- Welcome, everyone, to Wednesday Nite @ the Lab.  I'm Tom Zinnen. I work here at the UW-Madison Biotechnology Center.  I also work for UW-Extension Cooperative Extension, and on behalf of those folks and our other co-organizers, Wisconsin Public Television, the Wisconsin Alumni Association, and the UW-Madison Science Alliance, thanks again for coming to Wednesday Nite @ the Lab.  We do this every Wednesday night, 50 times a year.  Tonight, it's my pleasure to introduce to you John Yin.  He's a professor in chemical and biological engineering.  He also works at the Wisconsin Institutes for Discovery across the street.  Tonight he's going to talk with us about COOL, the Chemical Origins of Life.  He's been working on this since his life began, apparently.  That's how he likes to look at it. 

 And his life began in Boston, Massachusetts.  He also grew up for a time in LA.  He went to high school in Kensington, Maryland, did his undergraduate work at Columbia University in New York City, and got his PhD at UC Berkeley.  Then postdocked in Germany for a while and got his first professor position at Dartmouth College.  And then he came here to UW- Madison to improve his ice fishing potentials.  [laughter] I didn't hear any really cold areas there.  This is going to be pretty cool.  I love a cube as the central problem of biology. That's good.  A cube does have a center, does it not? Please join me in welcoming John Yin to Wednesday Nite @ the Lab.  [applause] - Thanks very much for the kind welcome. 

 Can you hear me all right in the back? Yes you can. Very good.  So, I'm delighted to be here.  I'd like to thank Tom Zinnen for inviting me, and it's really fun to be able to share some of our interests.  This central problem of biology.  This is supposed to be a figure of the universe.  So apparently people who study the universe make simulations of it.  And this creates a problem for biology, and that problem is perhaps stated here.  How could purposeful systems have emerged from a universe with no purpose? This was a question raised by Jacques Monod, a famous French biologist and part philosopher, in his work "Chance and Necessity," an essay on the natural philosophy of modern biology.  So, it's a rather deep philosophical question, I think, and we'll be trying in this next 50 minutes or so to try to answer it a bit more concretely.  So, how do we do that? Well, we have to say something about what we mean by purposeful systems. 

 So, what I have in mind, and I think what Monod had in mind, were systems like this.  Here's a jaguar chasing after its prey.  Or a Venus flytrap getting ready for dinner.  Maybe some colonies on a Petri dish of mold.  Or perhaps a snake finding its dinner.  Those aren't the only things of eating.  Here's a spider web.  Probably there's a spider waiting for its prey.  But there are also other systems that have particular purposes...  [laughter] such as reproducing. 

 And even bacteria in our gut are reproducing.  So, what we mean by purposeful systems here are systems that are alive.  They have this property of living systems.  We can contrast this with purposeless, purpose free systems.  Systems that are not purposeful.  What do we mean by purpose free systems? Well, ones that are not looking for dinner.  Right? Some minerals, quartz.  Or the moon.  Snowflakes.  Beautiful, nice symmetries, but we wouldn't assign particular purposes to those. 

 Or to the universe.  Or even to a beautiful sunset.  We're not looking at systems that try to find dinner here or try to reproduce.  And in this sense we might be considering purpose free systems.  All right, so, we'd like to think about how living systems might evolve.  And there is a framework for thinking about this.  So we can consider the simplest forms of life, those of perhaps the friendly bacterium here, E. coli.  And the framework for thinking about how this might have evolved is to think that it moved from simple life, single cellular life, to complex life.  We can think of this as multicellular life.  And there's some process for describing that. 

 Elucidating by none other than Charles Darwin, who thought about the various ways that accumulations of slight modifications can proceed.  So, if you can't see it in the back, I'll read this.  "If it could be demonstrated that any complex organ existed "which could not possibly have been formed by numerous "successive slight modifications, "my theory would absolutely break down, "but I can find no such case." So realize this was now 1859 in his "Origins of Species." He had no idea of what we today call DNA.  So he's just thinking about slight modifications that he can observe as expressed in particular biological organisms.  But he's imagining that there's some underpinning mechanism that can facilitate this, and certainly in the last century this is a major component of finding, at the molecular level, what Charles Darwin was able to observe at the macroscopic level.  So, this is how systems, living systems, evolved.  We'd like to try to extend this Darwinian theory from simple life to complex life but now beyond life and extending it backwards.  We might call that a biological phase.  If we want to extend it backwards, we might imagine that prior to simple life there was something we could call non-life and that there was a phase of change from non-life to simple life, which we'll call a chemical phase.  So the idea here is that that red arrow consists of chemical systems, not biological systems. 

 And that's what we're trying to elucidate a bit here.  So one way we'll take to do this is to imagine how we might extend Darwinian theory beyond simple life or complex life to chemical systems.  Could we imagine chemical systems that could exhibit biological properties that could evolve? That's what we'd like to try to do.  So, today we'll be focusing, then, on this aspect of the transition from non-life to simple life, and we'll take a couple of different approaches.  One is to start at simple life and try to deconstruct it a bit.  See if we can allow it to evolve toward something almost chemical.  And then we'll come from the other side of non-life, simple chemicals, and try to give them, mix them in appropriate ways that they begin to exhibit life-like characteristics.  So Darwin, in his own day, had no, made no attempt to try to describe how simple life would arise.  I think he would probably be delighted to see that his theory might have some application beyond living systems.  So that's what we're trying to do today. 

