Session 5: Chemical Evolution

Transcript of Part 1: The Origin of Life on Earth

00:00:00.00	My name is Jack Szostak,
00:00:01.25	I'm a Professor of Genetics at Harvard Medical School,
00:00:05.22	I'm an Investigator at Massachusetts General Hospital, where my labs are,
00:00:09.18	and I'm also an Investigator of the Howard Hughes Medical Institute.
00:00:14.17	In this lecture, what I'd like to tell you about is recent advances
00:00:21.06	in work from my lab on the origin of cellular life on the early Earth.
00:00:26.22	But before I get into those experiments,
00:00:29.08	I'd like to step back from the origin of life per se,
00:00:33.08	and talk a little bit about some insights from modern biology
00:00:39.00	that bear on this question,
00:00:41.01	in particular why the question has attracted so much interest and attention recently.
00:00:46.16	So, this is one of the iconic images of hydrothermal deep sea vents.
00:00:56.02	This is an environment characterized by very high temperature and pressure,
00:01:01.21	and of course the surrounding area is just teeming with life.
00:01:07.04	Here's another example: an image from Norm Pace.
00:01:12.04	You can see a layer of green cells growing inside the rock.
00:01:18.07	These are photosynthetic cyanobacteria,
00:01:21.29	and they're living in the pores of the rock at very low pH.
00:01:28.23	This is one of the famous hot springs in Yellowstone National Park.
00:01:34.26	Again, a very high-temperature environment; again, full of life.
00:01:43.29	And here's yet another distinct kind of extreme environment,
00:01:48.21	another very low pH environment.
00:01:50.14	This is the Rio Tinto in Spain.
00:01:53.27	Very acidic water, but again teeming with life:
00:01:59.00	microbial, eukaryotic life.
00:02:04.17	There are even more extreme examples of this kind of environment in acid mine drainage sites,
00:02:12.00	where the water that's flowing out is basically sulfuric acid at a pH close to zero.
00:02:18.24	And again there is microbial life.
00:02:21.11	So with all of these examples,
00:02:22.22	what it's telling us is just the remarkable extent which our planet
00:02:27.21	has been colonized by life.
00:02:31.17	And even environments that we would've considered incredibly hostile and extreme
00:02:38.20	are apparently easily adapted to by life.
00:02:43.10	And of course, this is a consequence of the power of Darwinian evolution,
00:02:48.10	to lead to adaptations to diverse environments.
00:02:53.16	So, if you put this together with recent observations
00:03:00.01	from our astronomy colleagues, in terms of the discovery of extrasolar planets,
00:03:06.02	it really puts into focus the question of whether there is life out there,
00:03:13.13	apart from our planet.
00:03:16.07	So this is an image of the Milky Way, of course.
00:03:22.20	Up to a couple of years ago,
00:03:24.21	astronomers had discovered on the order of 500 extrasolar planets,
00:03:29.04	planets orbiting other stars.
00:03:32.08	But more recently, as a result of the Kepler mission,
00:03:36.00	a space telescope that is just pointed continuously at a very dense starfield,
00:03:45.22	a large number of additional planets have been found,
00:03:48.24	about 1200 candidates at the last count.
00:03:52.28	And these are detected as the planets orbit around their star,
00:03:57.29	and if they eclipse the star, if they transit in front of it,
00:04:00.27	they block out some of the light, and you can detect that little dip in the intensity of the light.
00:04:06.23	So this has given us a big enough sample to actually make extrapolations,
00:04:12.02	and what I've heard from scientists associated with the Kepler mission
00:04:17.17	is that those extrapolations suggest that there could be roughly on the order of
00:04:23.06	500 million, perhaps even a billion, Earth-like planets
00:04:27.00	orbiting sun-like stars out there in our galaxy.
00:04:32.13	And so, if you put that together with the fact that we know,
00:04:37.03	on our planet, that at least microbial life can live in incredibly harsh and diverse environments,
00:04:44.28	it's pretty clear that there will environments out there on
00:04:49.12	these other planets that could support life.
00:04:52.03	So the question is, and the thing we all really want to know is:
00:04:56.01	Is there life out there?
00:04:58.01	Are we alone, or is the universe, is our galaxy, full of life?
00:05:03.15	So this really comes down to the question you see here.
00:05:07.25	Is it easy or hard for life to emerge from the chemistry of early planets?
00:05:14.13	And, unfortunately, it's going to be a long time before we can answer that question
00:05:18.28	in the most satisfying way, by direct observation.
00:05:23.16	Even to get indirect evidence from spectroscopy of planetary atmospheres
00:05:30.27	may take 10, 20, 50 years, to look at Earth-like planets.
00:05:38.28	So what can we do in the meantime to try to get some clues to answer this question?
00:05:46.27	So, what we've been doing, and other people have been doing,
00:05:49.29	is to go into the lab and do simple, chemical experiments
00:05:54.29	and try to work out a complete, step-by-step, plausible pathway,
00:06:02.17	all the way from simple chemistry to more complex chemistry to simple biology.
00:06:08.02	And if we can actually show that there's a continuous pathway
00:06:13.26	with no super-hard steps along the way,
00:06:17.20	then I think we can conclude that it's likely that there is abundant life
00:06:22.14	out there in our galaxy.
00:06:25.03	On the other hand, it could be that our experiments show
00:06:29.14	that there are some steps in that pathway that are extremely difficult,
00:06:35.01	there are bottlenecks that might be very hard to overcome,
00:06:38.29	in which case the emergence of life might actually be a very rare phenomenon.
00:06:44.04	And in the extreme, we could be it.
00:06:47.23	This could be the only place in our galaxy or even the universe where life has emerged.
00:06:53.28	So we would like to try to get some insight into these questions
00:06:58.11	by doing simple laboratory experiments.
00:07:00.20	Now, there's a related question, which is shown down here.
00:07:06.03	If there is life out there,
00:07:07.25	is it likely to be pretty similar to what we're familiar with on our planet?
