SpudCell is a masterful demonstration of bottom-up engineering that successfully blurs the line between complex chemistry and biological function. However, its inability to evolve reminds us that assembling the machinery of life is not the same as igniting the spark of living autonomy.
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SpudCell: Newest Breakthrough in Synthetic Biology (Featuring Kate Adamala)
Added:Hey everyone, many of you know that in between debunking science denying charlatans, I like to highlight new and innovative research being done by the scientific community. You may have seen headlines regarding a synthetic cell named Spud cell. What's that all about?
Let's go over some information and then chat with the scientist behind it all.
Kate Adamala is a synthetic biologist working at the University of Minnesota.
For anyone who is unfamiliar with this field, it essentially entails using modern knowledge in a variety of scientific fields in order to physically construct biological systems from an engineering perspective. This could mean redesigning existing organisms or even creating totally new systems completely from scratch. It's an incredibly bold field which promises a wide variety of potential applications. Most obviously, this includes the capacity for engineered microorganisms to synthesize useful compounds such as life-saving drugs, biofuels, plastics, and more, all in eco-friendly sustainable manner. In fact, we have highlighted research in this area in other content when discussing genetically modified microorganisms that can express a desired set of enzymes which allow them to synthesize certain materials in as straightforward a manner as brewing beer. But beyond these applications, the field inevitably brushes up against territory of a philosophical nature, given that one of the stated goals of the field involves creating life from non-living materials. In other words, life from non-life. Given my extensive efforts combating anti-science propaganda surrounding origin of life research, it's worth noting that synthetic biology has only some overlap with the notion of abiogenesis. Methods that can be devised to synthesize life in a modern lab, as remarkable as they may be, are very unlikely to bear any resemblance to the processes by which life initially evolved on Earth several billion years ago. And those are the specific processes that origin of life researchers are hunting for. It's a question of what is possible versus what specifically happened. Nevertheless, illustrating a variety of potentiality for the assembly of a living cell does help us better understand the possibilities that are available to natural systems and which ones are more probable than others. So, what is this so-called spud cell? In short, it's some water enclosed in a fatty membrane that is filled with DNA and other cellular components, which is capable of growth and cell division. Not quite to the degree of an actual living cell, but it exhibits select behaviors that are of the nature of a living cell. So, we would not call it alive, but on a physicochemical continuum that spans from the completely inert to the completely alive, it sits somewhere in the middle and it is almost certainly the closest we have come to building a living cell from scratch. Other highly publicized achievements in this field, such as Craig Venter's synthetic organisms, have involved designing and synthesizing a novel million-base pair genome from scratch and then transfecting it into an existing bacterial cell. So, the genome was synthesized, resulting in a totally novel organism that had never existed before, but no other aspect of the bacterium was synthesized. Demonstrating that a living organism could be sustained by synthetic genome was an incredible milestone. Whereas, Kate's spud cell appears to be a milestone of a different nature. Spud cell is not a pre-existing cell at all, but rather involves droplets forming, fusing, and replicating of their own accord. Cell division is not reliable over many generations, so the process is clearly not as robust as what occurs in even the simplest extant living cells. But, it is a remarkable result that can be regarded as a stepping stone towards a more concretely viable fully synthetic organism. Spud cell's genome consists of only 36 genes taken from various existing species across several domains, making it much simpler than the simplest bacterium. Some of these genes encode molecular tags that present on the surface of the droplet, kind of like membrane surface proteins. Some of these tags act as attachment points for feeder vesicles or smaller liposomes that contain enzymes and other crucial molecules for the core droplet, which is incapable of biosynthesizing its own building blocks. Other tags bind to a protein named streptavidin, which creates enough repulsion among the surface molecules to force cell division in a crude and inefficient manner. One obvious barrier to extended division and replication involves the fidelity of genome replication. Living cells have systems in place to segregate replicated chromosomes such that each new cell has a full copy of the genome. Spud cell can't do that, so only 30% of spud cells carry the full genome after five division cycles. But it remains the first achievement of its precise kind, the first instance in which a complete cell cycle has been demonstrated by this sort of bottom-up system, which is totally unlike the more common top-down approach of deconstructing an existing microorganism. This means that the door is wide open for iterative improvement of this approach.