 So, we can think of that to the right, everything to the right of simple life as being purposeful, and everything to the left of non-life being purpose free.  And I'll let you decide where purposeful comes in in that transition chemical phase.  I'm not going to try to define that tonight.  So, the title of my presentation here is "Chemical Origins of Life." I kind of like that, COOL.  So this is the COOL research project.  I'm here in the Department of Chemical and Biological Engineering, and I also lead the Systems Biology Theme in the Discovery building.  So I'd like to start off by suggesting a nice book that I read last September.  This is "What is Life?" by Addy Pross.  Some of you might know that the famous physicist Erwin Schrodinger also wrote a book by this title.  Pross comes at it, though, from a perspective of a chemist, a card-carrying organic chemist. 

 And I think he offers some real insights into how one can be thinking about how biology could emerge from chemistry.  And one of the observations he makes is that there are, well, at least two kinds of stability.  He focuses on two kinds.  One kind of stability is what one could call thermal dynamic stability.  It's non-reactive. It's like this bottle of water.  There's no reaction going on here.  Or it could be a few stones there.  Nothing happening there.  But there's a different kind of stability which he calls dynamic or kinetic stability.  And this is a highly reactive kind of stable system. 

 That might sound contradictory, so we have to try to unpack that idea of what a dynamic stability could be.  Something that's constantly changing but somehow also maintaining something about its behavior.  And here I have chosen a figure of a couple of living cells here.  So those would be an example of systems that exhibit dynamic stability.  Other examples might be-- This is a fountain in Mexico.  I was in Mexico last week, and so here, what you see in the white here, are the water, where the water is coming in.  And here's the stone or part of the fountain sculpture.  And what I'd ask you focus on is the water part.  And you have to imagine that this is spraying out and creating this pattern of a couple of areas of water, which appear to be quite stable, but any given water molecule that you see at one instant in time you won't see for another few seconds, perhaps after it circulates through.  Yet the pattern here is quite stable. 

 So this is one where the water is constantly changing, yet the pattern of the water is maintained.  What are other sorts of examples of dynamic or kinetic stability? This is a little bit hard to see.  I've got to find a better picture for this.  But you have to imagine kind of a conveyor belt here where this conveyor belt is moving from top to down here.  And these objects here are cookies.  So this is a process if you go to the cookie factory.  Way way upstream, up there, is where they mixed up the batter and the sugar and all the ingredients.  And they put it on this conveyor belt, and the conveyor belt goes through a continuous oven.  It's got openings at the entrance where the cookies move in, and an opening at the end where the cookies come out.  And here they're starting to leave this conveyor belt and then go on to a cooling rack. 

 And this is, I would claim, an example of dynamic stability because if you stare at this and you take pictures of this at every instant, it'll look something like this.  There'll be different cookies, but the same pattern will be reproduced over and over again.  If you bake cookies at home, you might be more akin to something like this where you only have one door.  And we might call this a certain kind of-- What do we call this for cookies? - Batch. - Batch. B-A-T-C-H.  That is not an example of dynamic kinetic stability.  We put the batch into the oven. It's constantly changing.  When we peek in the oven at different times, we see it's brown to different extents.  So, over time, that is not an example of dynamic kinetic stability.  What might be another-- Oh, this one.  So, you look at me up here and you might think this guy is-- How is this guy an example of dynamic kinetic stability? Well, I do have to inhale in order to speak. 

 So as I am inhaling. I'm taking in oxygen.  Fortunately there's oxygen in this room.  And as I exhale and speak, I'm producing these words for you.  So I am also a dynamic stable system.  Some of my family members may have some questions about the stable part. [laughter] But I am taking in the oxygen and producing carbon dioxide.  So I too am an example of a dynamic stable system.  Now, I come from the area of chemical engineering, so I have to teach you at least a little bit about chemical engineering.  So this would be an example of a reactor, which we call a continuous stir tank reactor.  It's stirred tank because we've got a little mixer here, and you can think of that as a propeller.  And when that propeller is spinning around, that means everything in the tank is well mixed and of the same composition. 

 This tank also has some feed here.  Those of you who might be from the more quantitative sciences might see something that looks like changing of velocity with time.  So this would be a volumetric flow rate.  So many gallons per hour might be the flow rate into this vessel.  And this might be also at some concentration of some component, concentration in.  And then within the tank we have a concentration of that component.  Maybe it's sugar within the tank.  And then there's a volume of the fluid in the tank.  And then coming out there's some flow rate-- volumetric flow rate coming out.  Now, if the flow rate coming out is the same as the flow rate going in, the volume within the tank will not change. 

 And this will be an example of dynamic stability, in the sense that the volume is constant even though the contents of the tank are constantly being renewed and being drawn off.  Notice that the composition of what comes off will always reflect whatever the composition was in the tank.  If we take it even another step further for the mathematically inclined, we can try to think about things that might grow in the tank.  So if it's sugar water, I might introduce some bacteria in there, and the bacteria might grow or the yeast might grow, if I'm interested in fermentations.  So we can call those bacteria or yeast replicators.  That's a more generic term.  Something that replicates or grows.  And one way we might represent how that concentration of replicator changes as a function of time in here is this is a term called a derivative.  Something we teach our undergraduate students in calculus.  And we're saying how rapidly or how this concentration changes depends on two kinds of terms. 

