Ep 94: Synthesizing life on the planet (with John Glass)
What’s the smallest number of genes that cells need to grow and reproduce? Is it possible to synthesize minimal genomes and insert them into cells? What do minimal genomes teach us about life?
In this episode, we talk to John Glass, leader of the Synthetic Biology Group at the J. Craig Venter Institute. Over the past decade, Glass and colleagues developed techniques for manipulating and synthesizing entire bacterial genomes. Starting with Mycoplasma bacteria, which have very small genomes, they determined the minimal number of genes (473!) required to support life. They experimentally confirmed this number by synthesizing genomes from scratch, containing just the essential genes, and putting them into other bacteria whose genomes were removed. Cells in this lineage, called JCVI-syn3.0, grow and divide approximately like wildtype cells do.
We talk with John about how they pulled it off and what this minimal genome tells us about life more generally. We also chat about the functions of essential genes and what so-called non-essential genes may do in the wild. Finally, we touch on what if anything minimal genomes say about the origin of life and on the group’s ongoing efforts to synthesize entire cells – not just genomes! – from scratch.
Cover photo: Keating Shahmehri
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SPEAKERS
Art Woods, John Glass, Marty Martin
MM: What is a model in biology?
AW: Or even better question, what is a model at all?
MM: OK, here’s an all-purpose definition…
AW: go for it…
MM: A model is any kind of simplified representation of a more complex real thing.
AW: Reasonable…but let’s think through what that means. Some models are physical. An example is the model airplanes I built as a kid, all the time huffing plastic glue, alas [MM: explains a lot!].. Those plastic planes were small and extremely simplified, but I loved them because they still evoked the real thing.
MM: Most models are more abstract – they use ideas or structures in one medium or space to compactly represent objects or processes in the real world. For example, an architect’s blueprints are a 2D drawing that represents a 3D structure in the real world..
AW: Even more abstract are statistical and mathematical models, which scientists often use to describe the relationships among parts of the systems they study.
MM: For example, over time, well-fed baby birds grow, and if we weighed a set of birds daily for a few weeks, we could then fit a line, or maybe a curve, to the relationship between weight and time.
AW: That line then becomes a model of bird growth - all of that feeding and pooping and cell division and growth collapsed into just two parameters – a slope and an intercept! Almost magic..
MM: Which leads us to a deep philosophical question – what’s the relationship between developing good models and understanding the biology that one is modeling in the first place?
AW: Weirdly, understanding doesn’t mean making models that describe every last aspect of a data set. Think about this in terms of the number of terms in a linear statistical model. The simplest description of a data set using that kind of model is just one term – the mean.
MM: The next step up in complexity is to describe the data in terms of a line. This kind of model requires two terms, a slope and an intercept.
AW: And so on…I could use three terms, which would introduce a simple curve, or four terms, which would give a more complicated curve. AND…I could keep going so that I used so many terms that the squiggly line I called ‘my model’ went through every point in my data set. Perfect, right??
MM: Alas, no. In biology, as in other quantitative sciences, we put a premium on finding the minimum sufficient model. In other words, we value simple over complex, as long as the simple models capture enough of what we care about. And whether enough is enough is virtually always a judgment call…
AW: So…spelling this out, I feel like I understand more about important relationships in biology from a simple model that doesn’t account for everything going on in the data than I would from a complex model that got it all!
MM: This favor-the-simple philosophical stance underlies the approach to biology that we discuss today with Dr. John Glass, a professor and leader of the Synthetic Biology Group at the J Craig Venter Institute.
AW: Glass and his team have spent a good chunk of the past decade trying to determine the minimal set of genes required by cells.
MM: Their idea is that by identifying the minimum set of genes in a cell, we will kick open the door to understanding the core set of structures and processes that operate in all living things. Note that there is a built-in – and perhaps objectionable! – kind of genetic determinism here – which is that a cell’s minimal genome will map in a comprehensible way onto the minimal necessary cell physiology.
