it towards different colors. There’s actually an even another layer of the coloration, which has to do with the acidity of the vacuole. These anthocyanins, they move into the vacuole, which is quite acidic environment. And then depending on the pH of that, they can change from blue to pink. Like hydrangeas that you may have in your garden if the soil is really acidic, it’s more blue. If it’s more basic, it’s more pink.

McCarty: And what else? Let’s see. You brought a lot of petunias, right? What’s going on with this petunia?

Desnoyer: This one. You have Queen of Hearts, King of Hearts. This one, we didn’t know actually what it’s called. My colleague called it Silent Prince. As you can imagine, this is also post-transcriptional gene silencing.

McCarty: This looks much more controlled.

Desnoyer: It looks much more controlled, but the breeders still don’t even know why. It’s in this star pattern. And so with gene silencing in petunia, it’s the reason for almost all the patterns. But they don’t know why it arises in certain places. They’re learning more and more about that though.

McCarty: Just to be clear, this flower would normally be purple. It’s just the gene encoding the purple gets silenced at a certain point in development. And so that the cells that become these white part of the petals look white. And you were telling me too, while I’ve been here, that most flowers are just naturally white, right? White is the default state of flowers.

Desnoyer: I would say white is, you could say, the default state of all the organs and that you just have pigments that are expressed over it. And so sometimes you get an effect called virus-induced gene silencing in leaves. And scientists often target the gene called PDS to know if the virus-induced gene silencing is working. And in that case, you get all these white sectors in the leaf and that’s because the chloroplasts are being degraded where the chlorophyll isn’t accumulating and so it goes back to white. You can get a fully white leaf.

McCarty: And so last petunia here.

Desnoyer: Oh yeah.

McCarty: I’m interested in this one because it has this really beautiful—the color flows through the veins. It looks like veins. What’s going on here?

Desnoyer: This one, I don’t actually know. But I would assume that you have more anthocyanins accumulating in the vasculature. Probably the phloem companion cells. There is a promoter called SUC2 that’s a really famous promoter for phloem companion cells that you can drive the expression of different genes. And so perhaps it’s more stressed within the vasculature and so you have more anthocyanins. There’s actually a gene expressed there. But it’s an interesting exercise to think, if I want to now bioengineer this flower, how do I access the different domains of the petal? How can I just get it along the margins? How can I get it just within the veins or the center or these spots?

McCarty: It’s basically when you think about your design, you’re looking to nature. You see things that pop up naturally. And then in your head, you’re like, “Oh, I bet I could figure out a way to use that!” Like getting color in the vasculature or adding new layers of petals like this, right? Double stacking petals.

Desnoyer: Right.

McCarty: Or using gene silencing to get these really beautiful patterns, which is just amazing, right? It’s like you look to nature, you see the natural variation. Then you’re like, “Oh, I can cross these things to get the features I want.”

Desnoyer: Or you think, how does the plant make this? How can I reverse engineer that with bioengineering?

McCarty: Which also makes you look more closely, probably.

Desnoyer: Totally. It completely actually changes how you view nature. And I think that’s the most beautiful part of the project. It’s like how your job influences your perspective on life. If you’re a carpenter, maybe you’re just always looking around at the wood and taking a closer look at that. I probably didn’t even think about what type of wood this table is made of. But it influences how you see the world. And so as a flower designer, you really start to look at all plants as amazing inventions of evolution. And it really sparks your imagination as to how they make these things.

McCarty: This is technically a petunia, even though it doesn’t look like it, where the leaves are forming...

Desnoyer: There’s basically no petals.

McCarty: So it’s leaves. One thing I’ve noticed is why don’t we see flowers that have green? Surely there are green pigments or there’s ways to put chlorophyll back into the petals. Why do we not see green flowers?

Desnoyer: If you don’t find something in nature that means either it hasn’t evolved because it’s not fit or because it’s something really difficult to evolve. This is the case of the former. It’s just not very fit. As I mentioned before, petals have the sole purpose of attracting insects and having them pollinate them. And so a green petal may not stand out to a pollinator. In fact, it may attract more herbivores that want to eat that petal. Obviously there’s many ways you can make a green petal. All you need to do is have it revert back to sepal identity or not lose its chloroplast. There’s tons of mutations that you can do to make that. But that doesn’t typically evolve.

McCarty: But if you wanted to, could you breed this in the lab to enlarge these so that it looks like a flower that is green?

Desnoyer: Yeah. There’s a flower that we don’t have here, but it’s called the Picasso petunia. It’s actually my favorite and it’s like a lime green, with pink pigmentation in the center. It’s less dramatic than this, but I would imagine that those petals have a bit more leaf identity. There’s also quite a few pathogens that actually infect plants in order to revert the flower back to a vegetative state. And these bacteria are usually transmitted by insects. And so it’s kind of co-evolution of the flower, the insect and the bacteria where the bacteria is trying to revert the flower back into food so that it recruits the insect. And then when the insect eats the flower, it obtains the bacteria and then moves to another flower. There’s also some ecology in flower design.

McCarty: The other color that I basically never see is true blues. There’s a lot of purples. We see blues in animals, right? There’s blue lobsters. Why do we not see blue flowers?

Desnoyer: I was looking for the most blue one we have here, but it’s a bit more mauve. And actually when you call something blue, you have to be very careful because it can be a bit scandalous. There was the first blue rose that came out. It’s called Applause. It came from a company, Floragine. It took 10 years to make. And when they produced it, they said, this is the first blue rose. But anyone with eyes can see it’s purple. And so the blue, it’s like, as you said, it’s really rare to have true blue pigmentation. You’ll find a lot of blue in nature, but a lot of it is structural color. It’s some kind of co-evolution between underlying pigment and then bending that light using structural variation on the cuticle or the waxy surface of the petal. And so that tells you something: that tells you that blue actually is fit, right, because it evolves.

And so it’s really that second category of it’s just difficult to evolve. And that’s probably because there’s something about blue compounds that are hard to biosynthesize or we don’t have the code for or the chemical is unstable. The most classic true blue in flowers is a flower called, I think it’s butterfly pea. It’s known as Clitoria, so you can imagine what it actually looks like. And there’s a guy here at the John Innes Center that actually did his whole PhD on Clitoria and defining what are the anthocyanins that lead to blue in this flower. And so he actually shared his PhD with me. And it’s amazing because he has the whole lore of blue pigments in his introduction. It’s also a beautiful thing that you can do storytelling about all the different colors. We could sit here for the next two hours and talk about every single color and all the organisms that have evolved different ways of making those colors and where they’re from.

And blue is an interesting one.

McCarty: And there’s also this flower that you were telling me about that turns translucent when it rains and it’s native to Japan. What happens with that flower? Why does it turn transparent?

Desnoyer: Yeah. That flower, it’s called the skeleton flower. And actually most petals, if you soak them in water or infiltrate them so that they become completely full of water, they will become transparent. If I take a white petunia and inject in water into the air spaces or the mesophyll of the petal, you’ll be able to see through it. That’s because it’s not an actual white pigment that the flower has. It’s more that it’s just diffuse light. And so that’s caused by the difference in the refractive index of the cell wall of the cell in that air space. And so the air’s refractive index is somewhere around one, and the plant cell wall is like 1.5. And so when it goes through the plant cell wall, it bends the light and then this hits another plant cell wall, bends. And so you get light scattering everywhere.

Of course, this looks white. But when you fill it with water, the refractive index of water is one. It’s very close to air. And so it just goes right through and is transparent. And so I imagine with the skeleton flower, it has large stomata or has some way of becoming soaked really easily.

McCarty: Have you thought about designing flowers that turn transparent?

Desnoyer: I haven’t actually, but that would be a cool one. You would need to probably get rid of the waxy cuticle on top of the flower because flowers don’t want to become soaked. When you get soaked, it’s really easy to get a pathogen infection because it’s full of bacteria. Most plant surfaces have a waxy coating to prevent that.

McCarty: Do you feel like we’ve mapped all the levers? So you also have this thing with smell, right? You have an ongoing project. But smell—are there, beyond smell, are there other levers as well? How big can we really go with flower design?

Desnoyer: I think you’re kind of limited in what code we have and what code has been discovered. And with bioengineering, I see it as complementary to breeding; you can create traits that you wouldn’t normally get within that plant family. And then once you create that, you can start to introgress it into different lines with breeding. Flower design encompasses both breeding and bioengineering. The exciting part of bioengineering is you can create traits that would have never evolved within that plant family. For example, recently people made a glow-in-the-dark petunia; the firefly petunia from Light Bio that’s being sold in the US. It’s a bit dim, but still it glows in the dark and it’s literally emitting photons and recycling the substrate for the luciferase, which is quite incredible. And so things like that get me really excited about new to nature traits and also this adventure aspect of biology in which you look out over the entire tree of life, at what are all the molecular inventions we have, and then thinking creatively about how can we implement those to create new patterns, new colors, and new structures.

McCarty: And what is the smell project that you’re doing?

Desnoyer: The smell project, we first wanted to go for something that we are very sensitive to, which is the smell of rotting flesh. And so there’s a few carnivorous plants. They’re called malodorous plants because actually they want to attract insects and want to mimic rotting flesh. Like Rafflesia, which is the biggest flower in the world. It’s in Malaysia, this really large red flower. But it produces a chemical, DMDS, through a two-step pathway that was recently discovered. And so actually it was my professor now, Sophien [Kamoun], who knew the person that discovered these enzymes and was like, “You should make smelly petunia.” But this is also potentially cool because maybe you could attract new types of pollinators like flies. So we synthesize the genes and we always test them first in bacteria. We always use microbiology to do quick tests, and so we boosted the expression of these two genes in bacteria and the first thing I did was make a liter of this bacteria and I let it grow overnight.

It’s a bit of a funny story because the next day I came in so excited to see if it really smells horrible and I was actually a bit worried because when I walked into the building, the whole building smelled like sewage and people were even talking me about how they couldn’t work there. And I immediately went white in the face. I was like, oh no, this is all because of me. But there was also a part of me that was like, by God, we’ve done it. And I’m thinking that this is going to be the most legendary story of the Sainsbury lab. And so I get closer, I’m telling people, I’m like, I think it’s me. And I get closer to the shaker where we’re growing the bacteria and I open it up and it smells just like E. coli.

And so it just so happened that the same day that I grew this massive flask culture of this corpse flower gene bacteria one of the sewage pipes had broken. With that said, when I smelled the bacteria it still smelled a bit like sewage, and we did a blind smell test throughout [The Sainsbury Laboratory] where I brought people controls that don’t have the gene. And they did double blind smell tests, and seven out of seven people could distinguish them. Now we’re going to see if putting these genes in petunia, if it triggers that smell. You’ll need the precursor of the metabolite and the gene product will have to be in the right place of the cell. Those are always the two considerations. And if those work, then we hope to actually test it with different pollinators, seeing if we can do pollinator switch.

I would love to have petunia, which is normally pollinated by hawk moths, hummingbirds and bees to now be pollinated by flies.

McCarty: Why did you choose a bad smell instead of a good smell?

Desnoyer: It’s just the first thing actually that came up. Sophien just happened to know a person that was working on it. But later, after telling this story, I realized it’s actually probably the best thing to go for first because it elicits a really strong reaction. And some people really don’t like it and some people love it. And probably the best art is art that divides the audience or produces a really strong emotional response. And what produces a more emotional response than the smell of rotting flesh in a flower? But it’s also a beautiful art project because it questions what is beauty. To us, we’re like, oh, this is a disgusting flower and maybe also to the hummingbird. But now that it’s attractive to the fly—well, beauty is subjective. The fly may find that flower more beautiful. And so it brings up this interesting question.

McCarty: And also, of course, flowers did not evolve for our aesthetic sense. They evolved to look the way they look to attract pollinators, right? That’s the whole function of the flower.

Desnoyer: Almost every flower that you can find in nature which is insect pollinated is a physical manifestation of what that insect finds beautiful. And so over generations and generations, they keep selecting what they find the most beautiful. And it’s a physical manifestation of that insect’s aesthetic sense.

McCarty: Let’s talk about Arabidopsis. Your first flower design project was micro-roses, which were basically Arabidopsis that you bred and then you added a transgene to get color. And so let’s just start with the wild type. This is normal Arabidopsis, right? It looks so unremarkable. And that’s because you were saying plant breeders have just inbred it for generations. Why were they inbreeding it in the first place?

Desnoyer: Scientists continued to self it so that it became an almost completely homozygous line. That means all the seeds from that plant will have more or less the same traits and that makes experiments more reproducible.

McCarty: I see.

Desnoyer: Oftentimes if a scientist wants to adopt a new model organism for plants, the first step is to make it either double haploid where it’s completely homozygous or you just keep selfing it for like 10 generations.

McCarty: Basically they just breed it with itself until all the progeny are the same.

Desnoyer: Right. But still they are slightly different. If you were to find wild type in different labs around the world and sequence them, I’m sure that they would each be slightly different. And this actually may lead to some discrepancies in results. There’s also different wild type backgrounds. There’s Landsberg, there’s Columbia, there’s Erecta, and then there’s tons of other ones. But the most common one which you see here is Columbia, like Columbia, Missouri.

McCarty: If you were to walk around outside though, you would see Arabidopsis all over the place. But it wouldn’t really look like this, right?

Desnoyer: No, it would look very, very similar. I believe even in the wild, Arabidopsis thaliana is still mostly selfing. Which is a sad story because once a plant evolves a selfing strategy, it’s very efficient at the beginning because you can produce a lot of seeds. But it’s more or less an evolutionary dead end because you can’t create any new variation.