 Terms of growth, and the growth terms depend on how much replicator we already have in there as well as what is this M.  This M is the food. Concentration of food.  If we have zero food in there, there's no growth.  But if we have some non-zero positive value for M.  This is positive.  And k is a rate of replicator formation given the presence of replicators and food.  So all of those are positive values.  Likewise, g is a positive value.  It's a rate of decay or death.  And that would include not only if these cells are dying in here, but also it would include some kind of accounting for how they're leaving the tank. 

 So that g combines both those kinds of terms.  g is positive and X is positive.  So the term minus gX would be a negative term.  And what happens in cases of dynamic stability? Then this equation simplifies.  Do we have any mathematicians or engineers in the audience, or physicists, perhaps some chemists, who could tell me how this equation would simplify? - dX/dt will be zero.  - dX/dt will be zero Thank you.  Let's hear an applause.  [applause] I want you in my class. [laughter] All right, so that means that's zero, and if that's zero, then that means we have a balance between the growth and death, or we have a balance between growth and decay.  Those are equally balanced, and that means if we sit and look in this tank at any given point in time, there is no change in the concentration of our replicator, even though it is growing and it also dying.  It's just that those are balanced, quantitatively balanced. 

 I could take it a step further and put tank inside of a process.  Don't look at the details here.  Just realize that there are a bunch of tanks connected together with other things, and there are arrows here.  The main thing is in this process there are inputs to the process.  This happens to be a biomass process.  So you put in biomass and you get some fuel out of this thing.  But this has inputs and outputs, and if we look at any component within this process, it'll be like this one in the sense that it'll be a dynamic stability.  Likewise, I can look at a big chemical plant where there are many more of these operations, we might call them unit operations, where somewhere in this plant there's a feed, there are a bunch of distillation towers, there are a bunch of other processing components, and then there's some outlet.  Essentially, somewhere in here there's a way to feed in raw materials, and there's a way to pull out products.  And when this plant is running, then it's also an example of dynamic stability. 

 All right? So that's your chemical engineering for the day.  Now we need to move on a little bit.  And we'll just emphasize the point, from process perspective, Darwin's theory of natural selection should extend to replicator chemistry.  So now we're trying to look at the chemistry, and we need to say something a little bit about chemistry.  So just a little bit of chemistry.  I want to introduce a few terms.  So, one kind of chemical compound that you can find is a polymer or polyethylene.  It's a very common plastic.  And you can find your ice cream perhaps distributed in polyethylene containers.  And I already alluded to this term, that if you look at the plastic and ask what is the technical term for the plastic, you might encounter this term polymer, which is made up of monomers. 

 So the monomers are single units, and the polymers are stitched together.  Chemically stitched together monomers to make what we call this polymer.  And the process of chemically linking together the monomers to make this chain is called polymerization.  So that's a little bit of chemistry.  And the process of polymerization-- So the polymerization of monomers of something called ethylene, which contains two carbon groups, yields a polymer or plastic that we call polyethylene That's what we had over here.  In the chemical formulas, you have carbons with hydrogens connected to them.  And the polymerization process, which chemical engineers like to do, is to link together these monomers to make long chained polymers, and then process those polymers into nice shapes that can be useful.  So that's polymerization. That's unnatural polymerization.  You won't go into nature and find polyethylene, at least-- Well, I should be a little careful.  [laughter] These days you might find some plastic out there, but not naturally formed polyethylene. 

 Perhaps released by some living form.  But there are also polymers that exist in living systems.  And here we should say something about DNA.  You've heard of DNA.  For our purposes, DNA is indeed a polymer and it's made up of monomers.  Not the same single unit of monomer as we see for polyethylene.  But now we have four unique monomers.  And we won't go into the chemical details.  They have different shapes, and they're made up of different elements.  The purple is a common element shared by them, but the bases, these other colors, represent how they differ. 

 And these are sometimes abbreviated A, T, G and C for these chemical compounds.  Adenine, cytosine, guanine, and thymine.  We don't need to worry about those details.  The main point is DNA is a polymer.  So you imagine somehow stringing these together.  Chemically linking them together.  And chemically linking then I could make something out of solely A or solely C or mixtures of A and C.  What is important here is that I can begin to encode information using the different monomers.  I could do the same if I had just monomers of ones and zeros.  And that's what you have in your computer. 

 Ones and zeros essentially encoding information, except they're not chemical ones and zeros; they're electronic forms of ones and zeros.  All right, so this is just to iterate or emphasize the point that all life uses the same monomers.  So they're the same monomers of DNA.  What differs from the DNA of these various different organisms? Well, it all boils down to every organism has its own compilation of total DNA, which we call its genome.  And the corn plant has a genome.  You have a genome that was provided to you by your parents as when you started off as a fertilized human egg.  And that genome then defines the various processes of development that ultimately result in a mature corn plant when these seeds are placed in the appropriate environment, or when this fertilized egg is allowed to develop in the appropriate environment, to complex organism.  Key differences here are that the genomes have different lengths and they have different sequences.  They are chemically identical, though.  So that's pretty remarkable. 