AW: Perhaps reasonable for the core biocellular functions in a minimal cell.
MM: A few years ago, Glass and colleagues achieved their goal using cutting-edge molecular biology to manipulate the genomes of Mycoplasma bacteria, which live in the genitourinary tracts of humans and other animals and were known already to have very small genomes.
AW: We delve into Mycoplasma details in the show, but briefly here… the researchers used transposons to systematically knock out every one of the 900+ genes in the Mycoplasma genome. Then, they synthesized new genomes from scratch that contained just the genes that they thought were required, then popped those synthesized genomes into living cells.
MM: It worked, and they created a cell lineage called jcvi-syn3.0 that contains just 473 genes, which many labs around the world are now working on.
AW: We talk with John about how they pulled it off and, more importantly, what it means for biology. For example, we talk about how truly universal this gene set is by asking him if they would have arrived at the same core set if they had started with another distantly-related bacterium.
MM: We also chat about kinds of things essential genes do…the things that make them, well, essential!. John tells us about one critical but small group of genes involved in cell division.
AW: We also press John on origin-of-life questions…if the minimal required set is 470+ genes, then how did early life ever arrive at that set?
MM: We end by talking about his Build-a-Cell Consortium, which aims to build entire cells from scratch using off-the-shelf chemicals. That group hasn’t succeeded yet, they believe they’ll get there in the not-too-distant future.
AW: Altogether, the chat raises deep questions about how understanding is linked to minimal models. Stick around for more…
MM: I’m Marty Martin
AW: and I’m Art Woods
MM…And this is Big Biology
[Music break]
Art Woods 00:00
John Glass, Welcome to Big Biology, it's a thrill to have you on the show. We are really excited to talk to you about some of these epic papers that you've been publishing about synthesizing genomes, figuring out minimal gene sets, how to build minimal cells, building the other parts of cells besides genomes. Maybe let's get into that just by talking about the up first of all, just the motivation behind this idea of building a minimal cell. So what is a minimal cell? And, and why would you want to build one?
John Glass 00:33
Physicists and chemists, for the last 200 years have used the hydrogen atom as a model to understand the fundamental principles of matter. And the reason that they have to use the hydrogen atom is the technology to make these kinds of technical breakthroughs about the structure of matter. With things like uranium and carbon, they don't really work. So the hydrogen atom has been this model system. And the notion was, and it has since been thoroughly proven that what is true for hydrogen atoms is true for larger atoms. So similarly, in the 1930s, Max Delbrück, founded this thing called the Phage School at Cold Spring Harbor, and one of their ideas what was that if science could make a minimal living cell, it would be possible to understand maybe to cut through some of the incredible complexity of biology, if you can have just this absolutely minimal chassis organism. Now the technology in the 30's Certainly didn't exist. And people had been writing about this whole lot. For the last 50 years, before we actually created a minimal cell, there were still 1000s of papers about this idea of a minimal cell. And the idea is E. coli has 4000 genes. And that's the organism that beyond my minimal cell, I would argue, is probably the best understood living cell on the planet. But there are much much simpler bacteria in nature. And so the idea that we would use the simpler organisms and the simplest of these are a group of organisms called mycoplasmas. These are organisms that are not like primordial bacteria. They are like conventional bacteria like Streptococcus pneumoniae or bacillus or even E. coli that became obligate parasites of eukaryotes, higher animals, humans, plants, fish, etc. And when they became this obligate parasite, it allowed them to throw away really most of their genome because they lived in such incredibly stable environments. And so mycoplasmas started out with cell walls and a lot of genetic machinery that they were able to throw off. The simplest organism that we know of on the planet now that occurs naturally is an organism called Mycoplasma genitalium. I joke that it's a marine organism because it was originally found in a British Marine in 1980 as a urogenital pathogen.
Marty Martin 03:14
Not a typical kind of marine but okay.