Kate's team's work on spud cell currently exists in the form of a preprint on bioRxiv and thus has not yet been peer-reviewed or formally published. It's nearly 200 pages with all the data, so it's not a short read, but it is linked below should anyone be curious to get a closer look. And indeed, the intention is to make all of this methodology publicly available for other groups to mimic. For our purposes here, we can simply take a moment to examine some of the key figures. Figure one depicts the complete cell cycle that was observed, including replication of the multi-plasmid genome, gene expression, nutrient uptake and waste removal, as well as division and selection. Figures three and four depict five generations of the cell cycle and selection in populations of synthetic cells, respectively. But as this will get quite esoteric very quickly, we will do best to move along and speak with Kate directly. Enjoy this conversation now. Kate, thanks so much for joining us. So, we're going to talk a little bit about spud cell today, but maybe just to start, can you tell us a little bit about your background? How did you arrive at this research interest that you have currently?
>> Hi and hi everyone. Thanks for having me. I I am a synthetic biologist, which means I am interested in biology, but I recognize the limitations of biology. I I'm trained originally as a chemist.
And I really like to know where molecules go when I work with something.
And then when I started learning biology, I realized that biologists don't really know where their molecules go.
A natural cell is like a black box. We don't have a full chemical ingredient list. We don't have full blueprints of it.
So, I wanted to call myself a bioengineer, but I really can't with a straight face because what kind of engineer doesn't have like the full plans of what they're working with.
So, that was that that was what really motivated um my field, motivated my my work in this.
And I ended up wanting to build a synthetic cell for two reasons. Um one, to show that we can, to show that we can assemble molecules into something that looks like a cell, that there's nothing magical about life as a phenomena, that we can assemble those molecules and they start performing certain functions of life.
And that's the scientific kind of a big picture philosophical motivation. And then there was the practical motivation.
And um that motivation basically um came from the fact that if you think about it, the invention of an electrical light didn't come from a continuous improvement of a candle.
That's a quote that's very overused, but it explains our motivation really well.
If we want to improve biology, we want to build bioeconomy, we want to have a carbon neutral economy that allows us to produce everything we need, everything the civilization needs, using renewable biosynthesis methods with biology. And we're not going to get there by improving a natural heavily evolutionary constrained cell.
I do believe it's possible to run world economy on bioproduction, but I don't think it's possible to do that with natural cells, the cells that evolved in nature cuz they evolved for very different purpose.
>> Right.
>> So that was that practical motivation behind wanting to make a synthetic cell.
>> Yeah, I I totally feel you on the I I studied chemistry as well and so for me in learning biology, there is sort of that chasm when you get all even the most the simplest extant cell. I I think that a lot of people right there's a lot of heavily publicized stuff in synthetic in synthetic biology where I think the general public doesn't fully understand that it is very top-down just sort of the redesigning of a genome or something like that. This is totally bottom-up. So let's let's dig into Spud Cell. Please tell us a little bit about uh I we really want to understand the composition of Spud Cell, the functions it can perform, and how it compares to something like a modern prokaryotic cell. So maybe starting with like the genome, let's talk about that.
>> The genome is um multiple plasmids that contain all the proteins you need for DNA replication, protein expression, so transcription, um making all the um copies of the mRNA that you need, making some of the ribosomal proteins, although we do not make ribosomes in a Spud Cell yet.
Um all the proteins you need for growth, so the growth is genetically encoded, it's coupled to the genome, and all the proteins you need for uh replication, which also is genetically encoded. And that's pretty much it. Um there's some helper proteins like um reporter proteins that tell us something about the healthy that that organ that I don't know if you could call it organism that thing is.
Uh but that's the minimal absolute minimal amount of genes you need to to be able to complete a cell cycle.