 That tells us we are somehow all related, all lifeforms.   Okay, so where are we now? We've talked a little bit about how we are trying to extend Darwinian theory beyond life to chemical, chemical systems.  And we've talked a little bit about what sorts of chemicals we might be particularly interested in.  Some kinds of polymers that are made out of monomers, where the monomers are different and able to encode information.  So, let's take the next step and consider a particular biological system.  Recall we're going to go and take, start from the simple life here and try to go backwards to something simpler than simple life.  So, simple life is a single cell here, but it's being invaded.  And this is a virus particle.  So this touches a little bit on the sort of research we do.  The virus particle is a little bit of information. 

 It can be made out of DNA or that information could also be made out of a similar polymer called RNA.  But the main point is that information is delivered to the cell, and when that information is unpacked in the cell, it can direct the resources of the cell to make more virus.  All right? So the cell normally, when it's provided growth media, the cell itself will divide in two.  It'll grow larger and divide in two.  When the virus finds such a cell, it sees the cell as raw materials.  So here I am putting on my chemical engineering hat and saying this is actually perhaps like those processes where we have some raw materials being converted into products.  Except from the standpoint of the viruses, it's putting in the information that's informing the raw materials in this cell how to make viruses.  It's turning the cell into a virus manufacturing plant.  And you might make anywhere from a hundred to a thousand or 10,000 viral progeny from a cell.  And this could take anywhere from 15 minutes to 15 hours or 15 days depending on the virus that you might be working with. 

 All right, so this is how a virus reproduces.  What we want to do is deconstruct this a bit and reduce it to a little bit of its chemistry.  So I want to take a look at a little bit of what's going on in the deconstruction and construction of viruses here.  So this goes back into thinking this approach was an early stage of systems chemistry.  I would call this the chemistry of figuring out how biology might have come about from chemical processes.  So when a virus enters the cell, I alluded to the virus genome, and this is used as a template to make proteins.  Proteins then feed back on processes that allow the genome to reproduce itself, and then the genome gets together with these proteins and ultimately packages them up and makes virus progeny.  So this does not show all the resources of the cell, but it shows some of the components that are important for the virus.  If we take even a greater simplification and look at this virus genome, then we can ask what is chemically happening there.  So this virus genome for a particular virus, I'll be considering one called a phage, the virus genome was made out of a piece of RNA. 

 So you should think of this as a polymer made out of DNA or RNA like monomers.  So different monomers where they have a unique sequence.  And this plus strand, plus indicates that there's a certain kind of polarity.  If you can think of-- Well, we could also think of this as ones and zeros.  And the monomers then are components that can stick to the RNA and be stuck together, bound together by a particular enzyme or catalyst that the virus brings into the cell.  The virus also encodes this enzyme.  So when the virus genome gets into the cell, it instructs the cell to make this enzyme.  And what happens is the enzymes uses the genomic template that the virus introduce into the cell, and it uses monomers that are present in the cell to stitch together a complimentary piece of RNA.  So the red was what came in with the infecting virus, and the blue is something that is made within the infected cell.  So you can imagine if we think of monomers as being 1-1-0, the first few monomers here as being 1-1-0, on this opposite strand, coding in the negative sense, you would have-- Let's see, I said 1-1-0, so across from 1 I would have 0, and it would be 0-0-1. 

 So you can imagine how strings of ones and zeros on the red strand could be complemented by ones and zeros on the complementary blue strand.  So either strand encodes the same information.  And what happens within the cell as these strands separate during an infection, and the replicase can then operate the same way as it did on the red strand to make another blue strand.  But the replicase can also now operate on the blue strand to polymerize and make the complementary red strand.  So we started off with a single red strand, we made a red and blue, and now we have two each of the red and blue.  And this can continue on.  So you have the possibility for exponential, or you could call it explosive growth.  What the virus does when it enters the cell is it essentially sets off a chemical or a genomic explosion, making many copies of the genome.  So, what happened in the 1960s was a biologist by the name of Sol Spiegelman said this is a very interesting reaction, I wonder if we could deconstruct it and think of it more in chemical terms.  So what he did was he and his coworkers isolated this red strand from infected cells and the polymerase, this enzyme, and he put them into the test tube and he bought from the store the monomers. 

 So chemical stores you can buy the monomers and you can also put in there.  So we no longer have this reaction going on during an infection inside of a living cell.  He's trying to reconstruct this process of amplification in a test tube, in a little plastic tube here.  So he has a few strands of the RNA, excess monomers or building blocks that he bought from the store, and excess replicase which he isolated from infected cells.  And the question was, well, would this run or not? Maybe if you provide all the ingredients for the initial strand here and the enzyme, the catalyst that stitches together the monomers, and plenty of monomer, then you could keep on doing this process of molecular growth.  Would that be possible? Well, indeed he tried that.  This is Sol Spiegelman.  So at time zero he mixed the ingredients together, incubated them at, I think, about 37 degrees C, about a little warmer than room temperature, and over time he was able to measure the concentration of RNA in the tube.  You might notice that this scale here is on an log scale.  So this is one, that's 10, and that's 100. 

 So the RNA here is growing exponentially over time.  And this is over a period of two, three hours.  It just keeps on growing.  You see initially it starts off with the same slope.  So that's an exponential growth, but then it starts leveling off.  And you can imagine that it's leveling off because it's using up those monomers.  As you use up the monomers, the growth slows down.  So what he did next was an interesting thing.  He took these RNA molecules that were made in the tube and he introduced them back into living cells.  So, normally the virus would introduce these molecules into the cell. 