John Glass 03:16
Anyway, genitalium has the naturally occurring organism has about 500/485 genes, protein coding genes, as opposed to 4000 for E. Coli. And it's an extremely simple organism. It makes nothing except more Mycoplasma genitalium. It can't make fatty acids, it can't make nucleic acids. It can't make amino acids. It has to import all of those from its environment. Now, when we started this process, Craig Venter said, Okay, I want a minimal cell I want to this was back in the early 1990s or late 1980s. I want to understand life, I want to really understand life. And I believe that we need to make a minimal cell. And I realized that the mycoplasmas are the logical platform for this, but the technology to whittle away non essential genes for mycoplasma that are necessary for life in a human urogenital tract, but not in the lab, that technology doesn't exist. So instead, I'm going to be bold Craig Venter Maverick style, we're going to set this project up and we are going to synthesize an organism, we're going to design and build a minimal genome. And somehow we'll we'll boot it up and make a cell and we will then use that to understand the first principles of cellular life. That's what's driven our work.
Marty Martin 04:45
So I want to get into the the scope of the rest of the talk is going to be talking about the methodology of your first efforts to simplify and then subsequently start de novo. But I want to dwell on this simple, a little bit more, like two questions, but I I'll ask them in sequence the first one, it seems like you're saying simple is the fewest genes? Is there any other dimension of simplicity that is also captured in your thinking? Or is there any other way around that?
John Glass 05:14
I would argue that for any organism, any organism that we can grow in the lab, I would be able to whittle away or redesign it so that we got rid of only the genes necessary for growth in a certain environment. And that that is the model of simplicity, it is the ideas. Ultimately, we are getting down to a minimum number of genes, but we're just taking away any machinery that is not necessary for growth in a given situation. And so if I were to start with a sar 11 bacterium, one of the most common organisms on Earth and responsible for most of our oxygen, you know, if I were to minimize that, it would be a not remarkably different gene set, but it would be a different gene set. And what we are pleased to find out what we had hypothesized and we have found out is that as we approach the minimal gene set in mycoplasma, this seems to be not exactly but almost all of the genes that are essential for life and mycoplasma are essential for life and everything else.
Marty Martin 06:29
And when you're saying life, I mean, this is this gets really philosophical very quickly, but life, which is sort of persisting but not growing, not replicating?
John Glass 06:37
No, life, life growing, divided, making new cells, everything.
Art Woods 06:43
I just want to restate here what I think you're doing. And maybe you said this, but just make sure listeners are coming along. So you're starting with Mycoplasma genitalium?
John Glass 06:52
It is not what we started with. We started with that. But we had problems with it, and genitalium though it is the smallest organism, it has some disadvantages. So it is a human pathogen, although you would have to spill it in your lap, it only is a urogenital pathogen, but it takes six weeks to make a colony and the colonies you have to have a microscope to see them. So a brilliant postdoc that I hired in 2004, Carol Lartigue, to work on the process of installing an isolated bacterial genome into a suitable recipient cells so that the newly installed genome would commandeer the genetic machinery of this recipient cell and would produce new cells that only had the donated genome. So let us take a bacterial genome and boot it up by transplanting it into a new cell. And we put an antibiotic resistance marker in the donated genome. So initially, you have a cell that has two genomes, and one with an antibiotic resistance marker one without we return it to normal growth conditions, but with this antibiotic in it, and any cell that divides and just has the wild type genome will die and any cell with a donated genome, our designed genome will live we call that genome transplantation. That's one of the essential technologies we developed. Now we were struggling to do this with genitalium. But Carol did her PhD on a different species of mycoplasma, it's a larger genome, and it is a goat pathogen called mycoplasma mycoides, and she developed transplantation for Mycoplasma mycoides. And so our whole effort switched to that bacterium, which is much, much easier to work with, it makes a colony in two days, and you can see it with your eyes.