>> Right. Yeah, so I mean, I know that there's this sort of like >> [clears throat] >> fear theoretical minimum genome length for a living organism, and this is dramatically less than that, but but perhaps that's not surprising because it's not considered alive formally.
>> Yes. Um, I [clears throat] I'm I strongly believe it is not alive because it's not robust enough, and also it doesn't continuously replicate. Um, it can go through a few replication cycles and then it stops. And I think that's where the gap comes from in the genome size. Our genome is still smaller than that theoretically predicted um smallest genome size, and I think that gap will be filled by the proteins we need to be able to continuously indefinitely replicate.
>> Right. So, so would that be some kind of cellular machinery? Like obviously in in accident life, there there might has to be a way to kind of segregate the chromosomes to ensure that each uh daughter cell has the full So, you'd need to design some kind of apparatus, whether it be natural or something completely of your own invention, that would successfully perform that function. Is that kind of one of the main barriers?
>> That's correct. That's my personally the biggest obstacle right now is that we don't have something called cytoskeleton. Like every cell has this protein structure inside it that acts like a skeleton, and we don't have that in a cell cell.
It's significant that we've achieved replication without cytoskeleton, but it's also notably poor replication.
I think it's really important to introduce cytoskeleton, which is going to be some of those missing genes, and that's going to help with two things.
One is the indefinite growth and ability for the cell to be more rigid and robust, and the other one will be the segregation of the cellular components, and most notably the genome.
>> Mhm. Mhm. Yeah, it would be very fascinating if you could install something like that and then you had continued replication with full fidelity of the genome. Would that then be alive?
And if not, why not? And what would be the next uh you know, what issue metabolically would be preventing it from being called alive or something like that? Um yeah.
>> That's a tricky question because we don't really have a good definition of life.
>> Yeah.
>> There is no scientific definition of life that I would find sufficient.
>> I mean, I I find the I find the definition sufficient in in its ability to describe extant life. But when you get really, really granular, we're talking about systems that we've never observed before, then there is a point where it breaks down, obviously, because we've never seen the simplest possible thing that could possibly be considered alive.
We don't know what that is, you know. So >> Exactly. And we might There might not be a line, you know, it might be a continuum.
>> Yeah.
>> It's possible that there is no like a very clear boundary between life and non-life, and I would actually be very happy with that.
>> Yeah. I think that's probably the case.
Yeah.
Um >> life isn't anything special. Life is just behavior of molecules, so >> That's right. Yeah.
>> Yeah.
>> It's an emergent property of of a sufficiently complex system of molecules, yeah. Um I I would I'd like to know a bit about the membrane as well because it's it's not like a phospholipid bilayer or anything like that, right? What is Oh, it is? Oh, okay.
>> It is a very simple, plain phospholipid bilayer, which is different than extant cells because, as you know, in extant cells, the the membrane it's called a phospholipid bilayer, but it really isn't. It's It's a It's a protein, glycoprotein, lipids, sugar mix membrane. It's It's more more like a liquid crystal made in part from lipids, but also a lot of other things.
>> Yeah, teeming with with surface proteins, obviously, right? But there are But there are there are a small handful of surface proteins in Smudge cell, right? Can you tell us about those?
>> They are Those proteins have three functions. Um they're membrane channels, so they allow us to uptake nutrients from the growth media.
And they also present tags on the surface, and those tags are used for feeding, so inducing the process of the the feeding and division, inducing the process of division. And these are the three functions of the membrane proteins and nothing else.
>> Mhm. So, a channel protein so that it can uptake substance just from its surroundings, but then sort of a tag to to fuse with these liposomes, which that basically you you have to feed your Smudge cell intentionally, essentially, right? So, that that might also be considered another barrier to it being considered alive as it's it can't really self-sustain without being fed the the liposomes.
>> That's I mean, I I'm firmly that this is not a living system, but I do have problem with that feeding intentionally.