McCarty: And so when you started to think about designing Arabidopsis, what was the first thing that you did?

Desnoyer: Actually the first time I designed Arabidopsis was with fluorescent proteins. My PhD was all on plant reproduction and I was doing live imaging of double fertilization within the flower. But through this, I developed all these different fluorescent lines of the flower. And so I started to cross all of these and actually think of it as genetic painting with fluorescent proteins, trying to highlight different parts of the plant. And then a new tool came online that actually a postdoc brought into the lab. I still remember his journal club on this paper. And he brought in a tool called RUBY And RUBY is three genes from beetroot—CYP76AD1, DODA, and a glucosyltransferase gene—separated by P2A linkers that are self-cleavable so that you get one mRNA that can produce three proteins. It’s elegant. And they use this as a selectable marker or reporter for gene expression.

And so this postdoc, he wanted to put it under a pollen promoter because we all studied the pollen. He wanted to use it as a marker for tracking the pollen tube growth. But he noticed on the single cell level, the pollen tubes are still translucent, so it didn’t really work. But there’s a lot of serendipity that occurs when you transform a plant with a construct like RUBY. It can have multiple copies or it can go into different parts of the genome. And so he picked up all these transforming lines that had pink pigmentation in the full flower or just the petals or just the pollen. But for his experiment, it didn’t work.

McCarty: Right.

Desnoyer: He was ready to throw them away. But me, having played with genetic painting of fluorescent proteins for so long, I was like, wow, this is actually visible. At the same time, right next to these flowers, I had these agamous mutants. And in short, instead of producing petals, sepals, stamens and carpels, they produce sepals, petals, petals, sepals repeating. It becomes an indeterminate flower. And I was teaching a course. That’s why I was growing these flowers, and the students always love this one the most because it’s actually the genetic underpinning of a lot of commercial flowers that you see in the grocery store that have this double flower phenotype. They’re like little roses. I crossed a carrier of agamous—these don’t produce any reproductive organs—with this RUBY line. This is actually a funny story because it was a carrier for agamous, but this is a really old EMS allele.

And in fact, we have no selectable marker for this mutation.

McCarty: What does that mean, EMS?

Desnoyer: This is a chemical mutagen that can induce mutations. Back in the early days, people were mutating Arabidopsis to do forward genetic screens, where they would treat them with EMS. They put the seeds in the chemical and then look for interesting mutants that pop up. And you know if your EMS worked, if some of the leaves have white sectors, but also about one in 10,000 plants will yield an agamous mutant. They use this as a proxy to see if the mutagenesis worked. But to propagate these is quite hard because these ones don’t make seed. The only way to propagate these would be to vegetatively cut them, which you can’t do with Arabidopsis, or propagate them through carriers of the mutation. So you find wild type looking plants that would be heterozygous for the agamous allele. But because this is an EMS allele and we didn’t have any selectable marker for it and we couldn’t even genotype it, I do it through classical genetics where I plate all the seeds of a wild type looking plant and see: does the mutation pop up in the next generation?

And so all I did was cross a plant which I thought was a carrier for agamous. I had only two thirds chance that this was a carrier and crossed these two plants. And so in an alternate universe, that plant was the one third that was wild type and didn’t get anything. And I would have just trashed them. That’s what I mean by there’s a bit of serendipity in it. And so I crossed these two flowers. I grow the first generation, which is called the F1, filial one. And again, I’m not genotyping them. Also I don’t know if the progeny carry the mutation and they’re just a little less pink than this because now they’re heterozygous for that. I selfed that plant and then in the F2 hoped to find some pink little micro-roses popping up. In the F2 population, then deriving from this cross, I found a few plants that were homozygous for agamous, as in they had this double flower phenotype, and homozygous for the RUBY, which looked a bit like this.

I thought this could get a lot more interest within the course and that this actually might be a better way to reach the public than genetic painting with fluorescent proteins. And so I brought this through the entire institute showing everyone I could find and was met with mixed reactions. So the younger students, like the undergrads and the masters, they were like, “Whoa, that’s so cool. You transform this into this and now it’s big and pink.” But when I brought it to the postdocs and the professors, they were like, “Yeah, you made a cross. Now get back to work. What are you doing?” But I was quite convinced that people will find this cool especially when you compare the wild type and the new version to show people what you can do with biotech.

I had already been making scientific art that I put online for about four years up until that point. And I posted this post and it was the first time that people actually reached out to me offering money. And I had always hoped that this would happen one day. And so I was really excited after I made this micro-rose, I showed it to my professor and he was like, oh, you could introduce this mutation and this mutation to make it larger or to have more petals. And so I took that as inspiration to upgrade these roses over the next year. And so rather than looking at it as a potential startup, I was exploring it more from an artistic perspective of: is flower design a real thing that we can do? Or is it just a simple cross like the postdocs were saying? And this was one of the most exciting times in science because it really for me, because it started to change how I saw the science.

I was writing my PhD, but also exploring all of the literature of Arabidopsis research, which has over 10,000 papers on it. But now I was starting to see the utility of this research actually. When you try and make something out of a flower, you start to see what are the actual impactful papers that we can start to create stuff with. I started skimming these papers and looking at them more as catalogs of mutations: what could make these flowers a little more aesthetic? And there’s very few genes that actually make the flower a little more aesthetic. I went for about five and I just ordered some primers for CRISPR and started to transform these pink roses with the CRISPR. And I also went for a few low hanging fruits of what I thought could be achieved with bioengineering, but not breeding, which is making the flowers interactive; such as using inducible gene cassettes that you can add a small molecule and you can direct the production of pigmentation.

Over the course of the year, I explored many different combinations of mutations and many different transgenes to control the color. And all the while I had this vision in my head of a flower that’s—instead of being sepals, petals, petals, sepals, which makes it a little bit mangly—it’s much larger. It has sepals and just petals, petals, petals all the way down, is a bit more symmetrical and large, and has a bleeding red center, which I thought I could achieve with the inducible system. And so I remember clearly going to bed and having this burning vision of: I want to create this. And over the course of the year I explored a lot of funky things, realized what works, what doesn’t. And around December 2024, one line popped up that was homozygous for erecta, agamous, and superman and heterozygous for clavata3.

And it had the RUBY transgene as well in the background. It had about five different edits you could say. And this—I was extremely excited because it was much more beautiful than, in my eyes, than the original. And this time—and when I brought it through the Institute, I was met with much different reactions. In fact, I brought it to some professors that had worked on Arabidopsis their entire career. Like 40 years. And they were asking me what species it was. And so I took that as affirmation that I’m onto something.

McCarty: What were some of the interesting micro-roses that you got? And if you were still working on that, are there other colors or what else were you thinking in terms of expanding that?

Desnoyer: Right. Some of the other genes that I explored were more to do with organogenesis. There are two genes, DA1 and EOD1, that regulate the size of the petal. As I mentioned before, petals are dispensable and their shape and size don’t really affect their physiological function. And so you can introduce mutations like frl1 that make frilled edges or da1 and eod1 that make them larger. You can introduce mutations like clavata3 that actually affect the floral meristem size and balance. That’s where you also get some kind of freaky things that look like fasciated flowers or even tumors.

McCarty: We have a fasciated flower, right?

Desnoyer: We do, yeah.

McCarty: Show that.

Desnoyer: This is almost certainly a fasciated stem. And so the vegetative meristem likely became too large at some point in this mutant background and all the stems started to fuse together.

McCarty: But yeah, it’s like two stems. It’s like a very thick, flat stem. I’ve never seen a plant like this.

Desnoyer: But now that you’ve seen this, you’re going to start finding it in nature, especially if you look at dandelion. Dandelion clonally reproduce and so they don’t have much genetic variation. And so they’re very prone to making mutations. And sometimes they get mutants in clavata3 and start to fasciate like that.

McCarty: And that also happens in the meristem, right? Instead of one center, it has a split center.

Desnoyer: That’s right.

McCarty: Basically to sculpt the flower initially, you were doing crosses with mutants and your professor suggested some other things you could cross in. But then you started to do CRISPR. And I’m curious about that because before I came here to visit you, I had no understanding of the plant world. It was almost like a mystical thing when people would talk about tissue culture or whatever, or agrobacterium. And so maybe you could walk me through that. When you—we have some plates here, and could you explain what some of these are and how you actually get genes into the Arabidopsis?

Desnoyer: There are many ways you can get a gene into a plant. It depends on which species you’re working with. Arabidopsis is such a famous model because you can really easily transform it. And so you put your genes into a bacterium called Agrobacterium that occurs in the wild. This naturally infects plants and produces what’s called crown gall disease. Chemical signals from the wounded plant, such as acetosyringone, activate the Agrobacterium. The bacteria produce this secretion system, which is like little needles that poke into the plant cell, and they’re able to insert what’s called T-DNA. In the wild, this T-DNA carries tumor-inducing genes. And so the plant essentially becomes a home for the bacteria and starts to feed them metabolites. Some really clever scientists thought, “Oh, we should just take away those tumor-inducing genes and use this beautiful invention for inserting genes into plants.”

And then there was a guy who took that Agrobacterium and just dipped the flowers of Arabidopsis in the bacterial solution, collected the seeds, and found that, wow, this is enough to get that gene into the egg cell of the flower. The next generation then carries the stably integrated gene.

McCarty: You can just dip them into bacteria?

Desnoyer: Exactly. And that only works so well in Arabidopsis because of the development of the flower. There’s a stage very early on when the carpels, which eventually bear the seeds, are fusing and make a furrow. During that stage, the Agrobacterium can get in, and later the carpels enclose it. And that’s what infects the cells that become the egg cell. So it’s really based on the anatomy of Arabidopsis. If you dipped this petunia in Agrobacterium, it wouldn’t work.

McCarty: And so, speaking of petunia—to transform petunia, which I know we’re jumping back, you have to use tissue culture, right? How does that work?

Desnoyer: Essentially, for petunia, you take a cutting of one of its leaves and put it onto a medium with different concentrations of phytohormones, namely auxin and cytokinin. With the right balance of these phytohormones, the cells go from a differentiated state back to a dedifferentiated state, like stem cells. And they start to produce what’s called callus. Callus is totipotent. It’s undifferentiated cells that can produce an entirely new plant.

So what you do is, early on, when you cut the leaves, you co-culture them with the Agrobacterium. The Agrobacteriumstabs into the leaf cells and inserts its T-DNA. Along with that T-DNA, you add a selectable marker. This could be something like the RUBY transgene that colors it or an antibiotic-resistance gene. After the co-cultivation, you kill all the Agrobacterium with antibiotics and put the leaf tissue on a selection medium that again induces the callus. This time, only the callus that carries the transgene is going to survive and produce a whole new plant.

And so then shoots start to grow from this leaf and produce the next plant. Eventually, you move it from a shooting medium into a rooting medium, which has little to none of the phytohormones, so that the shoot can start to produce roots. The auxin and cytokinins actually have different modes of regulating genes in the shoot and the root.

McCarty: And so the process—if you have to do tissue culture, like for petunia—takes much longer, right?

Desnoyer: This one might even have a date on it. Actually, this is when we transferred it. But I can tell you this one is probably two to three months after cutting the plants. It’s quite remarkable. This whole plant came from a single cell from a leaf.

McCarty: There’s a physical limitation in how long it takes for a plant to grow. But when you dip Arabidopsis, you can immediately take it and regrow a plant, right? How much faster is it to transform and grow the next generation of Arabidopsis versus petunia?

Desnoyer: Right. Arabidopsis takes about a month and a half to grow. You can get flowers within four weeks. You dip those, wait about two to three weeks for it to produce the seeds, get those, and you have your transformed plant. You can go generation to generation in about a month and a half. And that’s how, within a year, I could squeeze in about five generations. You can never do that with petunia, but petunia is also a much larger, hardier plant. So it just takes longer to grow.

McCarty: And so with the micro-rose project, right? You went from this to petunia, presumably because you have a bigger flower to start playing with, right? But it also takes much longer, and researchers have mapped fewer mutations compared to Arabidopsis, right? What are the trade-offs when you choose a flower? What are you thinking about?

Desnoyer: Actually, when I was first making these micro-roses, I was kind of convinced that I was going to work on this for the rest of my life. I was calling it the Thousand Flower Collection. I was like, “I’m going to make a thousand different versions of this flower.” But I realized that even with Arabidopsis, there’s still a disconnect with the public. Most people don’t know this flower, and it’s just a bit too small for people to really get interested in. Mostly, they’re just not familiar with it.

This first project was also mostly impactful because of the sculpting of the flower. And that was possible because of all those mutations that we knew in Arabidopsis. So for my next project, I wanted to move from predominantly genetic sculpting to genetic painting, which is when I had this idea of the Paintunia.

And petunia is probably the second most studied flower, just after Arabidopsis. You know a lot more about the color. There’s a lot more standing variation that you can use. And it’s a beautiful canvas. So lately, I’ve completely switched to petunia. But after I make the petunia, I would like to switch to another system as well.

That’s what’s beautiful about flower design: it’s really endless. Once you get bored of one thing, you can move to a different medium. With each flower, you start to learn its growth behavior, how it reacts to certain treatments—even tissue culture you have to master. I like to think of mastering this organism. You have that in your tool belt, and through doing that, you develop a kind of deep connection with the plant. And you keep moving on and mastering different plants.

It’s like if you moved from watercolor to oil painting to clay.