Art Woods 08:51
I see so nearly as small and simple, but much easier to use in the lab and much faster growing great. So the overall sort of philosophy here is to start with something that has a very small set of genes, and then to go in and try to even whittle those away further. So you're systematically disrupting or deleting each of the genes in turn, and then finding out what's the minimal leftover number of cells that can still give a viable lineage is that a decent characterization?
John Glass 09:19
Right, except if we whittled it away one gene at a time, we'd still be doing it. So what we did is we used a technique that was developed as part of this effort called transposon bombardment, where we take a little piece of DNA that encodes its own enzyme that lets it insert itself randomly into other DNA, we would put that into the mycoplasma cells, and it installs itself in the genome. And if it installs itself in an essential gene, that cell dies, and if it installs itself in a non essential gene that cell lives and if it installs itself in a quasi essential gene. That means it's a gene whose protein is necessary for rapid growth, but not necessary for life. From that information, we figured out these are the genes that are essential for life and rapid growth. And based on that we synthesized a complete genome, starting from basically from four bottles of chemicals: Adenine, Guanine, Cytosine, Thymine. And so we made a wild type complete copy of the Mycoplasma mycoides genome. And we showed that we could make a cell with a chemically synthesized genome.
Art Woods 10:40
So you synthesize it exactly as it is in the wild type?
John Glass 10:44
Well, exactly, we took out some genes that we knew were related to pathogenesis. And we made a four base pair code that would let us do all of the ASCII characters. So we we watermark the genome. So you could always know that this was our organism as opposed to the natural organism. And we put in some, you know, erudite quotes from like James Joyce and Robert Oppenheimer and Charles Darwin, that kind of thing. Everybody who worked on the project, their name is in it.
Marty Martin 11:15
Yeah. That's, that's really cool. That's much, much better than getting an acknowledgement in a manuscript, right?
John Glass 11:21
Yes, it is. So this cell is called JCVI-syn1.0, we published on in 2010. And the world described it as a synthetic cell, although we don't say that we say it is a cell with a chemically synthesized genome, as opposed to building a cell from nonliving parts, you know, we install our synthetic genome in a living cell, and it commandeers that cell to make new cells. So first, we made the wild type organism because we wanted to make sure our methods work, and we knew that the wild type organism would work, then it took us six years, in part because we lost funding to figure out what the minimal gene set was, and we got that in 2016.
Art Woods 12:07
So tell us about that minimal set. So how many genes does that set consists of?
John Glass 12:13
We took an organism that was 1.01 7 million base pairs, mycoplasma, mycoides, and it encoded a little over 900 genes. And we whittled this down to about 480 some genes. This is the minimal gene set, it took us a long time to get there. But we produced this minimal cell that divides as opposed to the wild type organism divides in an hour, this cell divides in two hours, it still makes big, beautiful colonies on an agar plate, it looks and behaves like mycoplasma mycoides is in the sense of growing in the lab. But we now know that it would be completely incapable of growing outside of the lab. And so in 2016, our attention turned from developing methods to build the cell. Because we had spent, I guess, you could almost say we had spent 20 years developing the methods it took to build the cell. And that included developing whole genome sequencing, a lot of the foundational methods of modern molecular synthetic biology have come from this effort from from the J. Craig Venter Institute. So we have this cell. And now our focus has changed for the last six years to as opposed to developing methods. It is now more about analyzing how the cell works in every facet that you can imagine. And I had assumed that when we we would crossed this threshold, we've got ourselves, we will now do this. What I wasn't expecting is a couple of days after we announced this sell to the world with a paper in Science, people started writing and calling us saying they wanted to collaborate. They wanted to work with us to use this cell to investigate biology. I mean, it was fast. Every area of biology that you can imagine you might use one cell to work on, people are figuring this stuff out. And you're going to see just I think an avalanche of publications starting to show up over the next few years as we get closer. There are both wet sciences biologist who go in and grow the cells in their labs. And then there are also purely computational biologists who if you could hand them a plate of bacteria, they wouldn't have a clue what it was. But they have been able to make these remarkably detailed models to let you computationally model a cell. And the models are increasingly great at replicating the responses of the bacterium showing how it grows. Really, we're getting to the point where we may be able to model practically every atom in the cell through the cell lifecycle.