00:07:16.12	Will life that evolved independently elsewhere have the same
00:07:23.25	fundamental kind of biochemistry?
00:07:25.24	Will it be cells that are living in water,
00:07:29.00	using if not RNA and DNA, some nucleic acid to mediate heredity?
00:07:35.20	Will they use protein-like molecules to carry out biochemical functions?
00:07:41.18	Or could there be forms of life that are actually much different, much more diverse,
00:07:49.14	maybe using completely different kinds of molecules to mediate heredity
00:07:52.25	and to mediate function?
00:07:55.04	Or even forms of life that live in very different environments,
00:08:00.06	for example, in solvents other than water.
00:08:03.23	Again, this is the kind of thing that we can address by going into the lab
00:08:09.17	and doing simple experiments, and trying to build structures,
00:08:12.26	and assess the possibility of having living systems in
00:08:18.09	different kinds of environments and with different molecular bases.
00:08:25.16	So, let's try to think, then,
00:08:30.21	about how we can deduce something about early forms of life.
00:08:37.04	After all, if we want to experimentally investigate the beginnings of life,
00:08:41.26	we have to have some idea, some kind of conceptual model,
00:08:45.22	of what very primitive forms of life looked like.
00:08:50.17	And this has been a very difficult thing for people to think about,
00:08:55.03	because we're so biased by our view and our understanding of modern life.
00:09:00.25	So if we look at modern cells, they're incredibly complicated:
00:09:05.16	Just a lot of moving parts, very elaborate structures,
00:09:09.14	such as you can see here in this elaborate structure in a eukaryotic cell,
00:09:15.15	all the machinery involved in cell division.
00:09:19.00	If you go deeper and look at the underlying biochemistry,
00:09:23.09	if anything, it's even more complicated.
00:09:26.17	And this is just a small section of the chart of central metabolism,
00:09:32.09	so there are hundreds or thousands of enzymes that catalyze
00:09:36.22	all of the metabolic reactions that are required for cells to grow and divide.
00:09:43.10	Even the general organizational structure of modern cells is very complicated,
00:09:51.10	in the sense that it's highly self-referential.
00:09:54.24	So every aspect of this process,
00:09:59.03	this central dogma (the transmission of information from DNA to RNA
00:10:03.10	to proteins and then down to building structures with function),
00:10:08.21	every part of that depends on all the other parts.
00:10:12.12	So for example, the replication of DNA requires DNA,
00:10:16.14	but it also requires RNA and proteins, the polymerases.
00:10:20.11	The transcription of RNA requires DNA,
00:10:25.11	which is where the information's stored, but it also requires many proteins,
00:10:29.21	and it also requires many other RNA molecules.
00:10:33.02	And similarly, the formation of proteins occurs on a remarkably complex machine,
00:10:38.24	the ribosome, which is itself composed of RNA and proteins.
00:10:44.02	So, for decades, it was very hard for people to think of any reasonable way
00:10:51.07	in which such an internally self-referential system could emerge
00:10:57.25	spontaneously from a chemical environment.
00:11:01.16	And the answer to that really came from thinking about RNA
00:11:08.27	and the different things that it can do.
00:11:10.21	So this simplification in thinking came from the realization that RNA can not just
00:11:18.04	carry information but can also catalyze chemical reactions.
00:11:23.15	And that realization led immediately to the hypothesis that,
00:11:29.01	in primitive cells, RNA might be able to catalyze its own replication,
00:11:34.05	also carry out biochemical functions for the primitive cell.
00:11:39.10	And so then all you really need to think about is a cell with RNA molecules
00:11:45.14	encapsulated within some kind of primitive cell membrane
00:11:48.25	that itself could be a self-replicating structure.
00:11:52.08	So, the history of this idea actually goes back to the 1960s,
00:11:58.24	and three very smart people, Leslie Orgel, Carl Woese, Francis Crick,
00:12:05.05	hypothesized in part on the basis on the complex folded structure of tRNA,
00:12:13.01	that an early stage of life might've evolved RNA as the
00:12:19.01	sole macromolecular basis of evolved machinery.
00:12:24.25	And so, this lets you think of simple cells emerging with just a single biopolymer,
00:12:31.19	RNA, and that later on, as evolution
00:12:38.03	developed more complex cellular structures, information storage
00:12:42.14	became specialized in DNA,
00:12:44.18	and most functional activities because specialized as the job of proteins.
00:12:51.06	Now, although these ideas were put forth in rather elementary form in the 60s,
00:12:56.14	of course nobody took them seriously at the time,
00:12:59.21	because there was absolutely no experimental evidence for the idea
00:13:04.08	that RNA could catalyze chemical reactions.
00:13:06.23	At the time, people had just started to get very detailed,
00:13:11.19	high-resolution information about how proteins catalyzed reactions,
00:13:16.13	and the idea that a molecule like RNA could do the same thing seemed ludicrous.
00:13:22.26	So it wasn't until almost 20 years later,
00:13:25.05	with the work of Tom Cech and Sid Altman,
00:13:29.10	and the experimental demonstration that RNA molecules could actually
00:13:34.02	very effectively catalyze at least certain types of chemical reactions,
00:13:38.14	that people took this whole idea of an RNA-based early stage of life seriously.
00:13:45.00	And so that hypothesis, the "RNA world hypothesis,"
00:13:48.23	was really summarized by Walter Gilbert in an article in 1986,
00:13:57.18	and this has really become the foundation of a lot of thinking
00:14:02.12	about early stages in the emergence of life.
00:14:08.01	So, apart from the basic facts,
00:14:11.20	that RNA does and can catalyze chemical reactions,
00:14:15.04	is there any other evidence that early life might have been
00:14:19.17	based more exclusively on nucleic acids?
00:14:24.21	And in fact, there are several lines of circumstantial evidence.
00:14:28.24	So one of them is the structure of many cofactors.
00:14:33.07	So here you see acetyl-CoA, just one example.
00:14:39.03	But the working part of the molecule is the thioester out here,
00:14:43.27	and for no obvious reason, there's a nucleotide at the other end.