McCarty: Also, at one point while I’ve been here, you were talking about how there are also viruses that you can infect plants with, right? There are so many dimensions to engineering plants. If you think about it, it’s breeding, CRISPR, transgenes, pathogens, and all these things—you’re kind of tuning the development, I guess, of the plant. What were some of the viruses that you were thinking about? Although I know you’re not doing it anymore because people don’t like to hear about engineering viruses.

Desnoyer: Exactly. Actually, if you want to look at engineering a plant, one of the best places to go looking is at plant pathogens because they naturally hijack the plant machinery. Phytoplasmas, for example, revert the flower back into a vegetative meristem. They have all these genes that can regulate the plant at the genetic level or at the protein level, and pathogens make all sorts of patterns.

In fact, if you go out for a walk, just take a look at a leaf, and almost certainly you’ll find one that’s infected. One of the most famous infected flowers is ‘Semper Augustus,’ a tulip that had this fiery, flame-like pattern with red streaks in it. At the time, people had never seen this type of tulip. And so they called it tulip mania because this tulip became absurdly expensive.

However, it was a bit of a scandal because later they found out that a virus was causing this effect. And so it’s not heritable, and a lot of the flowers start to wilt over time. It was a big waste of your money to get this flower. Now, with breeding, you can get tulips that look like ‘Semper Augustus,’ but it’s post-transcriptional gene silencing now.

McCarty: It’s not stable?

Desnoyer: It is. It is stable. You can get stably unstable gene silencing in tulips. I used to think that viruses would be a really cool way of making all these different types of patterns. But as I started to learn about them, I realized that because they’re not alive and because they’re just particles, they don’t really have a way of actively moving through the plant. So they just move through the plant based on bulk flow or diffusion. They get into the vasculature, spread out through the veins, and then later through the plasmodesmata. A lot of the patterns that you see from viruses are actually more or less the same. It’s just diffusing through the vasculature. With that said, because they’re introducing new genes, you have what’s called virus-induced gene silencing, where you can get some interesting patterns.

And you can imagine how, in theory, you could engineer a virus to deliver a pigment as it travels through the plant to create cool patterns. I had thought about that because we actually have licenses to work with plant viruses. But that was an important consideration because whenever you’re doing biological design, you have to think not just, “Can we do this?” but, “Should we do this?” And I don’t think that is worth it, and it doesn’t send the right message either.

McCarty: We’ve been talking while I’ve been here, and you said that one of your dreams would be to build a greenhouse full of mutant flowers and maybe even mutant insects that pollinate different types of flowers than they naturally would. I guess my question is: Why is that your dream? Why build something like that? Isn’t the diversity and beauty of nature sufficient for our appreciation? Why do we need a mutant greenhouse?

Desnoyer: First off, there are already thousands of botanical gardens around the world where you can showcase the diversity and natural beauty of the living world. Those are my favorite things to go see. Anytime I go to a new city, the only thing I care about is going to their botanical gardens. It’s like a museum—a natural history museum of all the beautiful things evolution has created and what we’ve made with breeding. And there’s something really kind of magical…

But with this, it’s just admiration. You look at the flower and appreciate it for what it is. But I think there’s an added layer of beauty when you start to interact with the flower or even interface with its genome. You start to understand it at a deeper level that almost feels a bit magical. In fact, it’s the closest thing to fantasy in real life that I can find.

And so that’s the real motivation: to make the Studio Ghibli of biology. Something that instills that feeling of magic and fantasy when people see it. I think we can achieve that by looking at nature more through a scientific lens. There’s a school of thought that by learning more about nature, you actually diminish its beauty. But I think it’s the exact opposite.

There’s a famous monologue by this guy Richard Feynman. I’m sure you’ve heard of this guy—a very famous physicist. He has a whole monologue about flowers. It’s called “Ode to a Flower.”

Feynman [quoted passage]: I have a friend who’s an artist, and he’s sometimes taken a view which I don’t agree with very well. He’ll hold up a flower and say, “Look how beautiful it is.” And I’ll agree. And he says, “You see, I, as an artist, can see how beautiful this is. But you, as a scientist, take this all apart, and it becomes a dull thing.” And I think that he’s kind of nutty.

First of all, the beauty that he sees is available to other people and to me too. I believe, although I may not be quite as refined aesthetically as he is, that I can appreciate the beauty of a flower. At the same time, I see much more about the flower than he sees. I could imagine the cells in there, the complicated actions inside, which also have a beauty. I mean, it’s not just beauty at this dimension of one centimeter; there’s also beauty at smaller dimensions, the inner structure, also the processes. The fact that the colors in the flower evolved in order to attract insects to pollinate it is interesting.

It means that insects can see the color. It adds a question: Does this aesthetic sense also exist in the lower forms? Why is it aesthetic? All kinds of interesting questions, which the science knowledge only adds to the excitement, the mystery, and the awe of a flower. It only adds. I don’t understand how it subtracts.

Desnoyer: And so I would like to create a botanical garden that you walk into, and you don’t just appreciate the flowers, but you actually understand them a bit deeper through a scientific lens. And importantly, I want these flowers to only exist there. It’s like a magical moment where you realize you’ll only find this flower here.

I don’t want to use a typical breeder’s rubric of, “This one has really nice vase life,” or, “This one’s really full and big and colorful.” I want them to be weird and wonderful. When you walk through this garden, you get that feeling of magic, and with each flower, there’s a little description of what the mutant is. Almost certainly, each time you walk through the garden, you’ll feel compelled to take a closer look at what’s going on.

And that’s really the takeaway: once you leave this garden, you want to take a closer look at nature.

McCarty: It’s like when we were looking at the plants right before—the petunias—and every petunia has a different thing, has a different story. Some are gene silencing, and some are transposons.

Desnoyer: Do you watch Studio Ghibli, though?

McCarty: I love those films.

Desnoyer: And there’s a certain feeling you get, right, when you watch those films?

McCarty: You feel the humanity.

Desnoyer: You feel Hayao Miyazaki’s vision. If you learn a little bit about him too, you see that bleeding through into his story. And there’s that feeling that you get after watching, like, Howl’s Moving Castle or Princess Mononoke—I want to create that feeling in biology. How is that possible? And I think that is possible.

I think I told you one of my favorite podcasts is Lex Fridman with Neri Oxman. She said there are realists who are addicted to dreaming, and there are dreamers who are addicted to realism. And the people you want to hire are dreamers who are addicted to realism. They live for the dreams, they live for the fantasy, but they’re super grounded in reality. They just want to make that real life.

As a kid, I was a dreamer addicted to dreaming. I was having all these fantasies, and I had a moment, like when you lose your innocence, where I was like, “Damn, the world is a really boring place.”

As you grow older, you just get into all this monotony, and there is no Final Fantasy. There is no Kingdom Hearts. There are no grand adventures that you’re going to go on. And actually, it’s kind of stupid. But as a kid, because I had all those feelings and I could see the adults who clearly didn’t, I literally made a promise to myself: “This feeling is going to go away, so I need to remember it, hold on to that.”

I made a promise to myself when I was like seven years old. I was fighting with swords under a willow tree, and it was raining outside. I still remember that. And that came back to me once I started the flower design project. Now I’m like, “Oh, you can make a fantastical world that’s grounded in reality.” And that is biology.

That is science. Biology can be endless adventures. That is going out into nature, finding that thing, and bringing it back into the lab. The problem right now is there’s friction between the lab and nature. Nature drives you into the lab as you grow up loving all the biodiversity, and they all have their own special powers and stuff. Then you come into the lab and you just forget that because people don’t do that. You work on this single protein, but can you connect it back to what originally got you into it?

I feel like we’re kind of losing sight of that, and there’s a whole area of biology that’s completely missing at the moment, where the whole purpose is to just bring you closer to nature. Most of the tech we’re creating is driving us away from nature. But can I make tech that actually makes me feel like I understand nature better and feel closer to it?

That’s the future I hope we have as humanity: that we don’t have this cyberpunk future that’s just all these skyscrapers and robots, but rather a really high-tech future where we’re more grounded in nature. And the world looks a lot more like a garden with all these unique kinds of spaces.

McCarty: Some academics have kind of pooh-poohed what you’re doing, I would say. They’ve said, “What’s the point of this?” Is the argument essentially that by designing flowers in this way, you’re deepening our scientific understanding, or are you just deepening people’s curiosity about what’s going on? What is the pitch you make to people who maybe attack this or don’t understand it?

Desnoyer: I think there are many reasons, and a lot of their reasoning is justified. I don’t think everyone should switch to flower design. The world would fall apart, and we wouldn’t have as much food. But I do think there’s an interesting aspect going on, particularly in funding schemes: they’re really targeted at deliverables that are closer to things we just need and that are essential for our survival, like food and medicine.

But it’s actually the things that are least essential for our survival that make us human, like singing or dancing or laughing or gardening. Every summer, people go out and plant flowers in their garden, and some of the bulbs only pop up for like a week. You could ask, “What’s the point of that? Shouldn’t you be growing food?” But that’s not what makes us human. So I think beauty for itself is a justifiable purpose.

It enriches our lives. It adds to the quality of our lives. And so I feel there could be a bit more emphasis on that. I do see kind of a cultural shift, especially when you look at science a few hundred years ago, or even architecture a few hundred years ago: they put more emphasis on ornaments and creating beauty. I would like to see that a bit more in science.

But there are other angles that you can look at it from. Flowers are extremely familiar. So if you want to educate someone about biotechnology, there’s no better approach than a flower. They already know them. They already love them. They don’t have to eat them. These flowers aren’t going into the environment, and I’m showing exactly how I make them. It’s a very neutral approach.

You could also look at it through the artistic lens, which I think is justifiable in its own right: this is a new medium of art where the canvas is living cells.

That’s intriguing. And then, from a scientific lens, how much can we learn from designing and playing around with flower design? If we’re only focused on crop yield, most of the mutations and tools we’re going to use aren’t going to radically change that. Or most of them are going to be deleterious. Whereas flower design is like a creative sandbox. You’re implementing tools in new, creative ways that you wouldn’t normally go straight for if you were trying to increase the yield of a crop.

McCarty: Do you feel like you’ve made any discoveries from designing flowers?

Desnoyer: I wouldn’t say any groundbreaking ones, but I would say I’ve made a lot of observations that I didn’t know of before. I then go look them up and find that someone discovered this in a similar way. That happens all the time when you’re working with things that are super visible.

If you’re just working with fluorescent proteins, you’re only going to find a weird phenomenon if you dissect out that part of the plant, put it under the microscope, and look through a ton of samples. But if you’re working with something visible that’s growing in the glasshouse, it’s going to catch your eye, and you’re going to ask what’s going on there. That’s actually how people made a lot of discoveries. That’s how Barbara McClintock discovered transposons, with the different colors in the aleurone layer of the corn grain.

The white eyes that Thomas Hunt Morgan found in Drosophila—things like that.

McCarty: There are millions of gardeners. Gardening is an extremely popular hobby. And I do sometimes wonder why biotech doesn’t do more advocacy through gardening, right? Instead of having a community lab where people engineer E. coli to make insulin or something, why don’t we have a community lab where gardeners come and breed flowers? It’s biotech, but much more approachable. Is that something you’ve thought about?

Desnoyer: Absolutely. I think that’s an amazing approach because a lot of the pushback scientists get about genetic modification is because the general public either doesn’t understand it or just has no skin in the game. There are many years of education that you have to go through to even get into the lab. So it’s a big privilege, and you have this disconnect.

Whereas if the average person could already start to dabble in it a little bit, they would see that there’s nothing to be afraid of and that there’s nothing inherently wrong with modifying a plant. Just like anything else, it’s a tool, and you should use it responsibly. I think breeding is a nice kind of intermediate that anyone can get started with. And there are interesting things like the transposon line that has this active transposon that can mutate the flowers.

You don’t need to use CRISPR to find these mutations. You could already grow this in your garden, cross it with other flowers, and start to get cool mutants that you can introgress.

McCarty: Nick, what’s the next step?

Desnoyer: I want to complete this mission of creating the Paintunia. I think I’ve got about two more years before I finish the final product, which, again, is this petunia flower where you can apply copper, dexamethasone, or estradiol literally with a paintbrush onto the bud and create your own bespoke flower.

I would like to get this Paintunia into over 100 classrooms and have this be standard material for a university practical where people can visually see gene expression. They can modify a plant on a really short timescale, and they can blend art and science, so that even if that student doesn’t pursue biology, they’ll forever remember the Paintunia and how they triggered gene expression. That would be enough. However, to get there, I still need to fund the project because, as we’ve discussed, this is kind of hard when your goal is art and education and beauty.

I have a fellowship that I’m on right now, working on a completely separate research project, but that terminates next year, in August 2027. I’m looking to raise about $250,000 for that year to fund me, a research assistant, and an artist to tell the story of the making of the Paintunia.

I want to make this into a really accessible book and sell it very cheaply. Also, make a digital copy that has motion graphics that you can scroll through and see the entire story. And keep posting about it online so that people get live updates, and eventually they can get it into their own hands.

I’m seeking to do that fundraising, but also thinking: What comes after that? My grand vision is to make a flower design lab slash design studio that you walk into, and it’s a fusion of the modern lab and an art studio.

There are tablets for digital painting, cameras, and microscopes, but there’s also dirt for gardening. And just outside is a glasshouse where you can maintain all these plants. Now that I’ve been privileged enough to see the beauty of a flower and design it myself, I would like to have a place where you can invite others in so that they can do it themselves.