I mean, you have to feed intentionally, too. It Every organism has to feed intentionally, so I I actually don't think the feeding is a barrier. I think that metabolism and replication are bigger roadblocks towards aliveness.
>> Okay, yeah, let let's talk about metabolism then. So, so we have the we have metabolic processes that are occurring. Obviously, the there's there's protein synthesis happening.
Um what else in terms of like energy production? What else is going on in there?
>> Not much, really. It It makes It has a very simple energy regeneration pathway, but it also has to be fed some amount of straight ATP and GTP.
And it has um ability to obviously make RNA and proteins. It It's easier to to to list what it can than what it cannot, because it cannot do many things. It cannot biosynthesize building most building blocks. Um so, I mean acids and nucleotides have to be fed from the outside. And it also cannot break things down. So, once you made a protein on RNA, it's there to stay until chemical degradation takes over. And that's another big downside of that metabolism is that it doesn't take its own trash out. It doesn't recycle components.
>> Mhm. Mhm.
Okay, yeah. So, so certainly just like a lack of enzyme diversity would probably be one thing. Is that Which Which could we summarize? Is it possible to distill it into a short list of bullet points of what prevents Spud cell from being alive? We have the the lack of of continuous cell division. What How would you state that state this?
>> Yeah, to me it would be lack of continuous cell division, lack of the ability to evolve. The Darwinian evolution right now is not possible because the genome replication fidelity is too high to induce correct rate of spontaneous mutations, and lack of any sort of advanced robustness. So, there's no biosynthesis pathways for most metabolites, so it cannot really respond to changes in the environmental conditions. It cannot compensate.
>> Right.
Right. So, but I did read something about describing aspects of competition and selection for Spud cell. So, does that occur indeed? And And if so, in why does it not qualify as Darwinian?
>> It does have competition and selection, but it has to use mutations that are artificially introduced. So, we've shown that we can have competition. For example, we have a gene that allows for faster replication. And if you introduce that gene into the population, after a few generations that gene becomes more prevalent, like it takes over the population, which makes sense. That's what a competition is, but it's been introduced that mutation's been introduced artificially by me.
>> Okay.
>> It's not arising spontaneously, which is why it's not to me it's not a Darwinian evolution.
>> Right. It's non-random mutation, therefore, okay, that makes sense.
>> Yes.
>> Um interesting, but but yes, we could see yeah, if if the the cell division could be prolonged, then we might have enough time to see because you're you're I think you said it was about around five cycles before it becomes untenable.
So, what if that could be extended to several hundred, then then we start to see uh random mutation and and what that does.
>> That's what I'm hoping for. Yes, and I think that's why that that list of what it needs to be alive is is kind of all of it is tied to each other. None of those things by itself are going to do it, but I think all of it arising together will give this emergent property of of increased complexity.
>> Mhm. Mhm.
What what would you say it would might be the absolute next step in going from Spud cell to something even closer to a fully synthetic living cell?
>> Make cytoskeleton, make ribosomes, and make better metabolism.
>> Mhm.
>> Um then add genome construction tool.
Right now, the genome is and I I'm allowed to say that cuz I made it. The genome's messy as heck. It's um it's a a set of multiple plasmids and there are practical research considerations why it's like that cuz we had to iterate on many of those genes. It's easier to do it if they're smaller plasmids.
Eventually, I do want it switch to a single mega plasmid like a bacterial chromosome style.
>> Mhm. And that's that's more of a technical than conceptual research step, but I think that's going to help a lot in division fidelity.
>> Right. If you're on if you just have one circular chromosome and then you get two, what each gets one, that seems a lot simpler than how many is it seven plasmids or how many >> Depends on which version that's seven to nine is >> Seven to nine.
>> is is what we use.
>> Yeah, seems tricky seems like you'd need some more sophisticated machinery. Yeah, yeah, condensing into one could reduce the complexity of the machinery you'd need to install to segregate those.
>> the experimental complexity because one giant plasmid is incredibly difficult to make. It's >> Right.