00:14:48.13	And really the only way to make sense of that is the nucleotide is a "handle,"
00:14:53.11	either a relic of a primitive ribozyme
00:14:56.24	or something that was easy for primitive ribozymes to grab hold of and thereby,
00:15:04.10	using this cofactor, catalyze reactions in a thioester-mediated way.
00:15:11.14	Now there are other examples.
00:15:14.21	Here is vitamin B12, another very important catalyst.
00:15:20.24	Its working part is this complex corrin ring,
00:15:25.07	but down here you see, again, a nucleotide.
00:15:29.22	What's it doing there?
00:15:30.28	It's probably another relic of the RNA world,
00:15:34.02	when all of this complicated biochemistry was being catalyzed by RNA enzymes.
00:15:40.12	Yet another example is the very way that the substrates for
00:15:45.25	DNA synthesis are made, and they're not made de novo,
00:15:50.29	as you might expect if DNA came first.
00:15:53.27	They're actually made from preexisting ribonucleotides,
00:15:58.02	and so the transformation of ribonucleotides to deoxynucleotides
00:16:03.17	is catalyzed by the enzyme ribonucleotide reductase.
00:16:08.13	And this unusual synthetic pathway can be viewed as the relic of the fact that,
00:16:17.04	early in time, metabolism and RNA synthesis used ribonucleotides,
00:16:23.25	and only later when DNA was invented or evolved,
00:16:29.10	was there was requirement to make deoxynucleotides,
00:16:32.15	and so they're from the closest available substrate.
00:16:38.03	Finally, perhaps the most important and dramatic piece of evidence
00:16:44.14	for the early role of RNA in primitive forms of life
00:16:50.06	is the actual structure of the ribosome.
00:16:53.21	And so this is a slide from Tom Steitz showing a
00:16:57.27	view into the active site of the large subunit.
00:17:02.23	So this is the peptidyl transferase center,
00:17:05.06	and this little green structure in here is a transition state analogue
00:17:09.17	that marks it at the place in this giant machine where the chemistry is happening.
00:17:14.28	And what you can see is that it's these gray squiggles,
00:17:17.29	which are the RNA, that completely make up that active site.
00:17:23.23	So all proteins are generated by an RNA machine,
00:17:29.19	the RNA central region of the ribosome itself.
00:17:34.25	So again, this only makes sense in terms of an early stage of biochemistry
00:17:40.00	dominated by RNA functions, which then over time evolved the ability
00:17:45.15	to make proteins, which are now so important in all modern biochemistry.
00:17:52.05	So, if we want to understand the origin of life,
00:17:57.03	what we need to think about is not simply how to make
00:18:02.14	these incredibly complex modern cells, but we need to think about how to go from chemistry
00:18:07.23	to very simple, RNA-based cellular structures.
00:18:13.08	So, what would the process look like?
00:18:16.04	What's the broader picture?
00:18:17.17	When did this all happen on the early Earth?
00:18:20.17	So, what was the timeframe in which these events took place?
00:18:25.07	This is a slide from a review by Gerald Joyce, and it summarizes
00:18:30.02	the broad sweep of events that were important in the origin of life.
00:18:34.20	So we actually need to think of everything from planet formation,
00:18:38.14	the beginning of the Earth itself around 4.5 billion years ago;
00:18:44.07	over time as the Earth cooled, water could condense,
00:18:48.01	we have a stable hydrosphere, we have liquid water on the surface;
00:18:52.06	following that, increasingly complicated organic chemistry going on,
00:18:57.08	probably in many different environments on the early planet;
00:19:01.00	and then somehow that led up to the synthesis of RNA
00:19:06.09	or RNA-like molecules on the Earth,
00:19:09.13	which could start to carry out biochemical functions inside primitive cells;
00:19:14.24	and then eventually lead to the emergence of much more complicated cells
00:19:19.29	that would be biochemically similar to modern life.
00:19:23.14	Now, the first really good evidence we have about
00:19:27.04	the appearance of modern microbial life is roughly 3.5 billion years ago,
00:19:33.17	so there's a billion-year interval between the formation
00:19:38.17	and cooling of the planet and the first good evidence for life.
00:19:43.21	And basically, we have very little hard evidence about
00:19:48.00	where all of these important events that led up to life emerging from chemistry,
00:19:53.01	when they actually happened.
00:19:55.03	And that goes along with the fact that we have very little concrete evidence
00:19:59.25	concerning the environments in which those transitions took place.
00:20:04.27	So, this is one of the difficult aspects of studying this question.
00:20:09.12	We can't actually go back,
00:20:10.28	we can't know for sure what the early environments were really like,
00:20:16.13	we'll never know exactly what really happened.
00:20:19.15	So what's our goal in studying these questions?
00:20:23.00	What we're trying to do is really come up with a plausibly realistic
00:20:29.16	sequence of events so that we understand all of the transitions
00:20:35.00	throughout this whole pathway,
00:20:37.05	and we'd like to understand a complete pathway,
00:20:38.29	from planet formation through early chemistry,
00:20:41.28	more complicated organic chemistry,
00:20:44.05	up to the assembly of those building blocks into the first cells,
00:20:48.29	the emergence of Darwinian evolution,
00:20:51.04	and then the gradual complexification of early life leading up to what we see now.
00:20:58.10	So, let's look a little bit more closely at the chemical steps.
00:21:03.23	So in broad outline, what we think happened is that you
00:21:07.17	start off with very simple molecules such as shown up here.
00:21:14.02	There's still a lot of debate about the nature of the early atmosphere.
00:21:20.00	Scientific opinions have gone back and forth in terms of
00:21:23.09	the structure and how reducing that atmosphere was.
00:21:27.26	But it's also been recognized that there could be very important local variation,
00:21:32.22	so even if the atmosphere was globally fairly neutral
00:21:38.20	or perhaps mildly reducing or mildly oxidizing,
00:21:41.16	there could be local environments that were more reducing.