McCarty: It’s a great vision.

Desnoyer: Thanks.

McCarty: And you’re right that it’s so much more tangible than E. coli. When we teach biotech in schools, it’s like, “Oh, engineer the E. coli to have GFP.”

Desnoyer: Yeah.

McCarty: My experience of being here—everything is more visceral. When I walk around with you and see the different flowers, even the ones that people have just bred—flowers that they haven’t even engineered—you tell the story of, “Oh, here’s how they made this, and here’s why it looks like that, and it’s because of this molecular…” So you’re moving from the macroscopic all the way down to the molecular level.

Desnoyer: Totally.

McCarty: In a way that brings the biology together in a way that, for me, it almost never comes together.

Desnoyer: Right?

McCarty: And it’s not just the flower, but you talk about the ecosystem and insects that carry viruses. It’s just so beautiful to be a part of this. And thank you for hosting me.

Desnoyer: Thanks for being here. I’m going to miss you when you leave. And I’m sure we’ll work on more stuff together.

McCarty: And Nick, thanks also for doing the podcast.

Desnoyer: Thanks for having me.

I flew to Minnesota and interviewed Adamala for about three hours. First, I wanted to understand the bottlenecks with SpudCell. What engineering changes will they make to get it to reproduce continuously?

Second, Adamala is one of the leading opponents of creating mirror life, a program funded in part by Coefficient Giving through the Mirror Biology Dialogues Fund. I pushed her on the idea that SpudCell, or the ability to create life from the bottom up, could uniquely enable the creation of mirror life. I wanted to understand how we avoid that.

The third part of our interview was about understanding the point of making synthetic life. SpudCell, as you’ll hear, is nothing like cells on Earth today. I think it stretches the imagination to claim that making these cells teaches us much about biology. It’s more of an exercise in hacking biology to get the outcomes we want! I wanted to understand why that matters, and Adamala had some really good responses about how SpudCell could expand life’s chemistry, enable us to make new types of medicines, and help biologize the economy.

Watch on YouTube; listen on Apple Podcasts or Spotify.

Timestamps

(00:00:00) – Opening
(00:00:52) – SpudCell is not alive
(00:05:16) – How SpudCell works
(00:13:14) – Recycling as a major bottleneck
(00:19:24) – Genome inheritance and cell division
(00:34:19) – Bottom-up vs. top-down cells
(00:40:38) – What synthetic cells could be used for
(00:46:29) – Evolution and complexity of synthetic cells
(00:54:51) – Why Kate changed her mind about mirror life
(01:01:27) – Why life evolved a single handedness
(01:05:12) – SpudCell as an enabler for mirrored life
(01:14:38) – Biotic
(01:21:58) – China and 2050 goals

Transcript

00:00 — Opening

Kate Adamala (00:00) Life as a phenomenon is probably very easy, given how quickly it started on Earth. Many people were saying that even making growing, replicating cells from chemicals is impossible, that you need some mystery spark of life. And we just did it. We put together molecules, and they’re growing and replicating. There’s nothing magical to me in how molecules make themselves into life if you give them enough time and the right conditions.

Niko McCarty (00:25) I flew all the way to the University of Minnesota to interview Kate Adamala, whose group, about a month ago, published the first synthetic cell that eats, grows, and divides, built purely using molecules that the scientists put there. In this interview, I want to know not only how they built Spud Cell, as it’s called, but also what it’s good for. Kate, welcome.

Kate Adamala (00:51) Thanks for having me.

00:52 — SpudCell is not alive

Niko McCarty (00:52) My first question is: Very few science stories go viral like Spud Cell did. There wasn’t one New York Times article. There were three. I’m wondering what that’s like. In that first week, what did you make of it? Did you expect this would get as much attention as it did?

Kate Adamala (01:12) I definitely didn’t expect as much attention. It was very humbling that something we’ve done generates so much attention, most of it positive. That was very surprising, but also very happy-making. It was amazing to be able to talk about it. I always want to talk about my work, and it’s really interesting to find so many different people wanting to talk about it because it makes me think about it in different ways, from different perspectives. It was definitely weird.

Niko McCarty (01:46) What were some of the weird things that happened?

Kate Adamala (01:48) There wasn’t a single weird thing. Most of my life is pretty quiet; it’s the normal work of a scientist. Then suddenly, most of your day is taking calls and doing interviews, and that’s not the job I signed up for. That was definitely a new experience.

Niko McCarty (02:08) When these journalists came, you told everybody that this thing is not alive, right? It’s a synthetic cell that eats, grows, and divides, but it stops dividing after about five generations. You were tamping down on the hype that other people were writing about. What would be required for you to say this thing is actually alive—at the risk of upsetting other scientists, probably?

Kate Adamala (02:41) It has to keep going. It’s that simple to me. Life, to me, is defined by its robustness, by its ability to keep going—like the famous quote from Jurassic Park: “Life finds a way.” A Spud Cell could not find its way out of a straight tube. It’s just not robust. It’s capable of undergoing all those processes that we normally associate with life, but not continuously, constantly.

To declare this alive, it needs to be able to keep going, keep replicating as long as there are resources. I cannot say indefinitely because no life replicates indefinitely, but with an abundance of resources and no limiting factors like pH or the size of the vessel, it should keep replicating. The Spud Cell cannot do that right now.

Niko McCarty (03:32) What makes you confident that we can engineer robustness when the robustness of the natural world seems to have been emergently shaped over long timescales by evolution, which is pulling on many levers at once in this very multiplex, combinatorial fashion? Doesn’t it seem impossible that we could engineer robustness that matches evolution?

Kate Adamala (03:55) That might be the pride and overconfidence of a scientist, but I think we can do it. When I first started in this field, many people were saying that even making growing, replicating cells from chemicals is impossible, that you need some mystery spark of life, some mystery component we don’t understand. And we just did it. We put together molecules, and they’re growing and replicating.

Niko McCarty (04:16) Wait, you’re saying people believed in vitalism when you—

Kate Adamala (04:20) Totally. There are many biologists who think there’s something unique about biological life, that there’s some life force—who knows what—that is impossible to replicate in the lab. I always thought that it’s chemicals. Chemicals are doing it, so we can put together chemicals in the right way. Until I’m proven wrong, I’ll keep believing that robustness is also possible to engineer.

Niko McCarty (04:45) To clarify, you think, theoretically, it is possible to build a synthetic cell that is as robust as a natural cell if we just hit on the right combination?

Kate Adamala (04:56) Yes, I think so.

Niko McCarty (04:57) You see it as a big search problem in chemical space.

Kate Adamala (05:01) A huge combinatorial chemical problem, which makes it fun. But yes, I think we totally can. I don’t think there’s anything special about natural life in terms of its ability to solve problems and adapt to different environments.

05:16 — How SpudCell works

Niko McCarty (05:16) How long did it take you to make Spud Cell once you decided, “We’re going to try to put these components together and make a dividing organism”?

Kate Adamala (05:25) It was a trial-and-error process. This particular project’s been going on for about five years in my lab. We had a lot of ideas that failed, a lot of ideas that sort of worked and led us to other ideas, until eventually one of them worked. It wasn’t that one day I woke up, wrote up a plan, and we went and did it. It was all failed experiments that informed the next round of also-failed experiments, and so on until something started working. It was more of a Roomba-on-the-floor process. We didn’t go in a straight line; we just browsed.

Niko McCarty (05:59) What is Spud Cell? What are its key components, and how do they work together to give rise to this thing?

Kate Adamala (06:06) Spud Cell is a phospholipid liposome, so it has a membrane just like most natural cells. That membrane is very simple. It’s a two-component membrane. But we do know of a living cell that has a two-component membrane and can live fine with that. It’s not totally crazy; it’s not too simple.

Inside that membrane, we have a genome. That genome is 90 kilobase pairs. It’s tiny by natural cell standards. It’s encoded on several different plasmids, so it’s a multipartite genome. That genome gets replicated by a rolling-circle viral polymerase. We make copies of the genome inside the Spud Cell.

That genome expresses proteins. We have ribosomes, tRNA, all the enzymes that charge tRNAs, all the amino acids, all the small molecules. We have transcription and translation.

That translation produces proteins. One of the proteins it produces is, I think, my favorite protein in the whole world: alpha-hemolysin. It’s a bacterial toxin that creates a pore in the membrane. It’s a very dumb pore. It’s not a gated channel; it’s just a hole in the membrane. But the beauty of it is that it self-assembles. Because we make that alpha-hemolysin, we can have Spud Cells take up nutrients from the media by a concentration gradient and remove waste from the inside of the cell, again by diffusion.

The really cool thing is that alpha-hemolysin is pretty permissive to modifications. We’ve modified it by putting a small domain on one part of it that presents itself on a membrane. That domain is our feeding tag. It recruits feeder liposomes. The Spud Cell is a perfect heterotroph. It makes nothing; it doesn’t biosynthesize anything.

Obviously, then you run into the problem of how you add lipids, how you grow, how you make new ribosomes. We don’t. We feed it all. That membrane protein presents a tag on the membrane that attracts feeder liposomes. Those feeder liposomes bring in ribosomes, tRNA, and other nutrients that are too big to get in through the pore. They also bring lipids. Spud Cell does not make its own lipids; it has to eat all the lipids. Those lipids come in from feeder liposomes.

The beauty of the system is that, because the feeding happens as a result of that protein being displayed on the surface of the cell, and the protein is encoded by the genome, if the genome encodes for strong expression of that protein, the cell will grow faster because it’s going to have more of that feeder protein on the surface. If that feeder protein is encoded at lower levels, the cell is going to grow slower.

Then comes division, which is also induced by a tag—a different tag—on the surface of the membrane protein. We have two populations of those membrane proteins. One is for feeding; one is for division. That division, because it’s dependent on a membrane protein tag, depends on how much of that membrane protein you make. If you encode that division protein at higher levels, the cell can divide into more daughter cells.

It’s always daughter cells. They never talk about son cells in the literature, so we talk about daughter cells too. We always make those daughter cells, and the number of them depends on how much of the protein you make. That couples the genotype of the cell to the phenotype, which means how big they grow, how much they can eat, and how much offspring they can produce. That’s it. That’s all there is in a Spud Cell. It’s the simplest possible metabolism.

Niko McCarty (09:50) There’s a lot to unpack there. My first question is: Inside this lipid bubble you’ve made, you’re surrounding something called the PURE system. This is more than 20 years old. In the early 2000s, this Japanese—2001.

Kate Adamala (10:10) I think.

Niko McCarty (10:12) This Japanese team showed that they could reconstitute transcription and translation in a test tube. They figured out all the proteins and cofactors responsible, put those into a mixture, and they sell that mixture. You can buy it online. It’s called the PURE system.

It doesn’t seem so crazy to me to go from that to shrouding PURE in a lipid bubble and adding a few things. You’ve added a couple of clever proteins like alpha-hemolysin and these tags. I know progress takes a long time. I’m not poo-pooing progress, but why did it take 25 years for someone to get this to work if we already had some of the key components for a very long time?

Kate Adamala (10:58) I think part of the reason is that the description I just gave you was very simplified. For example, we’re not using the PURE system—the God-given, original PURE system. We’re using a heavily modified PURE system to make it compatible. It turns out that if you’re trying to replicate a genome and express proteins from that genome at the same time, you really need two different buffer compositions. To make it work in one pot, you’ve got to do a lot of optimization. Some people have already done some of that optimization, but we’re building on that.

Then the yields of expression from different parts of the genome have to be fine-tuned for this to work. There are a lot of annoying details that we give you now as, “This is the concentration to use.” But it took forever and many curse words to figure out what those actual conditions are.

Niko McCarty (11:54) But those things need different conditions. If different buffers are required for genome replication and protein expression, how do bacterial cells do both of those things in the same cell?

Kate Adamala (12:07) They do it in a smarter way than we do. They compartmentalize everything.

Niko McCarty (12:12) But this genome is just sitting there in the cytoplasm.

Kate Adamala (12:14) Most people don’t realize that even bacterial cytoplasm is very compartmentalized. It’s not a freely mixing bag or an aqueous bag. It’s something called deep eutectic, which means it’s not really a freely miscible water solution. It’s very, very dense—almost gel-like.

Water activity in a cytoplasm is pretty low. In theory, it is an aqueous solution, but really, everything has its place. Everything is stuck in different phases; everything has its own environment to be in. We did figure it out eventually—the Spud Cell does use one buffer—but it took a lot of figuring out.

When people originally started doing genome replication and then started doing translation, they thought, “We need different buffers.” But through a lot of trial and error—a lot of error—you finally found out that it’s possible to find one condition under which all of this works. It just took forever.

13:14 — Recycling as a major bottleneck

Niko McCarty (13:14) You went through the components. I think one way to understand how these components work is to start thinking about bottlenecks. I often like to think about problems as troubleshooting, and in troubleshooting something, I learn about the components. Why do you think Spud Cell stops dividing after five divisions? It sounds like it’s many problems.

Kate Adamala (13:41) To me, it’s one problem. Just to be clear, we published the five generations as a stopping point because that’s when we decided, “Okay, we’re going to characterize the hell out of it.” It can go on for a few more, but the yields go down significantly. It’s not like it goes for five generations and then drops down and stops completely. You could get a couple more cycles out of it, but the yields would keep dropping precipitously after each step.