 Here he had a way of introducing them into the cell so the cell could still remain intact.  And what he found was the cells would make more viruses.  So he's taking RNA molecules that were made in the test tube, introducing them into the cell, and the cell now makes viable virus particles that he can take and put on other cells, and they'll continue to grow.  So he's made, within the test tube, this molecule that is infectious.  This is 1965.  There were no companies like Promega selling these biological enzymes.  He isolated it from the infection and was finding, essentially, that he could make something that was infectious.  People called these molecules Spiegelman's Monster.  [laughter] Because they're RNA molecules that in some ways behave like life.  So he took the next step and said, "Well, "what would happen if we didn't allow them to "run out of materials?" How could you do that? Well, he wanted to ask the question. 

 So this is the-- This is a couple of years later.  Proceedings of the National Academy of Sciences.  An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule.  So this nucleic acid, that's the RNA.  Self-duplicating, you know how that works now.  And this is extracellular. It's outside of the cell.  And there's, well, potential for evolution maybe.  And the key point here is he was asking, what will happen to the RNA molecules if only the demand made on them is the biblical injunction: multiply? So you want to see, if you give them the resources to multiply, how they will do.  And that means that you don't want them to run out.  So how do you keep them from running out? Well, here's how they set up the experiment. 

 They set up what is called a serial transfer experiment.  There's the tube initially where they had their goodies of the strands of RNA and the monomers and the replicase, but then they set up a series of tubes here that had plenty of the monomers, excess monomers and replicase, but no templates.  So there's nothing going on in these tubes.  You have growth initially in this tube.  And before you're able to use up all of those monomers, you transfer a small fraction of that tube into the next tube.  So, some of those molecules that grew come into this land of excess monomers.  You can say this land of milk and honey.  They're ready to replicate.  So you do a serial transfer, and they start to grow.  They can grow, again, in this tube just as they did in the first tube except they're in this tube with all these fresh monomers. 

 And they're able to grow and before they grow and use up all those monomers, you transfer them again.  So you're constantly transferring these molecules, and you imagine those lucky molecules that happen to get transferred from tube to tube, the lucky large molecules, only see all this plentiful monomers.  So, what happens then? Okay, so here's what happens.  You start off with transfer number 0, and these are the various transfer numbers.  As he's doing the transfer numbers, they're counting or doing an accounting of how much of that monomer has been incorporated into the reaction.  So after one or a few transfers, you see there are more and more monomers being incorporated.  And up through about nine transfers it seems like each transfer is taking up about the same amount of monomer.  But around nine or 10 it seems like there's a change in this slope.  You're not continuing along the same pattern.  You're actually going a little bit faster, taking up more monomers. 

 So the system seems to be changing.  Up here it looks like things have slowed down, but actually that's a little bit of an illusion.  What we don't indicate here is now he's started transferring even more frequently because these molecules were taking up the monomers so rapidly they had to reduce the time that they were allowed to take up the monomers.  So what appears to be slower here is actually even faster growth.  All right? So, something is changing as we are doing this.  You have to admit this is basically a chemical experiment.  We don't have any living cells here.  There's an enzyme, there's a catalyst, it's a protein, and these RNA molecules, then some monomers.  Then what he did was also, as before, he took these templates and he put them back into the cell.  So, up through passage number nine, when he put these back into the cell, the cell was infectious. 

 It made plenty of virus just as before.  So the monster was intact during those first nine transfers.  But by transfer 10, and everywhere beyond, none of those molecules when put back in the cell was able to produce a viable virus.  Somehow this molecule, this system, lost the possibility of making virus.  So the monster is dead.  But some way there's a different monster here because it's growing faster.  What he did was to analyze what was finally coming out here.  And when he looked at that molecule, he found that it was much shorter.  83% shorter than the original starting material, starting molecule.  The starting molecule was about 4200 monomers in length, and this was only about 17% of that. 

 Much smaller molecule.  So, smaller and able to replicate or reproduce much faster than the original molecule, but now not able to instruct the cell to make virus.  It's lost the essential information needed to make viruses, but it's gained some capability to replicate very rapidly.  That's pretty neat.  And this, I would argue, is an example where the molecules are doing this selection process.  There are mutations that are occurring.  The mutations happen to shrink the molecule.  When the molecule is shorter, it doesn't take as long to make it.  So when you've got resources and you can grow faster than those that are growing slowly, then you get enriched, and you have a better possibility of being transferred to the next tube than the ones that are reproducing more slowly.  So that's a nice example of Darwinian selection at the molecular level. 

 So that's the example that we just considered.  Simple life, deconstructing it, putting it into the test tube, and showing that as long as we can replicate and create perhaps some kind of variation, then things can evolve.  Now I want to take it from this side, a system that is clearly non-life, and see if we can move it in this other direction.  How do we do that? Well, my second son is coming up to 15 years old.  So he's in ninth grade.  And in his biology book he's got this nice description of this experiment by Stanley Miller from way back in 1953.  Some of you might have heard of this.  The idea was to take what was thought to be a primitive atmosphere.  Gases in the primitive atmosphere of Earth had things like water, perhaps methane, CO2, ammonia, hydrogen, nitrogen.  No oxygen though. 