00:21:46.14	That, together with the input of various forms of energy
00:21:51.21	(for example, from electric discharges, lightning,
00:21:56.06	high-energy ultraviolet radiation, ionizing radiation)
00:22:01.08	these are all forms of very energetic processes that can basically
00:22:06.15	rip these small starting molecules apart into atoms,
00:22:11.26	which can then recombine to generate high-energy intermediates
00:22:15.17	with multiple bonds, molecules like cyanide and acetylene,
00:22:20.19	formaldehyde and so on.
00:22:22.18	And these molecules can then start to interact with each other
00:22:26.20	and gradually build up more complex intermediates,
00:22:29.13	ultimately leading to the things we really care about:
00:22:33.10	the lipids that will make membranes and vesicles,
00:22:37.25	the nucleotides that will assemble into genetic molecules like RNA,
00:22:42.16	amino acids that can assemble into peptides,
00:22:45.29	which may also play roles in primitive cells.
00:22:49.10	And somehow, and this is the question that my lab has really been focused on,
00:22:53.12	somehow all of these molecules come together
00:22:56.17	and assemble into larger structures that look and act like cells
00:23:01.10	that can grow and divide.
00:23:04.04	So how could that possibly happen,
00:23:06.17	and what would such a primitive cell look like?
00:23:09.24	So here is a schematic version of the way that we're thinking
00:23:13.21	about a primitive cell, or "protocell."
00:23:17.11	So what we think are the important components of a primitive cell
00:23:22.14	are basically two things:
00:23:25.01	a cell membrane and inside,
00:23:28.10	some kind of genetic material, maybe RNA, maybe DNA,
00:23:32.05	maybe something simpler, something more stable, we're not really sure.
00:23:37.12	So the first question is how could you assemble such composite structures?
00:23:43.23	So we want to be have a membrane boundary
00:23:46.13	that can keep important molecules encapsulated within
00:23:51.06	and essentially provide a distinction between the cell itself
00:23:54.22	and the rest of the universe.
00:23:57.05	We need to understand how these two components self-assemble,
00:24:02.09	how they come together.
00:24:04.07	And it actually turns out that that part is all fairly straightforward.
00:24:09.26	Self-assembly processes are critical in thinking about all of the steps,
00:24:15.12	and there are multiple different ways in which these components
00:24:19.06	can be made and can come together.
00:24:22.08	A much harder question and more interesting is:
00:24:28.08	Once you have structures like this,
00:24:30.16	how can they grow and then divide without any of the
00:24:34.17	complicated biochemical machinery that's present in all of modern life?
00:24:40.25	So since we're talking about the origin of life,
00:24:43.00	then by definition we didn't have highly evolved biochemical machinery around.
00:24:48.21	So it's sometimes hard to think about these problems
00:24:51.17	because modern cells use so much biochemical machinery
00:24:56.11	to mediate the process of cell growth and cell division.
00:25:00.12	It's almost hard to think of how could that be driven
00:25:06.04	by simple chemical and physical processes.
00:25:10.07	But that's in essence what we need to figure out
00:25:13.00	in order to understand this process.
00:25:15.07	There's no machinery around,
00:25:16.18	so we have to identify the chemical and physical processes
00:25:20.14	that will drive growth and then mediate cell division.
00:25:25.11	So that applies not only to the membrane,
00:25:27.11	but also the genetic material, whether it's RNA or something else.
00:25:31.13	There have to be simple chemical processes
00:25:35.16	that will drive the copying of that information,
00:25:38.12	that will allow the strands to separate
00:25:41.06	so that another round of copying can take place,
00:25:44.05	and that will allow that replicated material to be distributed into daughter cells.
00:25:50.10	So if we can identify chemical and physical processes that do all of that,
00:25:56.25	we would have a situation where essentially the environment
00:26:00.03	is driving a cycle of growth and division
00:26:04.15	that brings us back to this stage,
00:26:07.05	and you can go around and around that cycle again and again,
00:26:12.05	and that would be just very similar to the way in which
00:26:16.22	modern cells grow and divide.
00:26:18.23	The information within would be propagated and transmitted
00:26:22.23	from generation to generation,
00:26:25.08	and the important thing in terms of the emergence of Darwinian evolution is that,
00:26:31.00	during that continuous process of replication,
00:26:35.07	of course mistakes would be made.
00:26:38.18	Over time, more and more of sequence space would be surveyed,
00:26:43.28	and eventually we think, some sequence would emerge that did something
00:26:48.03	useful for the cell as a whole.
00:26:50.14	As soon as that happened, that sequence,
00:26:54.00	by conveying an advantage to its own cell,
00:26:57.24	whether in terms of growth rate or the efficiency of cell division
00:27:03.00	or the efficiency of survival,
00:27:05.22	it would have an advantage and it would gradually over generations
00:27:08.28	take over the population.
00:27:11.09	And so that is really the essence of Darwinian evolution.
00:27:15.05	You have a change in the genetic structure of the population as a result of natural selection.
00:27:21.01	And that is precisely what we would like to see
00:27:24.03	emerge spontaneously in our laboratory experiments.
00:27:27.17	We want to start with a chemical system
00:27:30.18	and watch it transition into the emergence of real Darwinian
00:27:35.18	evolution at a very simple level.
00:27:39.20	So, let's step back again and think about how all of these
00:27:43.25	molecules would be made in the environment of a primitive planet.
00:27:49.02	And of course, the first breakthrough in this research program
00:27:54.03	was the famous Miller-Urey experiment,
00:27:57.23	in which a mixture of reducing gases was subjected to an electric spark discharge,
00:28:02.10	and the products were analyzed.
00:28:04.12	And amazingly, in that mix of products were many of the amino acids,
00:28:11.19	which are major components of the proteins of modern cells.
00:28:16.28	So that was really a revelation.
00:28:19.29	It really took people by surprise that the building blocks of biological structures
00:28:28.05	could be generated in such an easy manner.