I think the biggest problem is that a Spud Cell does not break anything down. It makes proteins and mRNA, but it doesn’t have degradation pathways other than chemical hydrolysis. You keep accumulating trash: ribosomes that lose activity eventually, tRNAs that get broken one way or another because there’s some chemical hydrolysis error in them. There is nothing to recycle them, nothing to break them down and put those monomers back into circulation.

In a given volume of cytoplasm, with each increasing generation, you have more and more waste—freeloading passengers that sit there and do nothing. That decreases the yield per volume. That’s why I think the biggest bottleneck in a Spud Cell right now is ribogenesis: making new ribosomes. And part of ribogenesis—there’s no good word for it—is “ribo breakdown,” breaking down nonfunctional parts, including ribosomes. Taking out the trash and making new parts. This is a huge bottleneck that I think, once it’s solved, will let it keep going.

Niko McCarty (15:23) This is maybe a foolish question, but instead of breaking things down and recycling them, at least in the early part, wouldn’t it be easier to tag proteins somehow so they sequester on one side of the cell, and then you bleb the waste away every couple of generations? You take out that part, because you’re feeding in new parts all the time.

How do you plan to implement this? How difficult is it to get rid of waste versus recycling broken proteins, which seems harder than just getting rid of waste?

Kate Adamala (15:57) Both breaking down waste and getting the waste out in a little bleb have the same problem: How do you recognize waste? How do you recognize that this particular ribosome has been sitting around and doing nothing for the last two hours? It’s a really big problem that, in natural biology, takes a lot of time and money to solve. There are a lot of chaperones, a lot of proteins that do this quality control all the time. We don’t have any of that in a Spud Cell.

The biggest bottleneck is: How do you figure out who’s the waste and who’s still a productive member of society? I don’t have good ideas right now to solve it. I have some stupid ideas that we might be testing, but I don’t have anything that I know works. That’s definitely the biggest problem.

It’s really easy to break down proteins and RNA. There are nucleases and proteases that I can tag and direct to a specific target. Once I know what the target is, I can break that target down pretty cleanly. But I don’t know what the target is. That’s the problem.

Niko McCarty (17:05) Are you saying that the problem is a lack of basic understanding of biology? Why can’t we just take the known components that do this in cells? What happens when you try to put those into Spud Cells?

Kate Adamala (17:17) There are too many of them. Biology has too many steps. If you start trying to reconstitute all of the natural proofreading processes, you end up with a hugely bloated metabolism, which we’re trying to avoid here. My goal is to try to hack it, like we’ve done with all the other processes—to simplify it. That’s really difficult. That’s turning out to be a huge bottleneck.

Niko McCarty (17:42) But if evolution did not hit on a minimal solution to recycling waste, what makes you confident that you can hit on a minimal solution to recycle that waste?

Kate Adamala (17:52) So far, we got lucky with other things. Our genome replication system is one protein, and cells use huge protein complexes that allow for a lot more regulation but are also much more complex. Same with growth, same with replication. So far, we’ve managed to hack every one of those processes. I think waste removal is also hackable.

Again, that’s my belief. That’s not a fact, because we haven’t done it yet. But I do believe we’ll be able to find a simple way to identify waste. We just need to find it.

Niko McCarty (18:29) It almost feels like if you keep finding hacky solutions, which is possible in principle, you might arrive at a solution in the end that is not robust. It only works in the lab, and then it has none of the applications that the news media was reporting.

Kate Adamala (18:43) Yes. That’s the biggest challenge right now: The solutions we’re looking for cannot just be a one-off trick that works under very specific conditions. They have to be generalizable. That is the biggest challenge. You just identified that it’s not just the challenge of how to make ribosomes or how to break them down. It’s a challenge of how to do that repeatedly under various different conditions.

Niko McCarty (19:09) Seems like a very hard problem.

Kate Adamala (19:11) It’s a hard problem, but so far, every hard problem we’ve encountered that seemed super hard, we managed to solve one way or another. I wouldn’t be doing it if I didn’t believe it’s solvable.

19:24 — Genome inheritance and cell division

Niko McCarty (19:24) You mentioned that one big bottleneck is recycling or getting waste out because it accumulates with each division. Another problem you write about in the preprint is that you have this 90-kilobase-pair genome. It’s partitioned across many different plasmids or minichromosomes—I’m not sure what you’re calling them. Every time Spud Cell divides, they randomly segregate. There’s some probability during each generation that the daughter cell did not inherit the full genome. How big a bottleneck is that, and how are you thinking about solving that problem?

Kate Adamala (20:02) That’s a very easy problem to solve. The only reason it’s partitioned into small plasmids right now is for ease of working with it, because we were trying to figure out what genes are necessary. Adding and removing genes is much simpler when it’s a plasmid that you can normally clone in bacteria.

There is a way to make a megaplasmid, basically the thing that John Glass does for his mycoplasma-based cells. We already know how to encapsulate the megaplasmid in a liposome. Once we’ve settled on, “This is the genome that I want to persist,” we can put it all on a megaplasmid. I cannot say it’s trivial, because it’s still a technical project to do it, but we know how to do it.

The thing is, those megaplasmids are technically difficult to work with. You need to clone them in yeast. You cannot just amplify them in bacteria like any normal plasmid. That’s why we were using the multipartite genome at the optimization stage: I can clone a new gene or mutate that gene within a day. With a megaplasmid, it is about two weeks to make the whole thing. That’s purely a technical difficulty. That’s not a scientific problem that I don’t know how to solve.

Niko McCarty (21:15) As you add components to Spud Cell to make it more robust or to recycle waste, the genome will get bigger and bigger.

Kate Adamala (21:21) Yes.

Niko McCarty (21:22) Do you have any sense of how big the genome will be at the end of the—

Kate Adamala (21:29) I do, actually, thanks to George Church and Tony Forster. A few years ago, they published a paper where they speculated about the minimal size of an independently living, autonomous cell built from scratch, with the PURE system as an assumption. They speculated that about 120 kilobase pairs is going to be the size. It’s a very well-written paper. They reason through each function and how many genes would be assigned to each function. It all makes sense to me, so I agree with that.

Niko McCarty (22:03) When they wrote that paper, which I’ll link in the video description, they presumably were not thinking about all these hacky workarounds you’re finding. They couldn’t have assumed that the solution to cell division was to express alpha-hemolysin with a tag. They were probably making that genome size assumption based on existing biology.

Kate Adamala (22:26) It’s an upper boundary.

Niko McCarty (22:28) You see it as an upper boundary. You’re already at 90 kb. The upper boundary is 120.

Kate Adamala (22:34) We’re at 90 kb right now. The size of the genome is mostly driven by the fact that it’s eight different plasmids. Each of those plasmids brings its own junk—all the parts a plasmid needs to be a plasmid: the antibiotic resistance, the bacterial origin of replication. The actual protein-coding part of that plasmid is usually about a quarter of the plasmid itself. Once you put them all onto one plasmid, that is going to become much smaller.

Niko McCarty (23:04) How big?

Kate Adamala (23:05) About half the size. The megaplasmid that encodes all the genes we now have in a Spud Cell is going to be about 40 to 45 kbp.

Niko McCarty (23:15) Assuming you can put these onto a single megaplasmid, get that into Spud Cell, and it continues to work as expected—going back to this idea of robustness—now you have a single megaplasmid that you need to partition during division. That means you need to express many copies if it’s randomly segregating. If you only have two copies, there’s a very high probability that one daughter doesn’t get a copy. Even with four or five copies, you’re going to suffer the perils of noise in random division. You might need to express lots of copies, but then that throws off the energy balance and all these other balances.

Kate Adamala (24:00) Which is why random partitioning is not going to fly. I want a cytoskeleton. I want a very simple cytoskeleton. There’s already been great work from people like Petra Schwille and Marileen Dogterom that demonstrated that an actin-based cytoskeleton can be constructed inside a liposome. I want to anchor my plasmid somehow and then partition it into daughter cells in a more controlled way.

Niko McCarty (24:31) Can you say anything else? How do you think this is going to work?

Kate Adamala (24:36) We can have a plasmid with a DNA sequence that’s recognized by a DNA-binding protein, and then have some sort of tendril of actin, which we already know can be formed inside synthetic cells. That tendril of actin can go into the membrane. It doesn’t have to be perfect. You don’t have to have poles like in a natural cell. You just have to have two or three of those tendrils that go somewhere into the membrane.

The most likely scenario, just geometrically, is that they’re going to be going in opposite directions because of steric hindrance. When a cell starts dividing, they’re going to pull apart, and they might influence the geometry of the segregation. It won’t be perfect, but it’s going to be much better than this smoothie we have right now, where things partition randomly.

Niko McCarty (25:25) That’s also related to cell division. The solution you hit on for cell division is very strange. It’s really not how cells divide at all. It’s bulky crowding of proteins that repel each other and lead to a sort of schism. One thing I noticed in the preprint is that you have these proteins sticking out of your cell, and these proteins are grabbing onto the bulky molecules that cause cell division. My understanding is that that interaction is permanent.

Kate Adamala (25:59) It is. Like every interaction, it has a k-on and k-off, but it’s pretty tight binding.

Niko McCarty (26:06) What that means is that after the first division, the daughter cells already have these proteins attached to them. Does this make them divide faster? By the time you get to the fifth generation, is the cell just studded with all these things and completely incapable of dividing for that reason? How do you get them off?

Kate Adamala (26:25) These are two independent problems we’re looking at. We’re looking at one of those problems, the persistence of the bulkiness, with a modeling collaborator.

This division process is pretty well characterized. People act like this is the first time they hear about it, but it’s been really well characterized by Reinhard Lipowsky and others working on it for over a decade now. It was never genetically encoded before, but as a physicochemical process, they’ve done quite a bit of membrane dynamics to figure out how it works. There are some models of it. We’re following those models now to see how many of them there are and how that affects the daughter cell’s geometry.

There are two competing theories. One is that it makes it harder for them to divide because the new alpha-hemolysin is being made and the membrane’s already crowded, so it’s harder to go in. But then you also are possibly pre-poised to divide because you’re already coming in with a lot of those bulky proteins. One or both might be true.

That also circles back to this huge problem we have, which is waste removal. Ideally, I would love to start each generation with a clean slate. I would love to find a way to recycle those alpha-hemolysin proteins: have some sort of protease that goes into the membrane and either cuts the FLAG tag that holds that bulky protein or cuts the whole thing away. Right now, we don’t have that. That’s definitely limiting the number of generations.

When we want to get to a higher number of generations, we have to solve that problem. We have to find a way to either completely remove those proteins or at least limit their number at each generation. It’s one of the problems we’re still working on.

Niko McCarty (28:15) With Spud Cell, you have waste accumulating inside the cell because ribosomes and tRNA stop working. You have waste accumulating outside the cell, which is all these proteins that have bound to Spud Cell. Are those two completely different recycling problems?

Kate Adamala (28:32) I don’t think so. The membrane problem is obviously a little more complicated because of the presence of the membrane. You have to figure out a way for this protease to poke its head up above the membrane to be able to cleave it. But the general problem is the same: How do you recognize what’s waste?

I’ve been thinking of scenarios like, what if, between each generation, you just hydrolyze all of your hydrocarbons? Would that be possible? Then start from scratch. That’s obviously resource-intensive. I don’t have a good solution yet. That’s one of the problems we’re working on. But to me, it definitely will not be continuously capable of division, so it won’t be able to claim aliveness until we solve that problem.

Niko McCarty (29:24) Energy intensiveness doesn’t matter, right? You just want one of these things to keep dividing. Theoretically, you can supply infinite energy for a Spud Cell.

Kate Adamala (29:35) Right now, yes, because it’s in the lab. But eventually, we do want applications for it. They cannot be hungry little caterpillars all the time. They have to find a way to metabolize things and make their own energy.

Niko McCarty (29:48) Natural bacteria divide using things like contractile rings, where they express proteins that form rings toward the middle of the cell, and the rings pinch down and cleave it in two. That system has been so well—

Kate Adamala (30:03) Yes.

Niko McCarty (30:04) Right? Every microbiology department in the US has somebody who studies bacterial division. But earlier in this interview, you said that you didn’t even try that. From the beginning, you were using this bulky alpha-hemolysin approach, which is so unnatural. Why did you not try the contractile ring?

Kate Adamala (30:24) That’s because a contractile ring has been an obvious choice for synthetic cell division, and other people, better microbiologists than me, tried already. There are a few labs that have been trying to build a protein-based division system for—not forever, but a very long time—and they still haven’t succeeded.

To me, that was, “I’m not going to compete with the people who have been doing it since I was in undergrad, and they still haven’t figured it out. I’m not smarter than them. I’m not going to figure it out where they failed.” I still don’t think it’s a lost cause. I think there is a way to figure it out. We just need more work on it.

Niko McCarty (30:59) When you say they have not succeeded, I’ve seen papers where people get liposomes to divide.

Kate Adamala (31:05) Not by genetically encoding the division. That’s the key. There are many ways to make a liposome divide, including protein-induced division. But to me, the key is that you have to couple phenotype to genotype. You have to genetically encode what makes you grow and divide, because otherwise you don’t have the selection pressure; you don’t really undergo a full cell cycle.

At the beginning, you asked why Spud Cell achieved what others couldn’t. People have made liposomes grow and divide before, but we’re the first who actually made it happen as a result of the metabolic activity of the cell itself. It’s the same with the protein-based division systems. People have made the blebbing work, but not as a result of internal protein expression.

Niko McCarty (31:57) It’s a fine line, though, right? You’re providing a genome, but you’re also providing tons of nutrients and everything else.