>> There are ways to make it but they're pain in the lower back which is why we've been using smaller plasmids but it's on the on the to-do list.
>> Okay. Okay, that yeah, that makes sense as kind of the next step here.
>> [snorts] >> So I I have a question which you you may or may not be able to answer.
My viewers know that I've done a lot of work combating anti-science propaganda in the field of origin of life research.
And so among the propaganda peddlers there's a lot of conflation between origin of life research and synthetic biology where obviously there is some overlap there.
But work such as yours is not directly pertaining to right your your quest to build cell from scratch is not necessarily specifically elucidating the process by which life originally arose.
But um Can you speak to what you might see as potential overlap? Is there any kind of like functional simplicity to spud cell that you think does have some application to features of like early protocells? Is this completely exclusively bioengineering or or or do you think your work has application to origin of life?
>> It definitely has conceptual applications with origins. The spud cell itself is not an origins model because it uses modern enzymes. But it's a platform that allows us two things. One is you can imagine doing ancestral protein reconstitution and using the spud cell platform to for example test how an ancestral ribosome or some other ancestral pathway could work.
So, rebuild some of that earliest cell.
And it also is on a more kind of a conceptual level, it shows you how molecule behavior can lead to emergence of life-like properties. So, >> Mhm. Mhm.
>> even though it doesn't directly describe the identity of the molecules that were present 4 billion years ago on Earth, it does help us kind of a conceptualize that process, figure out, okay, we need this pathway, that pathway together in that order, in that kind of a type of interactions to reconstitute how early life could behave.
>> Mhm. So, we can we can elucidate some of the emergent properties that can more broadly apply to to to different sets of molecules, including the ones that would have been present in in the first protocell.
>> Yes, that's correct. Even though I want to make it very clear that the Spud cell itself is not an origins model because it is a modern >> Yeah, I I mean, it has a DNA genome already that disqualifies it, but but yeah, it is yeah, it it is quite interesting to see the propaganda conflating synthetic biology with origin of life research and then having to kind of go in and and and and separate the two without without denying the conceptual application, right? There is something here. We have very very minimalistic sets of of molecules and we're seeing how life can arise from that. So, obviously that has some appli- cation, but just with a totally different set of molecules.
Yeah.
Um what would you see I I think that with synthetic biology in general, there are a lot of applications. So, I'd love to hear you talk more broadly about the applications of of synthetic biology, but also very specifically in terms of Spud cell, what kind of practical applications there could be beyond simply the the the you know, the this incredible task of synthesizing a cell.
>> Short term, it can be a platform to create biologically active molecules, mostly drugs, um high value added molecules that use non-canonical building blocks.
Um it runs on a translation system called pure, which allows for incorporation of many non-canonical amino acids into proteins, for example.
>> Mhm.
>> And there's many drugs and drug candidates that use those building blocks and they're right now difficult to synthesize because you have to make them chemically. So, that's kind of a short-term, in the few years time scale, um when we start seeing first applications of this technology.
Long-term, the our 2050 goal and beyond is bioeconomy. It's being able to move all the atoms that our economy needs with biology instead of dead biology, the petrochemicals.
>> Mhm.
I've done a little bit of work elucidating how we use uh synthetically or sorry, genetically modified microorganisms to kind of install suites of enzymes to then build So, what what would be the difference here with a bottom-up cell, like really on the on the molecular level? How how would it How would a spud cell-like um system up approach synthesis differently from like E. coli or something like that?
>> It allows you to go farther. Um for applications that are not toxic to cells, so like products that are not toxic or >> Oh, okay.
>> or chemical transitions that biology already knows how to do, E. coli is your first choice because it grows the fastest, it's the cheapest, we know how to work with it.
>> Mhm.
>> But for there are many products that we cannot access right now with with live cell biosynthesis because they're either toxic or there just are no enzymes in biology to make those products.
>> Okay.
>> And that's These are the two things that we can do in a bottom-up cell is one is we can develop new enzymes that use novel non-canonical chemistries, novel building blocks, and we can make products that would be toxic to natural metabolism because we can design the metabolism around that toxicity.