 So the early planet was thought to lack oxygen in the atmosphere.  But there was certainly water around, so there's also water down here.  So the gas is able to communicate or exchange material with the water.  And what Miller did as a graduate student, 23-year-old graduate student at University of Chicago, was to put a spark in here.  And when he sparked it, he found that there were compounds that were formed in the water.  And those particular compounds were amino acids.  So, amino acids, it turns out, have a special place in biology.  Amino acids are the building blocks of proteins.  And when I say building blocks, another term for that would be...  - Monomers. - Monomers. 

 And so there are different-- Boy, you guys are great.  [laughter] There are different amino acids.  Some of you might know there are 20 some amino acids, typically, that we use to build up the proteins in our hair or skin or muscles or tears.  We're just chalk full of proteins, but those proteins are all made up of amino acid monomers.  And the proteins of all lifeforms are made up also of amino acids.  So this was a huge triumph to go from these very simple gases and to realize that the building blocks of biology could be produced.  So I was very curious to turn the page and see what was next in my son's biology textbook, and they move onto the next topic.  [laughter] Okay.  That leaves you in suspense.  But it says to me also that maybe this field hasn't really moved a lot since 1953. 

 And that's both a challenge but maybe it's also an opportunity.  So we've begun to think about this a little bit, but we also have some help from some giants in the field to think about how can we start stitching together these amino acids, maybe to make proteins and maybe to move a little bit from non-life in the direction of simple life.  So, if you look at the problem, then you immediately hit a wall, and here's what the wall is.  I have to go a little bit more into the chemistry here.  The main point here is I have two amino acids.  They're both the same amino acid.  There's an amine group and there's an acidic group, or acid group.  There's the acid group and amine group on this other amino acid.  And what happens, in order to chemically stitch these together, we have to take a water.  You might know water has a chemical formula H2O, and if we steal away H2O from these two, then they can stitch together and form a bond. 

 Notice this has CCN and this has a CCN, and if we read all along the line here, we have CCN and CCN.  We just formed a bond here, and that's called a peptide or amide bond.  And in the process of making that bond, we kick out the water.  So the water appears down here.  Now, there's a problem here in that if you go to your freshman chemistry student and ask, "What direction is this chemistry "favored if your amino acids are in water?" If you have lots of water present, then the chemistry favored is in the hydrolysis direction, or moving upwards rather than moving downwards.  Moving downwards is what we want.  We want to stitch together these monomers to make two amino acids joined together.  But what is favored in actual chemistry is, in water at least, is a hydrolysis or a lysis or lysing or splitting of a molecule by inserting a water.  So the water gets inserted here to make the two separate amino acids.  So each of us is very unstable. 

 If you go to the swimming pool and sit there long enough, this is what's going to happen.  You will be decomposed into your amino acids, as long as there aren't other bacteria there.  But the chemistry at least favors your decomposition back to your monomers.  All right, so this is a problem, and this is a serious problem.  In your body, you routinely stitch this together.  And this is happening as we speak.  You are digesting, you are making proteins, but the machinery to do this is many orders of magnitude larger than the amino acids.  So something the size of this room is the enzyme that helps to stitch together amino acids of this size.  So a highly evolved, very complex machinery made of both protein and RNA.  That we don't have present on the primitive Earth. 

 So we've got to figure out a way of trying to do this chemistry in a much more primitive way.  And that's where I allude to the giants.  One of the giants in the field is Bernd Rode.  So he is an emeritus professor now from Vienna, Austria.  He's a theoretical chemist.  But he thought, you know, there's this problem of stitching together the monomers, I wonder if we could do it in a simple way by putting in some copper chloride.  So this is a little hard to see.  I'm sorry the color is a little washed out here.  But the copper here is indicated by this little trapezoid here.  And the amino acids now are shown by the circles here. 

 So it turns out that if you put some copper chloride into solution, it forms a nice blue solution, but the coppers have this tendency-- Well, copper is positively charged.  It has a two-plus positive charge.  The amino acid could have a little bit of positive and negative charge.  It has enough negative charge so opposites attract, and that amino acid may become associated with the copper.  Not only that, another amino acid might associate with the same copper.  So now you have two amino acids, two monomers brought into close proximity.  You can think of the copper as kind of a matchmaker for the two amino acids, and they're sitting down to lunch here.  [laughter] Now, if the appropriate conditions are such that it's not too acidic, then these two potential partners jockey around, look at each other in the eye, and realize that they might like to come together.  And if they actually come together, if you could remove a water at this point, then you can actually drive the chemistry so that these two monomers come to the same side of the table and form that amide or peptide bond.  The trick here is that you've got to remove the water. 

 So, maybe we've just shifted, maybe it's just a semantic point here, but a key aspect here is that you brought these guys in close proximity.  And the removal of the water is where Rode, I think, was particularly clever.  One thing he did was to have very high concentration of sodium chloride, salt, table salt, which, in solution, likes to pull on water.  Sodium chloride likes to have water around it.  So it can be stripping away water.  These are water molecules around here.  But what he also did was leave the tube open to the environment, so the water could just evaporate.  So he said, all right, leave the tube open to the environment, allow the water to evaporate, and maybe you can get the chemistry to go so now there are some di-mers.  These are two unit now monomers.  We'll call it a di-mer. 