00:28:33.01	Now, in fact that result was so powerful
00:28:36.08	that it might have actually been a little bit distracting.
00:28:40.15	Probably the really important thing that's made
00:28:43.19	in this kind of experiment is not amino acids per se,
00:28:48.03	but high-energy intermediates like cyanide and acetylene.
00:28:53.06	Those are the kinds of molecules that can assemble in
00:28:57.25	subsequent steps into nucleotides, the building blocks of genetic materials.
00:29:07.16	Those molecules are thought to have been made in primitive environments,
00:29:14.11	so that was an electric discharge experiment,
00:29:16.08	which is very analogous to the kinds of lightning displays
00:29:21.12	that you get in volcanic scenarios.
00:29:24.12	So this is the lightning that's going on in the ash cloud
00:29:29.14	of a currently erupting volcano in southern Chile.
00:29:34.02	So since the early Earth was thought to be highly volcanically active,
00:29:38.15	this seems like a very reasonable scenario.
00:29:42.13	What about some of the other molecules that we need
00:29:44.22	to build our primitive early cell?
00:29:50.29	We need to have lipid-like molecules, amphiphilic molecules
00:29:55.29	that can self-assemble into membranes and generate compartments spontaneously.
00:30:00.16	So these are molecules that are amphiphilic:
00:30:03.07	They have one part that likes to be in water,
00:30:05.26	and another part that doesn't like to be in water.
00:30:09.11	And the way that those preferences are balanced
00:30:12.29	is by forming membranes in which the nonpolar parts are on the inside
00:30:17.29	and the polar parts of the molecule face out into the water.
00:30:21.16	So it turns out that it's actually, again,
00:30:24.19	very easy to make molecules like that in a variety of different scenarios.
00:30:30.02	In fact, Dave Deamer and his colleagues showed that you can
00:30:34.08	extract molecules from the Murchison meteorite
00:30:37.11	(it's one of these carbonaceous chondrite meteorites that's rich in organic materials),
00:30:41.23	you can extract molecules that will self-assemble into a vesicle,
00:30:46.10	as you can see here.
00:30:48.04	So they spontaneously make membrane sheets that close up into small vesicles.
00:30:53.19	Here's another example.
00:30:56.00	This is an experiment that was done to
00:31:00.11	mimic processes going on in interstellar molecular clouds,
00:31:05.03	where you have various gasses that have condensed
00:31:07.22	on the surface of silica particles.
00:31:10.11	They're subjected to irradiation by ultraviolet light and ionizing radiation.
00:31:16.03	So if you make ices like that in the laboratory,
00:31:19.18	subject them to ultraviolet radiation,
00:31:22.29	you get a lot of complicated chemistry going on,
00:31:25.01	and then in that vast mix of products,
00:31:28.28	you can extract molecules which again will form membranes
00:31:32.01	and self-assemble into these vesicle compartments.
00:31:37.10	Here is yet another scenario.
00:31:39.03	This is a hydrothermal synthesis done by Bob Hazen and Dave Deamer.
00:31:46.05	Again, in hydrothermal processing,
00:31:50.00	you can grow carbon chains with oxygenated groups
00:31:55.05	such as carboxylates at the end,
00:31:57.05	and these self-assemble into membranes and make many compartments,
00:32:02.03	as you can see in this beautiful image.
00:32:05.29	So, what would be an example of an early Earth
00:32:09.29	environment where something like this could take place?
00:32:14.03	There are a series of experiments from the Simoneit Lab that
00:32:19.14	suggest that hydrothermal synthesis could happen deep down
00:32:24.28	in regions with high temperature and high pressure,
00:32:29.25	on the surface of catalytic minerals such as transition metal sulfides or oxides,
00:32:35.27	and those reactions would basically turn hydrogen and carbon monoxide
00:32:40.27	into fatty acids and related compounds.
00:32:45.05	So the next slide here is a movie that was prepared by Janet Iwasa,
00:32:50.29	that illustrates this process.
00:32:52.15	So we're going deep into the Earth,
00:32:54.23	down through the water channels of a geyser,
00:32:59.00	and here we're looking at the surface of these catalytic transition
00:33:03.28	metal minerals, and you can see hydrogen and carbon monoxide molecules
00:33:08.24	bouncing around the surface, and the mineral is catalyzing
00:33:13.11	their assembly into chains, which eventually will be released and float up,
00:33:21.00	and they'll be caught up in the flow of water
00:33:23.02	and thereby brought to the surface, where you can imagine these fatty acids,
00:33:28.15	fatty alcohols, and related molecules being aerosolized
00:33:32.22	and concentrated in droplets and perhaps even
00:33:35.20	building up into large deposits on the land surface.
00:33:41.05	So it doesn't seem like the prebiotic assembly of molecules
00:33:46.07	that could spontaneously form membrane vesicles is all that difficult.
00:33:53.03	It's definitely an understudied area of prebiotic chemistry, it needs more work,
00:33:57.16	but it looks, I think, reasonably plausible.
00:34:01.13	So the most prebiotically likely molecules
00:34:04.15	would be things like capric acid that you see down here.
00:34:08.24	Short chain, saturated fatty acids.
00:34:12.15	So we do experiments in the lab with molecules like this,
00:34:16.28	but we also use longer chain, unsaturated molecules
00:34:22.07	like myristoleic acid and oleic acid,
00:34:25.05	as model systems because they're just generally easier to work with.
00:34:29.16	So what happens if you just take one of these fatty acids
00:34:34.20	and shake it up in water with some salt and buffer?
00:34:38.06	Is it hard to make membranes? No.
00:34:40.20	What you can see if that you just spontaneously make vesicles
00:34:47.27	in a huge variety of complex structures, a huge range of sizes,
00:34:53.25	all the way from 30 microns (this large vesicle)
00:34:57.19	to many, many smaller vesicles ranging down to 30 nanometers.
00:35:02.29	Many of these vesicles are composed of multiple sheets of membrane,
00:35:08.04	so stacks of membranes.