Marty Martin 15:02
Well, John, this is this is really neat. I can't help but hear everything you're saying through through my evolutionary biologist filter. I promised you another question that I didn't get to. We'll table that. We'll do that one later. Anyway, let's talk a little bit more about the essential genes. Just a minute ago, you talked about the sort of mystery genes that you're still or maybe in this consortium working out the functions of those things. We've talked to Nick Lane, we've talked to Sarah Walker, we talked to many people in the past on the show about the origins of life. And clearly your motivation in doing a lot of this work. Maybe not exclusively, clearly, not exclusively, but partially is about that. How do we understand these non essential genes? How do we understand these partially essential genes, these things that we don't really know about the fact that you don't instantaneously start with hundreds at the origins of life? How are you thinking about connecting all of those dots? How do we get from no life to life, or an understanding of that via the synthetic path that you've been taking?
John Glass 15:59
Okay, we'll do this in two parts. So first, I'm going to talk about genes of unknown function, basically, our bacterium in codes 400, about 450, protein coding genes. And if you take each one of those genes, and do a technique called blast, which means you are comparing the amino acid sequence, the order of amino acids that make up this protein, if you compare that to E. coli, yes or no is there are a equivalent gene in E. coli, most of the minimal cell genes are present, like you know, 90 plus percent are present in all bacteria, and about 80% are present in yeast, arabidopsis, the plant, you and me. So, you know, it is just huge conservation. This is the kernel of life. So that tells you that these things are everywhere.
Marty Martin 16:55
One thing before we go on that I'm a little bit confused about. And maybe this is about the mechanics of how you produce the synthetic version. Isn't that to be expected? Because at some point in the past, everybody shares an ancestor. So how do you know the difference between evolutionary legacy versus minimal for life? I mean, are you talking about life on Earth, or life in general?
John Glass 17:14
Well, so the common feature of life as we know it on Earth is the ribosomes. And after that, everything gets a little dicey. And that bacteria evolves so fast, they have found other ways to do things. But what we say is that the essential set of genes that our organism evolved from the first life like we know it on Earth, these are the things that are still largely conserved and have not diverged so far that they are unrecognizably different in the sense that you might have a protein in humans that does the same thing. And it's a protein in my organism, but that those proteins no longer look similar to each other. For the most part, we can still see that similarity, even after 3 billion years of evolution. So 450 genes, and we say that they are closer to what's common in bacteria, but it's the same in all of life. And we divided those genes into five classes, about half of them are what we call equivalogs in that we are almost absolutely certain what they do, you know, based on wet science, biology, not necessarily done in my organism, but of genes that look very similar in other organisms, or done in my organism. We know what these genes do. Another third of the genes, or maybe six are probable or putative, we are pretty sure what they do, but not absolutely certain, because it would take more experimentation to get that. And those sorts of genes are slowly being filtered into the best understood. But what we were unprepared for is that a third of the genes 149 out of 450, are either completely unknown, we have no idea what they do, or I know they are like, it probably encodes a hydrolase. But the actual function of that hydrolase I have no clue.
Art Woods 19:14
And that was one of the more amazing things that I read in your paper. And just to think that in this age of molecular biology, that that fraction of this core set still has unknown function. It's just kind of mind blowing.
John Glass 19:25
Yeah. And so it also begs the possibility that after what 70 years of thinking about genes and proteins and what things do and all the advances of modern biology, there could be genes that are conserved from mycoplasma to man, that are essential for life. And we are completely oblivious to there may be tasks that living cells have to do, and we don't even know they exist.
Art Woods 19:58
Are there labs all over the world that are going after the functions of these genes, and are they making progress such that you know, in 10 or 20 years, we're gonna know the answer in about all of them? Or is it a much longer problem than that?