Kate Adamala (32:04) Wait.

Niko McCarty (32:05) It’s kind of like moving the goalposts.

Kate Adamala (32:07) Totally. That’s why I don’t know what alive means. On one hand, I don’t think it’s alive because it doesn’t keep going, and I have to provide everything, including ribosomes. But then every life form needs something provided to it. There is no life form that’s going to completely live on its own.

Even if you have, for example, HeLa cells in a dish, they’re alive. No one questions that. But if you forget to come on a Saturday to passage them, on Monday they’re going to be dead because you didn’t provide for them. Life always needs to be provided for. That’s why I don’t have a good definition of the limit of what we should provide.

Niko McCarty (32:50) Going back to the contractile ring and people who have been trying to make cells that divide with the contractile approach, that system is so well studied. As someone who has looked at that field—you might caveat and say, “I’m not an expert”—why do you think that’s not working? Is this a problem of unknown unknowns? Are there other factors involved that we don’t know about? What is it? Why is it so difficult to get this to work?

Kate Adamala (33:25) Obligatory: I’m not an expert. I think the protein cytoskeleton is very close to working. I don’t think it’s an unknown-unknown problem. I think it’s an engineering problem, a stoichiometry problem. Some other groups, for example Cees Dekker, have shown that they are getting really close to totally autonomous, multiple cycles of blebbing. It’s just pushing it through this final finish line.

That’s why, when people ask me what’s the future of Spud Cells and whether they’re going to be dividing by this protein crowding model, I keep saying, “I don’t think so.” I think in the next-generation tater tot cells, we’re going to be able to replace this protein crowding system with something better, some actin-cytoskeleton-based division. I think we’re really close.

34:19 — Bottom-up vs. top-down cells

Niko McCarty (34:19) What would falsify this program for you? Your goal is to get continuous divisions. Let’s say it’s 2030, and it’s still only seven divisions. Would you ever admit defeat and say, “Actually, maybe it’s not possible to create a synthetic cell that divides in perpetuity”?

Kate Adamala (34:46) Two answers to that. One is that I think we’re going to have a perpetually dividing cell by 2030, because we already have a cell that can grow and divide, and now we can have more selection pressure on it.

But if we get to a few years from now—and not just me; I’m not the only lab working on it, there are other labs working on this technology—and we all fail as a field, then that means there is an unknown unknown. There’s something about a living cell. At that point, I would say the bottom-up approach has not proven viable, and we should focus on the top-down approach, the Craig Venter approach, the minimal cell approach.

That cell is growing and dividing. We still don’t understand it fully. But that’s more of a tractable engineering problem because that’s a limited set of components, and we just need to figure out what they are. I hope we don’t get there, but if we do, and if it really looks like we can’t hack it from the bottom up, then I would switch to putting all the resources into the top-down approach.

Niko McCarty (35:53) What else needs to be done in the top-down approach? I haven’t carefully followed the J. Craig Venter Institute’s progress. They’ve been working on it for so many years. All I ever see in the media is that it has 400-and-something genes, and they still don’t know the function of X number of these genes. But surely there are deeper problems limiting it. What else is there?

Kate Adamala (36:15) That’s the biggest problem: What are those essential genes of unknown function? Right now, they already have a defined medium for that cell. It’s no longer a kitchen sink. They can use chemically defined media to grow it. They can minimize the lipidome. That’s what I meant earlier when I mentioned there is a living cell that uses two lipids in its membrane. That’s the Craig Venter cell grown under certain conditions. It can have a membrane made out of two lipids.

Niko McCarty (36:45) This has been published?

Kate Adamala (36:46) Yes, it’s been published. I’ll send you the link. It’s work out of James Saenz’s lab. It’s really minimal. The biggest bottleneck keeping it from being fully understandable and engineerable is the fact that there are several dozen genes we know are essential, but we don’t know what they do. We have not even the faintest idea what the hell those proteins do. They have to be there because if you knock them out, the cell gets dead, but that’s all we know about them. Figuring out the functions of those is what stands between that cell being fully knowable and where we are right now.

Niko McCarty (37:23) But after throwing tens or hundreds of millions of dollars at a problem—and maybe I’m taking too aggressive an approach on this question—why is it so hard to figure out the function of proteins? Why can we not grow these things in a hundred little flasks, give them to people, and do some super-resolution microscopy? Well, they do. So what’s the holdup?

Kate Adamala (37:47) That’s the unknown unknown. I don’t know. I’ve been very closely following that field, and I’m friends with a lot of people who have been in it for a long time. It’s a very difficult problem, partially because biology has only two states: live or dead.

That’s the beauty of a Spud Cell: It can be mostly dead; it can be a little bit dead. You can figure out a lot of functions in a suboptimal way. Right now, the Spud Cell divides very slowly. If you break something, it’s not going to completely stop dividing; it’s just going to divide slower. I can still figure out what went wrong because my system is still working. It’s experimentally possible.

With the minimal cell, if you break something, the cell gets dead, and you have no cell. That’s the problem with living biology in general: To figure something out, you have to do it on a cell that’s still viable, because if it stops being viable, you don’t have a cell anymore. I think that bottleneck, the fact that we do not have a slightly dead biology, makes it much harder to work with because you have to keep it viable in order to work on it.

That’s why I think this gray area where a Spud Cell sits right now, where it’s not really dead but it’s not yet alive, is a very comfortable place to be in. I can break a lot of essential things. I can mess with the fundamentals of metabolism. With the minimal cell, they’re stuck with either studying a fixed, dead cell or trying to figure it out on a living metabolism without making it dead. I think that’s just technically really challenging.

Niko McCarty (39:30) Isn’t it so sad that so many of the tools of molecular biology require that we kill cells, extract their molecules, and study their molecules? Even then, almost everything we study is in isolation. We study RNA on its own; we study proteins on their own. We sequence the genome only to later realize that the genome has a particular 3D shape, a topology that also really matters for how the genes are expressed.

Kate Adamala (39:59) Mm-hmm.

Niko McCarty (40:00) Isn’t this also a rallying cry that if we actually want to understand biology, we need methods that enable us to study it across space and time on living samples?

Kate Adamala (40:11) Or somewhat living samples. That’s the thing to me. I think that’s why it’s so hard to study living biology: You have to keep it alive. If we had a state in which we could study it, kind of like a breadboard for biology, where we could see if a particular circuit is ticking without turning the whole thing on, then at least some of those problems might become easier.

40:38 — What synthetic cells could be used for

Niko McCarty (40:38) That’s a very good segue, because the next thing I was going to ask you is: What is the point of Spud Cell? The argument I really understood was that Spud Cell could be a very interesting platform, like you said, to test things. I want to add a new genetic circuit in my cell: Does it work or not? You’ve stripped away all the complexity, so it’s good for troubleshooting. But the question I always had was: If you made a circuit work in Spud Cell, does that have anything to do with making that circuit work in an actual organism?

Kate Adamala (41:11) No, it doesn’t.

Niko McCarty (41:13) You’re saying that’s not the point. It’s that we would actually move over large swathes of the biotech industry.

Kate Adamala (41:19) Large swathes of it. Not all of it, but big swathes of it.

Niko McCarty (41:22) We would have bioreactors not of CHO cells making drugs, but of Spud Cells making drugs.

Kate Adamala (41:28) Probably not the Spud Cell in its current iteration, because it’s just—

Niko McCarty (41:31) Something very robust.

Kate Adamala (41:33) Once Spud Cell becomes more robust, once it can actually replicate under perfect conditions indefinitely, then it can become a biomanufacturing strain.

Niko McCarty (41:44) Can you say what you think some of the likeliest applications would be?

Kate Adamala (41:48) Catalysis that’s not possible with natural proteins. If you need an industrial process that requires very high pressure and temperature, those are very difficult to turn into a bioprocess right now because of those physicochemical limitations. But we know that, for example, if you add fluorinated molecules—basically make Teflon proteins—they can withstand much higher temperatures. We can only do that at a small scale right now because you have to do it in vitro, in a PURE system in a test tube. There’s no other way to introduce those fluorinated amino acids, for example. They’re not compatible with being introduced naturally.

Enzymes that require more chemistry than natural life can give you—that’s one huge field. I think now that the technology is catching up, that field might explode, because people doing protein design were working with what’s available to them. New proteins were being designed with the building blocks that are available. We already know from in vitro studies that there are multiple hundreds—I don’t know the current number, but it’s over 300—of different noncanonical amino acids that can be translated even by a natural ribosome. That huge chemical diversity doesn’t exist in biology right now. We’re not designing proteins taking advantage of that chemistry.

That’s why I firmly believe we can replace the petrochemical industry with bioprocesses. Not with bioprocesses using modern life as we know it, with the 22 puny little amino acids with low chemical diversity—sorry, biology—but with the actual huge diversity that’s available, that’s possible. Bioproduction, especially of molecules that are very far outside the constraints of natural biology, is going to be a big application.

Another one is drugs and biomolecules that are bioorthogonal, that are not made out of natural building blocks. You can, for example, inject a drug into your system, and your proteases don’t chew it up immediately. That’s going to be a big one.

Another one is that right now, Spud Cell needs to be fed everything, and it’s incredibly picky about its nutrients. But because it’s a platform we hope to bioengineer, I want to be able to engineer it so it can eat anything. I want to go from a toddler to a teenager that eats anything you put in front of it.

That enables a globally distributed bioeconomy, because different places, different climates on Earth, can grow different types of biomass. That’s a limiting factor right now in the development of the bioeconomy, because those bioreactors need to ferment a very particular set of biomass. You have this bioreactor that can ferment biomass from soy but not from prairie grass. If you can build a Spud Cell that has enzymes that can chew up a lot of different food sources, then they can ferment anything. That’s another area.

Obviously, we’re far in the future. We’re not talking about a five-year horizon. But by 2050, I think we’ll get there. If we don’t, we’re in trouble as a civilization. We have no choice.

Niko McCarty (45:08) It’s interesting that when I asked you what the point of Spud Cell is, you focused on the technological applications. You did not say what is normally the rallying cry for synthetic biology, which is, “We are building this to understand life”—which honestly has always struck me as a more tenuous position.

I can accept your premise that, yes, if there were a robust Spud Cell, we could engineer with very interesting new chemistries, and we wouldn’t have to worry about crosstalk and all these other factors. But building life to understand it—Spud Cell is so different from natural biology. Does it really tell us anything about natural biology, or does it tell us more about chemistry?

Kate Adamala (45:52) I think it tells us more about chemistry. If you take a pathway from biology and study it in isolation in a Spud Cell, then you can study that particular pathway much better. In that way, it does teach you a little bit about a natural pathway, because you can look at it separately from all the other pathways. But the Spud Cell does not teach us how a complex natural cell works. It’s just too different. Because of all the hacks we did along the way, and more hacks we’re hoping to do, I don’t think it’s going to be a reliable model that teaches me how my own cell works.

46:29 — Evolution and complexity of synthetic cells

Niko McCarty (46:29) Another thing I was wondering: You’re building Spud Cell, and it will improve over time. Let’s say it’s 2030. You have a Spud Cell, and it can still only divide ten times. It’s still not robust. You all get together as a group and say, “I know how to make this more robust. We’re going to evolve it. We’re going to put it in a bioreactor and pressure it, and—”

Kate Adamala (46:52) We’re going to do that way before 2030.

Niko McCarty (46:55) Okay, but then the question is: Hasn’t that destroyed the whole point of Spud Cell? As soon as you let evolution act on this, you don’t understand the components anymore.

Kate Adamala (47:06) That’s the problem with natural evolution, because you’re starting with something you already don’t understand. With a Spud Cell, I can sequence the hell out of it at every generation.

Niko McCarty (47:15) We can do mass spec on all the components.

Kate Adamala (47:18) And I know I have a baseline that I fully understand. Every new thing that pops up, every point mutation, every new functionality will be compared to the baseline. If I don’t understand it, then I throw it out the window, because I’m not going to have something I don’t understand in a system that’s designed to be understandable.

Every tiny improvement, every way to deal with a selection pressure, is going to be compared to the baseline we now understand. It’s not like adding an unknown brick to something you already don’t understand. It’s going to be a baseline platform we do understand. Evolution might create unexpected solutions, but they won’t be unknown solutions.

Niko McCarty (48:06) That’s really interesting to think about: Spud Cell as a benchmark to trace evolution. That’s—

Kate Adamala (48:12) Mm-hmm. That’s why I feel—

Niko McCarty (48:14) Very interesting.

Kate Adamala (48:15) That’s why it’s key to me to couple genotype to phenotype. I think we’re not as smart as evolution. I really think evolvability is a key function that will enable us to improve Spud Cells faster. Now we have a genome that’s coupled to the outcome, to the number of offspring, so now we actually can evolve it.

Niko McCarty (48:36) You could build some kind of assay of robustness. You measure robustness, take Spud Cell, and evolve it. Every few generations, you sequence it and do mass spec. The thesis is that you could actually map what makes things robust under different— That would be very interesting.

Kate Adamala (49:02) Right now, nobody’s doing that because the Spud Cells still need to keep replicating. That minor detail of it not replicating fast enough. We’ll start doing it the moment I have continuous replication. That’s the goal. I have several collaborators who are tippy-tapping right there in their labs now, waiting for it to happen so they can start doing it. But until we can stop worrying about housekeeping—waste removal and the number of cycles—we cannot do that yet. That’s why the first problem is to make it more robust.

Niko McCarty (49:38) Do you think evolution might be required to make it divide longer?