 So, that allows you to-- It shows you how you can go from monomer to di-mer.  And then you can imagine the next step might be, well, if you add backwater, and then these guys, this di-mer can go back into solution.  But it can associate over here on the side.  So you could have a di-mer over here, and then the next guy adding here could be either a monomer or a di-mer.  If you go around the whole cycle again, evaporate, then you could form two di-mers coming together would give you a tetra-mer, or a di-mer and a monomer coming together would give you a trimer.  So, by just going around here, essentially drying and then rehydrating and then drying again, we have a machine to be able to stitch together these monomers.  Here we've considered monomers that are all the same.  But you can imagine that we can now put in different monomers.  Any drawn for those natural 20 amino acids.  And you could imagine that, depending on their particular chemical affinities for copper, that we might have any array of different kinds of polymers that could be formed from different monomers. 

 So, we had to try this on our own.  Back about 10 years ago, I had a master's student, and I said why don't you give that a try and mix some amino acid, in this case alanine, with some copper chloride and water.  You form this nice blue solution.  And let's just heat it to dry it.  So you bring it to 60 degrees C. You just put in on a block.  And you leave it open so it evaporates.  But to make sure we could do some kinds of measurements on what's going on, I said, well, let's weigh this thing.  So here's the mass of the water.  We started off with half a gram of water in there at time zero when we initially mixed this together.  And then over a period of, oh, what, four to eight hours, took periodic samples, weighed it, and because it's open to the environment, you can imagine this water level just dropping, dropping, dropping as you're evaporating, and that's what you're seeing right here. 

 Mass of water in there is decreasing.  At the same time, we were sampling that water and doing some analysis, some chemical analysis to say do you got any dialanine in there.  And so the dialanine axis is over here, and during that drying process as the water is dropping and evaporating, we don't see any dialanine.  We don't see any dialanine after eight or 12 hours, but if we incubate this now 16 hours and then we rehydrate it and analyze, lo and behold there's a little bit of dialanine.  And if we incubate even longer, there's more dialanine.  So this solid here is reacting.  That condensation reaction is actually occurring in the solid.  We're making polymers in here.  We're not making any polymers over here, but we are doing that here, as we incubate this solid.  And we don't have to stop at 20 hours. 

 We could go out to 200 hours, and it keeps on going.  If we go out to 400 hours or so, it doesn't maintain the same pattern.  This reminds us that maybe we're starting to use up those monomers, as we saw with the RNA experiment.  So you can imagine other sorts of serial transfer experiments you might want to do.  That's as far as we went in 2006, but Rode did a series of other experiments that were very intriguing also.  What they did was to put in other amino acids.  So, histidine is another amino acid.  This has some interesting side chemistry.  It's able to become acidic or basic depending on its side.  It has some more interesting chemistry than the alanine that we are considering. 

 And the main point here is when you put in that additional amino acid, this particular amino acid, it has a catalytic effect.  That means that it accelerates the reaction without being consumed.  So you imagine bringing in that histidine.  Somewhere the histidine might associate a little bit over here or over here or maybe in the solid phase.  The key point is if I've got histidine in that system, then this growth curve of dialanine will be even steeper, will make much more dialanine in the same amount of time than we made in the absence of histidine.  So histidine is not being consumed.  It's serving as a catalyst.  Those of you who have studied some biology or biochemistry know that enzymes or proteins that have histidine, oftentimes the histidine will play a catalytic role, that it can actually do some chemistry in the enzymes.  So maybe it's not surprising that the histidine alone in this particular system could do some chemistry.  What was really surprising, though, was when they took glycine. 

 So glycine happens to be the simplest amino acid you can imagine.  It's chemistry is just-- It's side group is just this H, a hydrogen.  And inside of you there's no enzyme.  I've found no-- We've got a great biology department, biochemistry department here.  No one-- None of my biochemistry colleagues can tell me of an enzyme in nature where glycine is active as a catalyst.  All right, it's boring chemistry.  All right? But here, it's catalytic.  How could that possibly be? So you've got this boring amino acid that normally, in our body, doesn't do anything interesting, but in this particular scenario can do something interesting.  And we have some thoughts on what's going on here because when we look at these solids, we see at least two kinds of solids.  One kind of solid looks kind of crystalline, like if you pour a little salt out of your salt shaker. 

 It's kind of crystalline.  Another kind of solid is kind of glassy.  So it's kind of amorphous.  And it looks like melted glass.  In that case, it turns out that the reactive solid is more reactive when it's glassy than when it's crystalline.  And we would hypothesize that when glycine is present, perhaps it acts as a bit of a plasticizer and allows the material to even flow a little bit and do some chemistry.  So that's a guess at this point.  We haven't demonstrated that, but we think that even the most boring amino acid, a single monomer, can now be an enzyme, and that's really quite remarkable.  Okay, so where do you go from there? Well, we're starting to mix amino acids together and cycle them and do all sorts of things.  And we've talked about how we started from the simple life and move down towards non-life. 