00:35:10.04	You can see some of these vesicles have smaller vesicles inside them.
00:35:14.17	So it's a very heterogeneous, complex mixture.
00:35:19.29	Now, the other thing that's really important about this is that these vesicles,
00:35:25.25	these membranes, have very, very different properties
00:35:29.02	from modern biological membranes.
00:35:31.26	Modern membranes are basically evolved to be good barriers,
00:35:37.09	so that cells can control the flow of all molecules in and out
00:35:42.04	using complicated protein machines.
00:35:47.26	For a primitive cell, you wouldn't want a situation like that...
00:35:51.03	that would be suicidal.
00:35:52.15	These molecules have to let stuff get across,
00:35:55.03	they have to have dynamic properties
00:35:56.26	that can let them grow and equilibrate.
00:36:00.16	So the next slide is actually a movie, again prepared by Janet Iwasa,
00:36:05.13	to illustrate the dynamic properties of these vesicles,
00:36:09.29	which are so different from modern membranes.
00:36:13.06	And so what you can see here is, first of all,
00:36:15.08	the motion on the surface, a lot of oscillations, diffusion.
00:36:20.27	In the membrane itself, these molecules, the individual molecules
00:36:25.05	are rapidly flip-flopping back and forth from inside to outside,
00:36:29.23	they're constantly entering the membrane, leaving the membrane,
00:36:34.16	so there's a lot of exchange reactions that are
00:36:37.29	going on on very rapid timescales, on the order of a second or less.
00:36:42.23	So they're very dynamic structures.
00:36:44.23	And these dynamic motions are also probably
00:36:49.09	very important in terms of permeability.
00:36:51.26	They allow the formation of transient defects in the membrane,
00:36:55.20	which let molecules get across spontaneously
00:36:58.21	without any complicated machinery.
00:37:02.19	There's another property of these vesicles which I find quite fascinating.
00:37:09.02	So as you saw in the illustration, the molecules that make up
00:37:12.28	any given vesicle come and go and therefore exchange between vesicles
00:37:19.07	on the timescale of roughly a second.
00:37:22.09	In this slide what you see are two populations of vesicles
00:37:25.16	that were labeled with phospholipid dyes,
00:37:28.18	so they're not exchanging between vesicles.
00:37:31.18	The picture here was taken after about a day,
00:37:35.18	and so you can see that they haven't all just fused and mixed up,
00:37:39.01	there are still red vesicles and green vesicles.
00:37:42.11	And yet we know from our other experiments that the molecules
00:37:45.27	that make up any one of these vesicles are changing
00:37:50.29	on a very rapid timescale, yet the structures themselves
00:37:54.23	maintain their identity on the timescale of weeks or months.
00:38:02.03	What about the nucleic acids then?
00:38:05.05	We've talked a lot about the building blocks of membranes,
00:38:07.27	the way they self-assemble,
00:38:09.12	and the properties of the membranes that they assemble into...
00:38:12.27	let's go back to the genetic materials and think about
00:38:15.21	what kinds of building blocks we need to assemble molecules like RNA.
00:38:22.06	Now, again, we have a difference between the molecules used in modern life...
00:38:28.12	so these of course are nucleoside triphosphates,
00:38:32.11	they're almost ideal substrates for a highly evolved cell
00:38:37.13	with very, very powerful catalysts.
00:38:41.15	These molecules are kinetically trapped in a high-energy state.
00:38:47.13	They don't spontaneously act very well at all,
00:38:51.29	so it takes a very sophisticated catalyst to
00:38:54.27	use molecules like this as a substrate.
00:38:57.26	They're also of course very polar, the triphosphate group is highly charged,
00:39:02.16	and that prevents these molecules from leaking out of the cell,
00:39:06.23	which would be a bad thing.
00:39:08.14	On the other hand, in a primitive cell,
00:39:11.19	if you imagine that substrates, food molecules,
00:39:15.05	are being made in chemical processes out in environment,
00:39:19.15	it needs to be possible for those molecules to get across the membrane
00:39:23.17	spontaneously and get into the interior of the cell.
00:39:27.18	So then we to think about different kinds of substrates,
00:39:31.19	molecules that are less polar so they can get into the cell,
00:39:36.25	and more chemically reactive, so that they can polymerize without the need
00:39:43.15	for very sophisticated, advanced, highly evolved catalysts.
00:39:47.24	And so molecules like this were first made by Leslie Orgel
00:39:52.20	and his students and colleagues 20-30 years ago,
00:39:57.13	and studied in quite a bit of detail as models for the early replication of RNA.
00:40:06.17	So, this brings us back to the question of
00:40:12.02	what was the first genetic material?
00:40:14.17	Was it RNA, in fact?
00:40:17.14	Or is RNA so complicated,
00:40:19.24	or its building blocks so hard to make,
00:40:23.03	that life more likely began with something simpler,
00:40:27.18	something easier to make,
00:40:29.12	maybe something more stable that could accumulate,
00:40:31.24	like DNA for example?
00:40:34.16	So this is an area of active debate and investigation,
00:40:39.10	we really don't know the answer to this question,
00:40:43.13	but lots of people are doing experiments and trying
00:40:45.22	to work out chemical pathways leading up to RNA,
00:40:49.09	for example, the Sutherland Lab in the UK has made a lot of progress in this area.
00:40:55.16	We're studying how these molecules could be assembled and replicated.
00:41:01.27	So one of the satisfying thinks about thinking about RNA
00:41:04.22	as the first genetic material,
00:41:06.10	is that we actually have two different chemical physical processes
00:41:12.29	that can lead to the polymerization of activated building block
00:41:17.01	into long RNA chains.
00:41:19.16	The first of these was discovered by Jim Ferris, working with Leslie Orgel,
00:41:26.27	and that was the discovery that a common clay mineral
00:41:30.20	known as montmorillonite can catalyze the assembly of
00:41:34.19	nucleotides into RNA chains.
00:41:37.04	So this illustrates the structure of this clay,
00:41:39.25	it's a layered hydroxide mineral.