>> Mhm. Mhm. Mhm. So, you won't be constrained by what life knows how to do, and you won't be constrained by chemistry that doesn't kill a living cell.
>> That's correct. That's These are These are the things that I need I think are absolutely needed to realize bioeconomy because we won't be able to make everything with natural cells.
>> Yes. Yes, that's true. And And yeah, so so obviously just kind of the greening of of of industry, right? If we're able to make biofuels and obviously drugs, but all kind like are there any materials that we're targeting that aren't so hyped up in the news? Is there Or is it pretty much just just those couple?
>> Um the high-volume things like certain kinds of polymers, plastics, these are the the things that are in the news. The the one thing that sort of flies under the radar is fertilizers. Um right now we use fertilizers that use a petrochemically derived process to synthesize them. And those fertilizers are absolutely necessary for the crop yields we need to feed the current population of of the world. And that's Many people don't know that that's why there is a direct link between food prices and fuel prices and oil prices. It's not just because fuel prices, it's also because fertilizer prices. Those directly are tied to oil because that's a petrochemical process.
And those are compounds that are and reactions that are toxic to natural cells, which is why we don't have a biosynthesis pathway for them. So, to to this biologically accessible nitrogen cuz that's basically what a fertilizer is, um, into at the scale that we need to fertilize the fields to get the crop yield, right now we need oil, and that's one of the things that is not very media, like it's not it's not people don't talk about it much, but that's a huge thing when we think about carbon neutral economy.
>> Understood. Okay. Yeah, that's the really is the most, uh, incredible science that which really pushes the boundaries of of what we can know and understand about the the natural world while also having this incredible economic application. It's kind of the best of both worlds, which you you don't you don't always see, uh, in science.
Um, yeah, those are all the questions I had. I, you know, uh, feel free to take a moment if there's any anything you want to direct the viewers to. I know that, um, it's kind of a tumultuous time politically with the future of, uh, the funding of of science unknown. I'm not sure exactly where your type of research would fall on the chopping block with what's going on with the OMB and just generally with Trump with the Trump administration, but, um, anything else that that you'd like to share with the viewers?
>> Um, that funding is definitely a concern of ours and also the fact that this has to be a technology that needs to belong to an open source global community, and that's why those two reasons, the uncertainty of federal funding and the need to keep the platform in the public domain, is why we started a non-profit organization called the Biotic that is a funding organization that's going to support this work and also steward the open sourceness of it. Um, I if we're right that this technology really will be the basics of the next economical revolution, the bioeconomy, it has to belong to an open source international global community, not a single country, not a not a company single company.
>> Mhm.
>> And that's what Biotic is intended to do. So, to me, the research news is just like step one. It's cool, we've done it, but now we have to move on and actually make it useful. And Biotic is what is going to enable making it useful.
>> That's fantastic. Very noble and uh yeah, I'll be sure to uh to uh provide the appropriate links in the description. Uh well >> know. I Actually, I want to pull on that thread. I don't know if it's noble. It's more of a self-preservation instinct.
>> Sure.
>> And I think we're not going to have a planet to leave to our kids if we don't do it right now.
>> I suppose that's a pretty good point.
It's actually >> [laughter] >> as much more of of self-preservation than than anything else. Where Where does it become the point where where we fight back for our our own survival? Um Yes, well, my viewers know that I've been talking about that quite a bit.
>> [laughter] >> Um yeah, that that's all the questions I had. Thanks so much for joining us.
>> Thanks for having me.
>> Pretty fascinating, no? While we're not yet in a place where we can construct a fully functional living cell that can reliably sustain itself and replicate indefinitely without any assistance, Spud cell is undoubtedly a huge step in that direction. As to the precise applications synthetic biology will succeed in offering and the degree to which this science overlaps with origin of life research remains to be seen.
But, I will be sure to update you with any other breakthroughs present themselves. As always, thanks for watching. I'll see you next time.
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