 And hopefully I've convinced you that maybe non-life could be moving in this evolutionary direction.  Maybe I have to elaborate a little bit more on how that would work.  I've shown you how non-life, how the monomers can be brought together to make polymers.  And I've suggested that certain monomers can be catalytic, even the most boring ones.  If that's the case, then you could imagine any set of polymers could possibly be catalytic.  So let's assume we have some building blocks, and here I've shown the building blocks are monomers in several different colors.  Red, blue, and green.  So we have-- We've considered three different monomers.  And just imagine that I put in the copper and do some chemistry and allow these monomers to form di-mers.  We already saw that for alanine, that you could form a homo di-mer made of the same monomers. 

 Or you could imagine maybe in some cases you'd form a hetero di-mer made out of two different monomers.  Or if we cycled a few times, maybe you could make penta-mers or even some-- I'm sorry.  This is mislabeled.  This should be-- What should this be? This should be quatra-mer or tetra-mer.  So, of course, I purposefully did that just to see if you were awake.  [laughter] All right, so you could imagine in this soup, depending on how many times one of these molecules has been gone through the process of being dried out and rehydrated, that we might have some di-mers or tetra-mers or penta-mers, and there might be some variation.  There's no kind of template copying here as we had in the RNA case.  So there's no template copying.  So you could imagine any number of different kinds of polymers arising.  And I just indicated a few variants here. 

 Now, what's interesting to think is that maybe this di-mer could be like glycine.  It could be a catalyst.  And when I say a catalyst, that means maybe if this is present, then it helps to make one of these B polymers.  So A could serve as a catalyst to enable B to be made more readily, one of these B molecules to be made more readily, more easily, without being incorporated, but just facilitate that chemical synthesis.  The same could be said of B.  Maybe B, one of these B molecules could help a C, and a C could help an A.  That's the interesting part.  If you have the possibility of somehow this loop closing because then if A enhances B and B enhances C and C enhances A, this is a positive feedback.  And a positive feedback has a capability then of growing out where these molecules enhance their own synthesis, while the ones that don't contribute so much to the chemistry are left behind.  So you might imagine the red variant here does a little bit better job than the blue variant. 

 And it would be perhaps enhanced by the chemistry here and allow certain members of each of these penta-mers, di-mers, or tetra-mers and di-mers to grow out.  So here, this is just an arm waving, but I'm trying to make the case that it's plausible at least that we could see some synthesis of polymers, hetero polymers made up of different monomers, enhanced in their synthesis and contributing to the bigger picture of self-replication.  So, I've tried to make the case that under different environments we might form different monomers, or, sorry, different di-mers or polymers, and these might react on themselves under different conditions.  If we make things a bit more acidic or change the temperature, you can imagine the chemistry is favoring some molecules over others.  So maybe there's an opportunity also for adaptation or evolution in this kind of system.  So there are a few broader impacts or extensions of what I've tried to elucidate here.  I've showed it for amino acids, thinking about how amino acids might come together and become functional, enable their own replication.  We're very interested in also doing this with the RNA monomers.  For those of you who follow the biology-- I'm sorry, this got a little bit scrambled here.  But we're testing the RNA world hypothesis. 

 Some people believe that RNA was actually the first biopolymer to be formed, and there are good reasons for that.  We're not convinced yet, but we think this might be a way to show that or find RNA molecules that are able to contribute to their own replication and evolution.  We could imagine taking the RNA monomers and mixing them with amino acids and doing this kind of cycling and perhaps allowing both kinds of polymers to arise.  I mentioned that the machinery that stitches together proteins in living systems is very much more complex.  That machinery is called a ribosome, and it's made up of RNA and amino acids or peptides.  Peptides being amino acids strung together.  So maybe it'd be possible to evolve that kind of machinery in a test tube, where these kinds of cooperation where there's a cooperation of RNA and peptides or proteins.  You don't have to stick with the amino acids or RNA, the monomers that nature gave us.  There are many kinds of fascinating amino acids that do not exist in nature.  We're not restricted to the ones that exist in nature. 

 We could carry out the same chemistry using non-biological monomers.  And we imagine that they could conceivably also replicate.  So you could imagine making polymers that are reproducing and are evolving and adapting but not made out of anything that arises in living systems.  So we don't have to also restrict ourselves to the specific kind of polymerization chemistry that I've shown here.  There are many kinds of polymerization chemistries.  So one could branch out to things that are not just hydrolysis condensation chemistries.  Alternatively, we could stick with the 20 amino acids, and just say let's repeat the experiment several times and see if we get the same monomers condensing to form the same polymers.  How reproducible is evolution? Or if we do it at a slightly higher temperature, will we get a very different kind of distribution of molecular species? Perhaps so.  So, what role does environment play on the evolution? This is that idea of rewinding the tape.  We are also very interested in computational chemistry. 

 So, the things that happen in the solution phase, this forming of amino acids coming together with copper, is very well studied.  It's been known how that happens for more than 50 years.  So people who want to try to simulate that behavior in computers have no problem with that.  It's just that when you dry and remove all that solvent and form that solid that's reactive, that's a complete unknown, and it would be a fabulous frontier, I think, of computational chemistry to try to compute how living systems or information containing systems could arise.  So that's something we're also currently working on.  So I try to make the point here that spreading these ideas of Darwinian selection from living systems to chemical systems might give us some insights into ways that life might have originated from chemistries.  I'll end with this particular quote from Richard Feynman: "What I cannot create, I do not understand." Thank you.  [applause]