Kate Adamala (49:44) I hope not, because it’s chicken and egg then. You can’t really have evolvability unless you can go through multiple generations. I think we can hack it to the point where it will be replicating. It might not be very efficient at it; that’s why I say “hack it to that point.” But once we have multiple cycles of growth and replication, evolution can improve on it for sure. I think evolution is much better than me. Evolution is much faster, much more efficient than artificial design, than directed evolution that humans do.

Niko McCarty (50:20) This is a difficult question to pose, but bear with me for a second. There are all these knobs that evolution can pull on, even within a single molecule. There was just a paper in Cell where they were studying a particular virus, and they said the infectivity of this virus—how infectious it is—is not only a function of its sequence. It’s an RNA virus, but that RNA, when it enters the cell, folds into a particular shape that also plays regulatory roles in the infected cell’s genome. In other words, the structure and the sequence of the RNA are both playing functions for the virus.

If you look at the evolution of genomes, historically we just sequenced genomes and that was good enough. But we now know that certain types of cancers in human cells emerge not from sequence errors, but because the way chromosomes physically package in relation to each other is off. Clearly, there are these very combinatorial knobs that evolution is pulling on.

The vitalism that people speak of, which I don’t believe in either—I subscribe to the view that life is just chemicals computing—but maybe there is something to this belief that if you strip things down too much, you reduce the levers evolution can pull on, and you just won’t ever match the robustness or sophistication of natural life. I’m wondering if you have takes on that or subscribe to that.

Kate Adamala (52:03) I don’t mind complexity. I love complexity as long as I can understand it. I think both positions can be correct. Life can be an effect of molecules, just physicochemical behavior of molecules, but it has to be complex enough to be robust.

For example, a modern airplane is incredibly complex. I don’t think there’s a single person right now who can understand every single system of a modern airliner and explain every single subsystem, all the avionics, all the aerodynamics of the airframe, everything. There’s not a single person who can control all of that. But that doesn’t mean an airplane is a magical being. It’s still designed, engineered, and you can explain every function of it. It just became so complex. That’s how I think of life—

Niko McCarty (53:07) But the difference is that we can study airplanes because we can see all the components. We can put the transistors under a microscope and see them. But biology—if you were to evolve Spud Cell and it hits on a solution to the division problem, let’s say, and then you study its molecules, do mass spec, and sequence the genome, you’re not actually capturing the topology of the genome, the structures of those molecules.

Kate Adamala (53:32) That’s why you need to slice it and put it on a cryo-EM.

Niko McCarty (53:35) But what if evolution hits on solutions that our measurement tools are not equipped to even detect?

Kate Adamala (53:42) That’s a really interesting problem. I think we need a better measurement tool, and that measurement tool has to be computational. That’s another thing I think Spud Cell might enable: building a true digital twin of a cell. Now that we’re starting with something simpler, we have a collaborator who is building an atomistic-resolution model of Spud Cell. Because we can. I can tell you what the concentrations are and where those molecules are. You can make a model right now. As we build complexity, that model can grow.

With a natural cell, we don’t have that model because we don’t know where everything goes. But I think the problem you raised is really important: What if the evolutionary process finds a solution that we can’t backtrack, that we can’t figure out? I think computational tools will help a lot with that.

Niko McCarty (54:35) But how long can you run an all-atom simulation of Spud Cell? Even though Spud Cell is very simple, you probably can’t run that for very long at all, right?

Kate Adamala (54:44) Yep. My goal is seconds, which is very long by those standards, but I was told it might be possible.

54:51 — Why Kate changed her mind about mirror life

Niko McCarty (54:51) I want to go to mirror life now.

Kate Adamala (54:54) I don’t. I don’t want to make mirror life.

Niko McCarty (54:56) No, I know. When that big report came out, we covered it at Asimov Press. I wrote a long piece with Finn Morehouse about the report. If somebody were able to make a cell that has the opposite handedness of natural life, meaning all of its molecules had been replaced with their mirrored versions, that mirrored cell could evade the human immune system. It could evade viruses in the environment and proliferate out of control; there would be few things to keep it in check. Most scientists acknowledge that this is a very distant thing. We are nowhere near able to build such an organism.

But I want to go back to 2019. There was a conference, some kind of workshop event, where synthetic biologists got together. You were there; John Glass was there. Everybody looked around and was like, “Yeah, we should make mirror life. This would be amazing.” Why did you think at the time that it would be interesting or useful?

Kate Adamala (56:09) Because I didn’t know enough. I didn’t know enough to know better.

Niko McCarty (56:11) But what were people saying at the event? What was going to be the functional purpose of mirror life?

Kate Adamala (56:17) All the benefits we thought about getting from mirror life are the reasons we now think it shouldn’t be made. We thought it would be stealth to the immune system. Great, it would make a fantastic drug. It would not be possible to infect it with natural phages. Great, it would make a fantastic bioreactor.

We didn’t think about it from the risk-analysis point of view. We only thought from the benefit point of view. Only after we started talking to evolutionary biologists, ecologists, and experts in immunobiology did we realize that all those things we considered features are actually bugs. If it’s stealth to the immune system, it doesn’t just make a perfect drug; it also would make a perfect pathogen. If it’s not possible to eat it or infect it, then if it leaks out of your magic bioreactor, it’s just going to spread in the environment.

Niko McCarty (57:17) Who were the people who first approached you to tell you, “Hey, you should not do this”? Even the NSF funded it. It wasn’t just scientists in a room. Big funding agencies also gave money. Probably hundreds of people were aware of this.

Kate Adamala (57:32) Yes. It was public—NSF grants are public—so we were never hiding that we were doing—

Niko McCarty (57:37) Of course, but I just mean that to get an NSF grant, dozens or hundreds had to say this is a great idea. Who first approached you and was like, “Hey, I want to talk to you about this”?

Kate Adamala (57:48) It was very gradual. It was over a couple of years—really, over a year—of talking in the biosafety and security community about that idea. There was not a single person who came and said, “Hey, I think this is a bad idea.” People started genuinely asking questions. Not in this Midwestern ironic way of “I’m just asking questions,” which means “I’m criticizing you.” No, no. They were genuinely asking questions about, “How do you make sure it doesn’t take over in the environment once it leaks out?” It was coming from curiosity, but also concerned curiosity.

We, the people working on it, realized we actually did not have a plan for that. So, okay, we have to come up with a plan for that. Then we started thinking: How would we prevent persistent infection or persistent replication in the environment? We started realizing that we couldn’t think of a way to do that.

Then we started going out to more people, asking ecologists, for example, “Hey, I have this problem. What if I make an organism that can do this? How would you limit that organism?” Those people could not come up with a way to limit it. Then we started realizing that we have a problem and we should not be enabling that technology.

Niko McCarty (59:12) What’s interesting is that after the big mirror life debate kicked off a couple of years ago, people went and looked in the history books. Louis Pasteur said this would be a problem. In the 1800s, Louis Pasteur was like, “If we made mirror-image life forms, it could be really bad.” In the 1990s—or in 1990—these Purdue chemists wrote a letter and warned about this. There was a Wired article in 2010 saying that mirrored organisms would wipe out the planet. George Church’s book with Ed Regis, Regenesis, devotes a huge share to mirror life.

It’s so confusing to me, the timeline of why, in 2019, despite even a very mainstream Wired article, people were like, “This is an amazing idea.” Again, I’m more techno-optimistic than fearful. I acknowledge that mirror life is so far away. I’m just trying to understand the timeline: How could it have been that these scientists in a room were not aware of this?

Kate Adamala (1:00:24) Now we’re aware of it. This Wired article, for example—I think it’s a great article, but I had no idea it existed until we started digging into the background on safety, when we started considering its safety. I think it became more mainstream as the problem became mainstream. It wasn’t an article everyone was aware of.

Obviously, I did read George’s book, but it was not—like, when we first started thinking about it, we thought, “Okay, we can put safeguards into the organism.” It took a long time to put all those things together. I had no idea Pasteur wrote about it until I was way into writing the Science paper. With all due respect to Louis Pasteur, I of course never read his original writings.

Niko McCarty (1:01:17) It was from a lecture, actually, so even harder to find.

Kate Adamala (1:01:20) Now we know those background materials exist, but they weren’t prominent. I think that shows a short—

1:01:27 — Why life evolved a single handedness

Niko McCarty (1:01:27) When the debate starts, people look for evidence. It’s selective bias. I’ve read books and articles that state as a fact that there’s no reason life adopted the handedness it did. It’s just a fluke of evolution that the cell that evolved to the present day and gave rise to all living organisms adopted those chiralities in its molecules. It chose those handednesses.

Kate Adamala (1:01:59) I agree with that, actually.

Niko McCarty (1:02:01) My question is: How do we actually know that? You’re making the assumption that it could be reversed and that there are no emergent properties or utility of the existing handedness. Also, why would only one handedness survive? It also insinuates that the evolution of life is rare. I’m curious what you make of it.

Kate Adamala (1:02:28) That’s a four-part question.

Niko McCarty (1:02:31) The question was terribly posed.

Kate Adamala (1:02:33) It’s actually a really good question. It’s four really good questions. Let me answer the second question first. The reason we need one chirality is that life has to be interoperable. Life has to be able to eat other life. A pretty strong hypothesis I support is that if you want a biosphere to work, everything in that biosphere has to be interoperable. If you die, you have to decompose to elements that other cells can eat. If a predator comes at you, that predator has to be able to eat you. You have to be able to eat food. Everything eats everything else, so one chirality is kind of necessary.

On the metabolic level, you have to be homochiral, because otherwise the proteins would just not work. You cannot have mixed chirality because you would have too many different stereoisomers, different possible configurations, different possible molecules that wouldn’t physically interact with each other. That’s the reason life had to pick one.

How do we know it probably doesn’t matter? Because we have a lot of evidence that opposite-chirality proteins and nucleic acids interact with each other just like the normal-chirality ones. That’s why we think it could have happened either way.

The third question in your string was: Does it imply that the evolution of life is really rare? I don’t think so. I think the universe might be lousy with life. Obviously, there’s the Fermi paradox, and I think that’s a very different discussion. Intelligent life might be very rare, but life as a phenomenon is probably very easy, given how quickly it started on Earth and how easy it seems to be. My small lab made molecules into a lifelike system. There’s nothing magical to me in how molecules make themselves into life if you give them enough time and the right conditions.

I don’t think life is a particularly difficult process to get started. We have n equals one because we only have one on Earth, but it started so quickly. The moment Earth had liquid water and a crust, life started. Either aliens came with a salt shaker, or life spontaneously started really quickly—and I take the easier solution: Life started quickly.

Niko McCarty (1:04:58) If it started quickly, it could start often.

Kate Adamala (1:05:01) It could start often, and it could pick a chirality at random.

Niko McCarty (1:05:05) We’ve just never detected it, or it peters out, or it’s outcompeted in its environment. That’s your thesis.

Kate Adamala (1:05:11) That’s my thesis exactly.

1:05:12 — SpudCell as an enabler for mirrored life

Niko McCarty (1:05:12) Another point is: Why are people even having this debate? We haven’t made a synthetic cell, let alone a synthetic mirrored cell, which is even harder. To play devil’s advocate, what is even the point of worrying about this?

Kate Adamala (1:05:30) Because now we can actually do something about it. People wanted to do it. We were funded to do it; others were funded to do it. If you get too close to it, there’s no stopping it. It’s really hard to stop scientific progress when it takes one or two bad actors to get there.

Right now, we’re so early that we could stop this whole field in its tracks by creating peer pressure: All the experts in the field don’t work on it. We’re not building the capacity that gets us closer to it. Now is actually the only time we can stop it. Once we get too close to making a mirror cell, a single bad actor can do it. Right now, we’re too far from it, so we can stop it as a field.

Niko McCarty (1:06:15) One thing I’ve always wondered about this is: If we had the technology to create mirror life, that insinuates that we’re very advanced in biotechnology. If we could make a mirrored organism, surely we could make a mirrored phage.

Kate Adamala (1:06:30) That’s a very safe assumption.

Niko McCarty (1:06:31) Mirrored antibiotics and mirrored—so is it actually as big a threat as people think it would be?

Kate Adamala (1:06:39) That’s a debate. That’s the argument against us being against mirror life that makes the most sense to me: If we can make mirror life, we can also make something that eats it and infects it.

But on the off chance that we’re both right about the dangers of mirror life and wrong about our ability to make a phage for it and release it globally—if those two are true, then we’re totally screwed. There’s nothing about mirror life that would be worth taking that risk. That’s it to me. It’s not like mirror life is completely worthless. It would have applications, but they’re not worth taking that risk. I’m not 100 percent sure we’re right about all those dangers, but I would rather not find out.

Niko McCarty (1:07:37) Personally, I struggle to envision exactly what the point of making a mirrored organism would be. I totally get a mirrored ribosome to make peptide therapeutics. That’s obvious. What do the proponents of making actual, full mirrored cells say are the applications?

Kate Adamala (1:07:55) Biofermentation: You cannot contaminate a bioreactor if it’s made out of mirror life. And drugs, medicine, cell therapies. Imagine a cell therapy where you have a cell you can inject into a patient that has all the properties of a cell. It can detect metabolites, it can produce a drug, and it’s stealth to the immune system. These are the two practical arguments, and—

Niko McCarty (1:08:20) Those are all things you’re saying we can make other ways. It just might be more expensive.

Kate Adamala (1:08:23) Exactly. Which is why I’m now on board for not making mirror cells, because I think the risks are much bigger than the possible benefits.