John Glass 20:09
I hope it's not a much longer problem. So in 2016, 149 genes, as of today, 85. That's good progress. Now, most of that progress has been with the generics, the things where now I know it's a hydrolase that does this. But some have been with the unknowns and new technologies, Google developed a protein structure analysis software called Alpha fold, which is really changing our ability to look at a protein sequence and understand how it is likely to fold in its natural state. And then when you look at the structure of a protein, you can say, Oh, well, this has evolved greatly from the original primordial protein, but they look almost exactly the same in terms of structure. And that gives you a solid clue that this protein probably does this function. And then it's something that we say, Okay, well, this mycoplasma, protein is probably the same as this hydrolase in humans and plants and stuff. And so then it's a matter that you take that gene and do biochemical analyses to confirm that. And so there are people doing that, ready for part two?
Art Woods 21:34
Yeah, let's do part two,
John Glass 21:35
The original organism that we made JCVI-syn 3.0, it is an incredibly wimpy organism, just if you pipette it with a lab instrument, you're going to destroy most of the cells. And when we did electron microscopy, those cells look really bizarre, as opposed to uniform 400 nanometer diameter spheres, like the wild type organisms, these things had blebs. And they, they would sometimes look like strings of spaghetti, it was just very weird. Now one of my colleagues, in the process of minimization, he made an organism that had 19 genes more than the minimal cell. And we happen to find out just by looking in the microscope, this organism look just like wild type. So it has 19 genes that are not essential for life, but are essential for a cell that divides like basically all the cells on the planet do. So ourselves, you meet almost everything on Earth, almost I mean, like, there are half a dozen known strains of bacteria, all of them simple organisms, like mycoplasmas looks like they've thrown away the genes for normal cell division. And by normal cell division, I mean that as the cell grows, it forms a septum, a protein and lipids septum between the two daughter cells, and puts a chromosome on each side and the cells divide. We think that 3.0 doesn't do that. What we think 3.0 does, is the cell gets so large that the membrane physics forces the cell to spontaneously divide on its own, the forces of membrane curvature, will compel the cell to split apart, but three A, which has the 19 additional genes doesn't. So now, okay, let's look at those 19 genes. And the first thing we noticed is there were two proteins that we knew were involved in cell division FTSZ, which is forms of the cell division ring, and another protein called Sep, F. So those are among those 19 genes. And we think, okay, it makes perfect sense, let's put those genes back in. And we bet it's going to divide like a normal cell, it didn't. So it turns out of the 19 genes, it takes seven to make a cell divide like a normal cell does on Earth. And five of those genes, we don't know what they do. Well, we got some ideas now, but we didn't at the time. And what this says is that it looks like inadvertently, we have recapitulated what cell division looked like before the invention of modern cell division. And those seven genes all have similar equivalent genes in everything. Now, they're saying they are sufficient for modern cell division, but they are essential for modern cell division.
Marty Martin 24:28
Another thing that jumped out in reading and thinking about the work that you've been doing, I don't remember exactly how you said it in the papers. But is it the case that it doesn't really matter the order of the genes, you know, when you stick that into you make the synthetic life does that matter? Because like as an evolutionary biologist, and we've done this on the show, too, we think a lot about epistasis. I mean, my lab works a lot on the role of DNA methylation and gene expression. So the sort of architecture being somewhat arbitrary was really surprising. Did I misread that or what do we need to know there?