00:41:43.03	In between the layer, the aluminum silicate layers,
00:41:47.21	there's water, and in these inner layers,
00:41:50.27	organic molecules can accumulate, and when they're brought close together,
00:41:54.23	they can react each other and start to polymerize.
00:41:58.25	So here is some of the experimental data.
00:42:01.29	So over a period of days, you start off with small chains,
00:42:07.08	and then gradually they get longer and longer, up to lengths of roughly 40,
00:42:12.18	and in more recent experiments up to 50 or 60, nucleotides long.
00:42:17.27	So I wanted to illustrate that with this movie,
00:42:20.16	another one of Janet Iwasa's animations,
00:42:24.16	to show roughly how we think this works.
00:42:27.15	So these chemically activated building blocks like to stick to the
00:42:31.13	surface of the clay mineral,
00:42:33.20	and when they stick in such a way that they're lined up with each other,
00:42:38.05	they can react and assemble a chemically linked backbone,
00:42:43.16	as you see here.
00:42:47.28	Now, there is another process that can do that same thing,
00:42:51.05	which is very interesting because it's so counterintuitive.
00:42:54.05	It turns out if you take these same building blocks and just have them
00:42:57.29	in a dilute solution and put that on your bench, nothing happens.
00:43:03.10	But if you take that same solution and put it in the freezer
00:43:07.08	and then come back the next day, you'll find RNA chains.
00:43:11.20	Why is that?
00:43:13.09	It's because when water freezes and forms ice crystals,
00:43:16.26	that during the growth of the ice crystals,
00:43:19.12	other molecules (solutes) are excluded from the growing crystal,
00:43:23.23	and so they end up concentrated as much as a thousand fold
00:43:27.21	in between the grains of ice,
00:43:31.04	and so when they're so concentrated, again they can react and polymerize.
00:43:35.08	So having two different processes that can lead the assembly of
00:43:38.23	RNA chains is actually a very satisfying thing...
00:43:41.29	that's something we look for in this field,
00:43:43.29	if there's more than one way of solving a problem,
00:43:47.04	it makes the whole solution seem more robust.
00:43:51.15	Now, the hardest problem, perhaps,
00:43:54.07	is once you've got RNA chains like this, how can they be replicated?
00:43:59.16	So much of our early thinking was based on RNA catalysis,
00:44:04.19	and in fact the whole basis of the RNA world is the idea
00:44:07.16	that RNA can act as an enzyme that could catalyze its own replication.
00:44:13.18	And Dave Bartel, when he was a student in my lab many years ago,
00:44:19.17	actually evolved an RNA enzyme with a catalytic activity,
00:44:25.11	that can ligate together pieces of RNA.
00:44:29.04	And Dave subsequently evolved this ribozyme into an even more complex structure
00:44:35.07	that is really an RNA polymerase made out of RNA.
00:44:40.09	Now, that's a very impressive proof of principle,
00:44:43.26	but unfortunately, despite many advances over the years,
00:44:47.26	we're still far from having an RNA molecule that can
00:44:51.09	completely catalyze the copying of its own sequence.
00:44:55.28	So, what we've decided to do is to actually again step back
00:45:01.07	and try to look at the underlying chemistry
00:45:04.03	and see if there might be ways of adjusting or playing
00:45:10.05	with the chemistry of RNA polymerization that would simplify this problem.
00:45:17.04	Ideally, perhaps we will be able to find a complete chemical process
00:45:22.00	that could drive RNA replication.
00:45:25.15	Now, that's a very difficult task,
00:45:28.16	Leslie Orgel and his colleagues worked on that for many years,
00:45:32.17	got partway to a solution,
00:45:34.22	but were never able to have complete cycles of replication.
00:45:39.23	But we have decided to go back and look at some model systems
00:45:44.16	and see if we can get some clues as to how to approach that problem,
00:45:48.24	perhaps in some fresh ways.
00:45:51.13	So, just to illustrate what we're really after,
00:45:53.24	I'm going to show another of Janet Iwasa's movies,
00:45:57.16	and so what you see here is an RNA template, a single-stranded molecule,
00:46:02.00	floating in a solution full of activated monomers,
00:46:05.05	which then find their complementary bases,
00:46:07.26	so they use Watson-Crick base pairing to line up on the template,
00:46:11.06	and then they basically click together to build up a complementary strand,
00:46:16.16	generating a duplex product.
00:46:20.25	So we're after some kind of simple,
00:46:25.03	chemical system that would drive that process very efficiently.
00:46:30.18	So, if we could get to that point,
00:46:33.06	then we would be back to being able to assemble this kind of model system,
00:46:39.10	a model protocell, composed of a membrane compartment boundary
00:46:45.07	and replicating genetic material on the inside.
00:46:50.28	Now, when we're thinking of a complex composite system like this,
00:46:56.13	the question often arises as to,
00:46:58.06	well, why really bother with the membrane compartment?
00:47:01.10	Why not just let the RNA molecules replicate in solution?
00:47:05.17	And one way of thinking about that is that,
00:47:09.22	for Darwinian evolution to emerge,
00:47:12.27	molecules that are in some way better than their neighbors
00:47:15.25	have to have an advantage for themselves.
00:47:19.01	So if we think about RNA replicases floating around in solution,
00:47:24.02	so these would be RNA molecules that catalyze the replication
00:47:27.24	of another RNA molecule,
00:47:30.14	it doesn't really help if you have a mutation which is faster or more accurate,
00:47:37.23	if all it's doing is copying random, other RNAs
00:47:41.01	that it bumps into in solution.
00:47:44.01	It has to have an advantage for itself.
00:47:47.18	And the simplest way to imagine that happening
00:47:50.13	is to encapsulate these molecules within a vesicle,
00:47:54.20	so that they're always copying molecules that are related by descent.
00:48:01.03	Now, the self-assembly of these kinds of complex structures
00:48:06.22	is something that's actually quite simple.