Niko McCarty (1:08:34) There are two ways to make a mirrored cell. There’s the top-down way, which seems extraordinarily difficult. I don’t even know that this would work, but maybe you could take a minimal cell like the JCVI cell and replace components one at a time, or swap in just the central dogma in a mirrored form. But because of the compatibility issue you talked about earlier, I don’t see how that would work. The only other way is to make it from the bottom up. Isn’t Spud Cell, in a way, the enabling technology to build mirror life?

Kate Adamala (1:09:14) Not really, because the biggest bottleneck in making mirror life is not the actual assembly. It’s the sheer amount of stuff you need that we cannot make right now. Spud Cell is difficult enough to do when all my components come pretty much free from E. coli. All my ribosomes, all the other proteins, everything I use to make a Spud Cell comes from E. coli. It takes pennies to grow it, and obviously it’s a pain in the lower back to purify it, but it’s doable. I can have buckets of it.

With mirror life, you would have to chemically synthesize every single thing because we don’t have a way to make that. That’s a huge technological barrier, and that’s the barrier we’re hoping never to cross. That’s the key enabling technology. That’s why I say a replicating, autonomous mirror ribosome would be my red line, because at that point you can start making all the components that will eventually become a cell.

Niko McCarty (1:10:14) But isn’t it a fear at all that if you know all the components exactly, you’re publishing a recipe where people could just recreate the—okay, so it’s expensive.

Kate Adamala (1:10:26) It’s more than expensive. It’s just not technically possible right now to make that amount of protein. Even state-actor-level resources would not be enough. We just don’t have a way to make that.

Niko McCarty (1:10:38) But what are the things we can’t make? Is it long proteins that are mirrored, too expensive, or—

Kate Adamala (1:10:44) Long proteins, it’s—

Niko McCarty (1:10:46) Because you have to make them using solid-phase synthesis.

Kate Adamala (1:10:48) Then stitch them together and have mirror chaperones that help them fold in the correct way. Resource-wise and technology-wise, we don’t have a chemical synthesis technology right now that would allow us to make those giant proteins. The biggest things we’ve made were those single instances of mirror polymerases. These are not that big an enzyme.

Niko McCarty (1:11:14) You have to make a high concentration of these.

Kate Adamala (1:11:17) High concentration, high amounts of all of them. Then you have to have all the nucleotides to make the mirror nucleic acids. Logistically, you would have to retool your whole scientific enterprise toward it.

Niko McCarty (1:11:32) Is that something you’re monitoring? You said your red line would be a mirrored ribosome that can make copies of itself. Are there other things where you’re like, “We would pause the Spud Cell work if we saw X”? If mirrored solid-phase synthesis becomes really good, what is your line for saying, “Okay, we’re not going to do this”?

Kate Adamala (1:11:53) I think mirror solid-phase synthesis would not give me pause. That’s why we’re pushing to codify what has become a sort of community-enforced red line into law before that technology becomes possible. So then we can—

Niko McCarty (1:12:13) Yeah.

Kate Adamala (1:12:13) We’re trying to frame that conversation. At least that’s my goal. It’s a diverse community. Some people don’t think it should be codified into law. But I would feel much safer if there were something like a Biological Weapons Convention, something that has similar power to the BWC but is about mirror life.

For example, right now no country can come out and say, “I’m making a virulent, weaponizable smallpox,” because international law literally tells you it’s illegal. I would love it if mirror life research got to that point. We’re not there yet. We might never get there, but that’s my goal. That’s the answer to your—

Niko McCarty (1:12:55) Don’t states still make smallpox? There are still bioweapons programs.

Kate Adamala (1:12:57) They do. They don’t admit to it.

Niko McCarty (1:13:02) Yeah, but okay, you know.

Kate Adamala (1:13:04) But also, it’s super cheap and easy to make smallpox, especially if you’re a state actor. That’s the good thing about mirror life now: We’re stopping the development of the technology before it becomes cheap and easy. It’s also a terrible weapon, because bioweapons only make sense if you can immunize your own population against them.

Niko McCarty (1:13:23) What, you mean mirrored?

Kate Adamala (1:13:24) Yeah, mirror life would be a terrible bioweapon.

Niko McCarty (1:13:26) But isn’t it a good ecological weapon?

Kate Adamala (1:13:29) Yes, but you cannot limit it. An adversary—

Niko McCarty (1:13:33) You would also be destroyed.

Kate Adamala (1:13:35) Would also be destroyed. That’s not a state-level weapon. That’s an individual-terrorist-level weapon, and those don’t have the resources.

Niko McCarty (1:13:43) Interesting argument. It’s interesting for me to examine how you justify working on things. Again, I’m a techno-optimist. I am a biotechnologist, but I live in San Francisco, so I’m sort of washed up into the discourse. It’s interesting to talk to someone like you who’s like, “We should stop mirror life,” and then, by the way, we’re making a synthetic cell platform that is the enabling technology.

Kate Adamala (1:14:16) That’s the thing. I don’t see it as an enabling technology, because I think the technical problems toward making mirror life—and I say that as someone who tried to make it, so I know how much it sucks to try to make it—are way beyond what normal-stereochemistry synthetic biology is facing. They’re just huge resource problems.

1:14:38 — Biotic

Niko McCarty (1:14:38) I think that’s a good segue to Biotic. After the Spud Cell preprint came out, you announced there’s going to be this big nonprofit initiative. The goal is to raise $100 million. Is that public? The goal is public.

Kate Adamala (1:14:52) The goal is public. The goal is to enable a global bioeconomy. Do the math.

Niko McCarty (1:14:59) There’s not a lot about Biotic that I’ve seen. I want to understand: What is Biotic actually doing? Is it a grant-making organization that’s trying to bring more people into the field? Is it going to be a building where you’re centralizing efforts? What is the goal here?

Kate Adamala (1:15:18) It’s a grant-giving organization. Right now, our goal is not to bring more people into the field; it’s to focus people who are already in the field. Synthetic cell engineering is an amazing, very diverse field. That’s the beauty of it: People have different definitions of what a synthetic cell is. But that makes the efforts rather unfocused. Progress is being made, but not fast enough.

We as a society really are struggling right now. The world is burning. The world is having a lot of societal problems that can be traced back to literally the way we’re moving atoms, the way our industry works. We think many of those problems could be solved by enabling a bioeconomy. We also believe it will not be possible to enable a bioeconomy unless we have a better way of moving atoms beyond the natural cell. That’s why we think synthetic cells have to happen for the world to become sustainable, for civilization as we know it to survive and be sustainable.

That has to happen soon—soon enough to matter. We’re talking about 2050 as the deadline when we have to start seeing things change. Right now, the efforts in the synthetic cell field are not focused enough. They’re not focused on a single interoperable platform.

At its core, what Biotic wants to do is fund the development of a robust synthetic cell that can create all those applications. All the people who work on developing modules and technologies that enable that synthetic cell have to agree on a standard, on a single platform. For example: This is the translation system we’re all using. This is the genome design and architecture we’re all using.

Those types of standards could be created by the community, with “Pretty please use those standards.” That could be one way of enforcing it. But a much more efficient way would be to fund research and say, “We’ll fund your research. We love what you’re doing for this field. We want you to keep doing it. Just please make your work interoperable with our platform, and we’ll pay you to do that.”

That’s what Biotic is. It’s a grant-giving organization, but the grants aren’t a free-for-all for anyone who wants to make synthetic cells. Those are grants for people who will make useful modules for synthetic cells that will work with all the other modules developed within that ecosystem.

It’s like saying we want to make apps for a Linux operating system, and those apps have to work on a Linux kernel. We’ll pay you to write that app, but only if I can boot it up on my computer. That’s an analogy.

Niko McCarty (1:18:11) Who decides what to fund and what the priorities are?

Kate Adamala (1:18:16) Right now, it’s the Biotic board that decides. As we grow, we’re hoping to build an international scientific advisory board, as the decisions will get tougher as we get more granular.

Right now, the guiding principle is that the modules you make have to operate on a Spud Cell. The only reason for that is that Spud Cell exists. There’s no other synthetic cell platform that grows and replicates. If someone makes a better one, and it’s compatible, we reserve the right to move. We’re not “Spud Cell is the one and only platform” people. We’re “Whatever works is the one and only platform” people.

Right now, we want to win by winning. We have a working prototype, so we’re asking people to contribute to making that working prototype better and better and better until it stops being a prototype. The standard now is: Make modules that will make this one thing that exists better.

Niko McCarty (1:19:19) Have you already shown that Spud Cell works in the hands of others? How reproducible is it? What other labs have made Spud Cells in their labs?

Kate Adamala (1:19:29) We’ve reproduced Spud Cells in Drew Endy’s lab. Right now, other people have reproduced other elements of Spud Cell. It’s been a little over a month since we made the whole thing public, so I don’t know of any other lab that has reproduced the whole thing. Elements of Spud Cell have been reproduced in other labs, but as far as I know, not the whole thing.

Niko McCarty (1:19:55) Even if Biotic raises $100 million, what is the plan to keep it sustained through 2050, especially when interest starts to die down? It’s one thing to fundraise when you’re backed by all the hype. It gets progressively harder and harder to fundraise as the progress becomes more incremental.

Kate Adamala (1:20:14) Hopefully, we will not be fundraising by 2050. The goal is to make it a useful technology. The only victory condition for Biotic is to make it into a commercially useful technology that enables biotechnology, that enables a bioeconomy. That’s going to bring in money.

We say this is an open platform for research, but we did file IP on it. It is not a platform that any company can use for free. We will license that and all the future improvements to any company that wants to make it into a useful technology. The royalties they pay back to Biotic will support further Biotic research. That’s the victory condition.

That’s why we have to succeed. Biotic is not designed as an ongoing, indefinite research operation. It has to start producing viable products that will bring in money, and that money will sustain it going forward.

Niko McCarty (1:21:09) Is the idea ever that you would spin out companies? Only licensing the technology may be interesting, but it’s very uncertain. Would you ever consider, “Hey, we did something very promising. We’re just going to spin out our own company”?

Kate Adamala (1:21:25) We do, and Biotic has this plan that once we start having viable product possibilities, we’re going to spin out Biotic Ventures. Think of it as something internal, almost like a family office run out of Biotic. We as Biotic founders will not spin out companies on our own, but we will support people spinning out companies, and their revenue will come back to the research ecosystem. That ties to our victory condition of making a useful product.

1:21:58 — China and 2050 goals

Niko McCarty (1:21:58) When this announcement came out, there was a lot of discourse about China: “We have to do this, and it’s so much better than China. China has its own synthetic cell effort, and we’re so far ahead.” What’s the deal with China? Who cares about China’s synthetic cell effort? Why not be collaborative? Why does it seem so antagonistic?

Kate Adamala (1:22:23) It really bugs me that there is this competitive narrative to it. It’s obviously tied to geopolitics.

Niko McCarty (1:22:29) But in Drew Endy’s Hoover Institution interview, a big chunk is about China and how we’re ahead of China. I’m like, “What does this have to do with geopolitics?”

Kate Adamala (1:22:39) It’s enforced by the political structure that governs the results. If Biotic is the first to produce a functioning synthetic cell that becomes technologically important and powers a bioeconomy, that bioeconomy is going to run by the rules of the country where Biotic is, or the system that supports Biotic. That’s going to be an open ecosystem.

If the first functioning, commercially viable synthetic cell comes out of research supported by a totalitarian government, then access to it and the ways it’s going to be used and deployed are going to be very different. That’s the biggest difference.

Niko McCarty (1:23:26) Are there Chinese labs that are really good that Biotic would fund but cannot fund because they’re in China?

Kate Adamala (1:23:33) Right now, we’re not funding any work in China, but there is a huge institute in Shenzhen led by Chenli Liu that has amazing expertise in synthetic cell engineering. In an ideal world, I want to work with them, not against them.

Niko McCarty (1:23:46) I visited the Shenzhen Institute, visited him, and saw his lab. They have two floors of robotic labs and very impressive scale.

Kate Adamala (1:23:56) Yes. We all would be much better off if we were able to collaborate. The sad reality is the geopolitics, and you can’t get around that.

Niko McCarty (1:24:07) But if Spud Cell is nonprofit, open-sourcing its technology, and publicly revealing things, isn’t the timeline for China to catch up to whatever you publish about a month? Considering how advanced they are—I was just there a couple of months ago, and I was even more impressed on the second visit.

Kate Adamala (1:24:28) Yes, but that’s why we filed IP on it. We filed protective IP. The Spud Cell is—

Niko McCarty (1:24:33) But that doesn’t matter, right?

Kate Adamala (1:24:36) It does and it doesn’t. We still have to pretend we believe in the law.

Niko McCarty (1:24:41) Assuming this works and Biotic becomes a self-sustaining organization, what is the end goal or the success case in 2050?

Kate Adamala (1:24:52) It has to work, because by 2050 we have to make all the products sustainably, and we have to be truly engineering biology. We’ll have a cell that people can work with, and bioengineering will become more democratized. I know it sounds like a utopia right now, but I really think it’s doable that this technology can become a universal jump-start to biological evolution.

People have been talking about the 21st century being the century of biology, and to me that is necessary. We have to engineer cells in an intentional and accessible way. That’s going to happen by 2050 or we’ve failed. I don’t like failing, so it’s not going to happen.

Niko McCarty (1:25:45) Awesome. Kate, thank you so much.

Kate Adamala (1:25:47) Thank you.