John Glass 25:01
You read it entirely correctly. So we said, we're going to reorder the genes in the genome. So it'd be like an engineer did it, we're going to put all of the genes involved in transport in this section, and glycolysis, here, and so on. When we originally built the genome, we built it in eight overlapping pieces. And we took one segment of that 1/8 of the genome. So it originally had about 100 genes. But the final, the minimized cell had 43, and we reordered that 43. And we took transcriptional. So if there were operons, meaning a pair of jeans that were transcribed at the same time, they were adjacent to each other, but they did two different functions, we would take an unused set of regulatory sequences, the genetic information immediately upstream of the gene that makes the RNA polymerase transcribe the gene, and the ribosomes recognize it and make the protein. So we know every gene has its own promoters, regulatory sequences, we built that and we substituted that 1/8 of the genome into a cell that was seven eighths not done that way. And it grew great. And this was in our 2016 paper. Now building on that success, we did the other seven, right, just to see what happened, only two of them grew. Now, I think the reason is, at the time, we weren't necessarily thoughtful enough about the regulatory sequences we put upstream of genes in order to govern their expression. And if we were to do this, again, it might work perfectly, but so many experiments, so little time, and that is a million, you know, that's a million dollar plus experiment. So gene order, I don't think it matters that much, except for a few genes that in every organism, you look at DNA, a chromosome, replication, initiation protein, is always adjacent to the origin of replication in every bacteria. So we know that that protein, pretty much has to be next to the chromosome origin of replication. And there are a few other examples like that, but that might comprise three or 4% of the genome.
Art Woods 27:24
Well, John, hey, I think we're getting to the point of needing to, you know, wrap but I want to ask one other, I guess, semi major question before we do. And that's something you alluded to, in passing about this sort of distinction between, you know, synthesizing a genome and installing it into a cell and then having it take over that cell versus synthesizing all of the rest of the components of the cell from scratch and putting those together into something that actually works. And as I understand it, you're part of this consortium, to build a cell consortium that's trying to do exactly that. Right. So maybe just tell us where what's the status of that? And is there any promise of success anytime soon?
John Glass 28:05
I will say that there is no promise of success. But I think there is a great likelihood of success. And build a cell is an organization, mostly a US organization. I think we have 70 or 80 different members, but it's academic, and there's some government labs. And the goal of this organization is to build synthetic cells. So some synthetic cells that people build are incapable of replication, but that you might make a vesicle of some sort that does some of the functions of cells in terms of protein synthesis, or product synthesis. But we want to, my particular team, which includes Kate Atamala, from the University of Minnesota, so Kate and I, and Wilhelm Huck from Radboud University in the Netherlands, we are trying to build a mycoplasma cell by making a synthetic lipid envelope from chemicals in bottles. So cholesterol, a carbon 18 fatty acid, a carbon 16 fatty acid, so we know that those three lipids are sufficient to make a functioning mycoplasma cell envelope, and then we will have a genome from a living cell or a synthetic genome or I'll get a genome and I want to put that inside this envelope. And I also want to take a cytoplasmic extract, meaning the liquid, the juice, the proteins, the everything from inside a cell, one living cell and take it out so it's dead as a doornail is just chemicals, ribosomes, etc. Put that all of those into the envelope. And our hope is that if we do this in just the right way, it will come alive. This is still taking parts from a living cell. In theory, the technology exists to put together RNA and proteins and make synthetic ribosomes, but I need a lot of ribosomes. And so, you know, eventually, we may make a cell where we go from a cytoplasmic, extract, a lipid envelope and a genome and make a cell that lives and survives. And that will be called a synthetic cell. And then later people may decide that that's not called a synthetic cell, because you didn't make synthetic ribosomes.
Art Woods 30:30
You cheated. You took some of the parts from somewhere else.
John Glass 30:33
And in 2010, some said we made a synthetic cell. But like now, that's that is terminology that we have.
Art Woods 30:45
Yeah, let me ask one, one follow up question here, too, which is like, can you imagine a situation where you were able to synthesize all of the parts perfectly, and you could arrange them and put them all in the right place? And yet, is that enough? In other words, is it enough to arrange all the parts? Or does there have to be some kickstart moment? You know, like the Frankenstein zap that sort of gets it all going? Even if everything is like, right in the right place?