00:48:09.28	So, at the lowest level,
00:48:12.26	the formation of a membrane vesicle can just encapsulate
00:48:16.01	whatever is there in the surrounding solution.
00:48:19.17	However, it's intriguing that there are ways of making the process more efficient,
00:48:24.02	and one of the most interesting ways of doing that is
00:48:28.05	to take advantage of that same clay mineral, montmorillonite,
00:48:31.25	that we've already seen can catalyze the assembly of RNA strands.
00:48:36.24	And so what you can see in this picture,
00:48:39.19	which was generated by Shelly Fujikawa and Martin Hanczyc
00:48:44.11	when they were in my lab about eight years ago...
00:48:47.03	what you can see is that we have here a clay particle,
00:48:51.15	which has RNA molecules bound to its surface,
00:48:55.21	so the orange color is a dye-labeled RNA,
00:48:59.02	and it turns out these clay particles can catalyze the
00:49:01.28	assembly of membrane sheets from fatty acids.
00:49:08.15	And what's happened here is that this clay particle has catalyzed
00:49:11.15	the assembly of this large surrounding vesicle
00:49:15.29	as well as the many smaller vesicles encapsulated within.
00:49:20.03	So what we now can see is that a single very common,
00:49:25.11	abundant mineral can catalyze the assembly of a genetic material,
00:49:30.17	it can catalyze the assembly of compartment boundaries (cell membranes),
00:49:34.08	and it can help bring them together.
00:49:36.13	So very intriguing as a way of simplifying the assembly of
00:49:39.14	cell-like structures on the early Earth.
00:49:43.02	Here's another picture: clay particle inside a vesicle.
00:49:48.01	Here the boundary is quite dramatically evident,
00:49:52.07	so this is a stack of many layers of membrane bilayers.
00:49:56.26	Here's yet another example where the large outer vesicle
00:50:00.15	is filled with hundreds of smaller vesicles, all assembled under
00:50:04.08	the catalytic influence of this clay particle in the middle.
00:50:10.11	So, assembling these things looks fairly simple.
00:50:14.02	What about the process of growth and division?
00:50:16.21	After all, that's what we really need to generate
00:50:19.07	cell-like structures that can propagate.
00:50:22.18	And at this point,
00:50:25.01	what I can say is that we've come up with a process that looks fairly robust.
00:50:31.09	We can start with vesicles and food in the form of fatty acid micelles.
00:50:37.16	They grow remarkably into filamentous structure,
00:50:42.13	which can then divide very easily into daughter cells,
00:50:45.19	and this generates a cycle that can go around and around indefinitely.
00:50:51.08	And in the next part of this lecture,
00:50:53.26	I'll go into much more detail about the nature of this process
00:50:57.09	and the mechanism by which this happens.
00:51:01.02	But, putting this cycle together with our
00:51:06.17	thinking about nucleic acid replication,
00:51:09.13	we can actually start to imagine what a
00:51:12.13	primitive cell cycle would have looked like.
00:51:15.12	And so this is shown in this figure from a Scientific American article
00:51:20.04	that I wrote with Alonso Ricardo from my lab,
00:51:23.03	and it summarizes some of our ideas about the ways in which
00:51:28.28	the early Earth environment might help to drive cell growth and division.
00:51:35.22	So the idea is that the general environment should be rather cold,
00:51:40.15	perhaps even an ice-covered pond,
00:51:44.24	something you might find in an arctic or alpine environment.
00:51:48.29	There are many examples on the modern Earth.
00:51:52.16	The reason for wanting a cold environment in general is that the
00:51:56.08	copying chemistry seems to go better at low temperatures.
00:52:01.06	The low temperature helps the building blocks
00:52:03.10	to bind to the template and facilitates the copying process.
00:52:07.10	But then we know that eventually, once copying is complete,
00:52:10.28	you have to get the strands apart so that you can
00:52:13.09	undergo another round of copying.
00:52:15.21	Simplest way for that to happen is to invoke high temperatures.
00:52:19.23	And so what we like to think about are
00:52:21.21	convection cells driven by geothermal energy;
00:52:26.12	so essentially in a hot spring type of environment,
00:52:30.13	you could have a pond that's mostly cold,
00:52:32.20	but every now and then, these particles would get caught up
00:52:35.01	in a plume of hot water rising from a hot spring.
00:52:39.01	They'd be transiently exposed to high temperatures
00:52:41.24	that would result in strand separation.
00:52:45.02	It also allows for a rapid influx of nutrients from the environment
00:52:50.02	to feed growth and replication through the next round.
00:52:54.08	And then that would generate a cycle in which the
00:52:57.25	entire process of growth and replication and division
00:53:01.07	is driven by fluctuations in the environment.
00:53:04.20	This is driving us to talk to geologists and to search
00:53:09.19	for analogues of this kind of environment on the modern Earth.
00:53:13.13	Here is a beautiful image of an Antarctic lake
00:53:18.19	in which you see stromatolites,
00:53:20.15	these mounds here are microbial growths on the surface,
00:53:25.18	and the reason that it's liquid is of course there is heat rising up from
00:53:29.18	below geothermally, so it's not a perfect analogue
00:53:34.15	of the scenario I described.
00:53:36.05	We'd like to find environments like this where there are hot springs
00:53:39.12	generating convection cells that could drive the whole cycle.
00:53:43.05	So that would be very satisfying if we could identify such environments.
00:53:48.29	So, what I've tried to show in this lecture is basically
00:53:54.13	the context of the environment and the chemistry
00:53:57.10	leading up to the assembly of primitive cells,
00:54:00.25	in a way that's plausible on the early Earth.
00:54:03.17	And what we'll head into in the next two parts
00:54:06.18	are a more detailed look at the chemistry of membrane assembly,
00:54:11.11	growth, and division;
00:54:12.16	and the chemistry of nucleic acid replication.
00:54:15.25	And all of this work is of course has been done through many
00:54:20.17	very talented students and postdocs in the lab
00:54:25.03	who you can see here on this slide.
00:54:28.13	Thank you.