John Glass 31:12
Yes. I mean, one of the characteristics, if you take a cell, there is a disequilibrium between what goes on inside the cell and what goes on outside the cell. There are chemical gradients, there are electrical gradients, all of that, I think. So just having, replicating, what goes on inside the cell. If you can't also precisely possibly replicate this disequilibrium. What you may have is a thing that looks like a living cell, but is dead. And I think that's a real possibility. Now, Kate, and I started this project four years ago, with National Science Foundation funding, and we had been whittling away at technical problems that we weren't expecting. So you know, so far, we have now solved three huge problems, none of which we anticipated at all. We didn't we turns out from mycoplasma as you couldn't make a cell free extract, or it took us three years to figure out how often. I actually, Kate and I published a paper this summer, where we reported, which is almost unheard of in science, we reported only negative results. You know, this, this is what we were trying to do. This is what we found, we were not able to do what we wanted to do. And if any others have you tried to go down that rabbit hole, this could say, don't go there, this is just not done in science. Now, I'm not going to retract the paper. But a Dutch graduate student trying to do something else figured out a strange way of actually solving this problem. But that was just a few weeks ago. But now we have faith that we can actually get to the experiment that we thought we would be doing three years ago. And I won't say that this is going to work. But this is our effort at this. There is a large group of scientists in the Netherlands who are trying to do the same sort of thing. They're trying to do it basically making a synthetic E. coli, I would think, and there are other groups all over the world who are pursuing this problem. Because if we can design and build cells, cells can be designed and built, we believe that will enable us to solve problems that biology as we know, of today can't, not necessarily that to be released into the environment. But things that can be put into reactors that will let us produce chemicals that just can't be done in nature for a variety of reasons. Because the organ, you might be making a cell that could never survive in nature, but can do something extraordinary, that may solve one or another kind of human problems. And I think that this is really important work. And I think it's going to become a major aspect of biotechnology over the next 20 years. We are a couple of experiments away from making the first synthetic cells. And I think someone will figure this out. I don't think there's anything magical about being alive. It's just figuring out the right conditions.
Marty Martin 34:23
Wow. So that's a very strong and inspiring statement to to end on. That's wonderful. We didn't plant that. That was completely organic. Thank you, John. Now, John, really, thank you. This has been a fantastic conversation. We really appreciate your time. Before we go, we want to give you the chance to say anything you didn't get to say that we didn't give you a prompt for Is there anything else that you wanted to make sure we touch before we wrap.
John Glass 34:45
We are in a remarkable time, where the technologies that my group and others have developed over the last 20-30 years, or more importantly, over the last 10 years, we're going to see this astonishing jump in what biology can do, and I think this is a huge deal for society. If you look at what's going on in Sharm el Sheikh now, with the Climate Change World Summit, it's pretty clear that humans are not going to be enticed into the kind of conservation that is needed to solve these problems. And it may be up to chemists and physicists and biologists to come up with technical solutions that will save what we sort of know of his life on Earth. And I think the scientific community is up to this, and I'm happy to be part of it.
Marty Martin 35:37
Excellent. Well, good. Thank you very much. Yeah.
Art Woods 35:39
Thanks so much, John. Yeah, really fun to talk it over.
[Music Break]
Outro:
MM: Thanks for listening to this episode! If you like what you hear, let us know via Twitter, Facebook, Instagram, or leave a review wherever you get your podcasts. And if you don’t, well we’d love to know that too. All feedback is good feedback!
CG: Thanks to Steve Lane, who manages the website, and Ruth Demree and Brad van Paridon for producing the episode.
MM: Thanks also to interns Dayna De La Cruz, Daniella Garcia Almeida, Kailey McCain, and Kyle Smith for helping produce this episode. Keating Shahmehri produces our awesome cover art.
CG: Thanks to the College of Public Health at the University of South Florida, the College of Humanities and Sciences at the University of Montana, and the National Science Foundation for support.
MM: Music on the episode is from Podington Bear and Tieren Costello.