15:02:28 I'm, I'm the only thing standing between you and your Friday afternoon libation so I try and make this quick. I've also brought a piece of fruit, if there's too much general introduction, come up, rather than.
15:02:39 Okay.
15:02:40 But I thought there should be at least some part of this is their students on a course here that should be at least some general introduction to evolution.
15:02:50 And so here's five. This is just to remind those of you especially physicists, that stars including our some own son have no non theological purpose, where whereas organisms are vehicles, designed or
15:03:10 strike that word from record involved in a way that can look suspiciously like design right and it's my personal belief that thinking anthropomorphic Lee about how organisms do things is actually useful.
15:03:24 As long as you remember to convert that thinking into what blind selection could have, how you could produce something that looks purposive in the sort of human sense, but organisms or vehicles that are evolved to disperse genes through time and space
15:03:39 so there are two obligatory quotations there's the Penske one.
15:03:46 But nothing in biology, makes sense except in the light of evolution.
15:03:50 But there is a sort of inverse statement, which is nothing in evolution makes sense except in the light of biology because evolution works on biological systems and biological systems have constraints which evolution is applied to either obey or find
15:04:09 crafty ways to circumvent.
15:04:14 Hey, This is what we're missing.
15:04:16 Sorry, different things showing my screen. This is
15:04:22 lived under a rock. This is the TARDIS in which doctor who travels backwards in time and space. So, if we had this device. This talk would be unnecessary.
15:04:32 Okay, an evolution two panelists on three things. Inheritance the offspring are more like their parents typically than they are anyone else mutation which generates variation and selection which means some genotypes leave more project.
15:04:51 I should also again sort of obligatory disclaimer disclaimer.
15:04:55 There's two sort of classes of evolution. There's evolution which is adaptive that is driven by selective pressure.
15:05:05 And there's evolution which is purely neutralist sort of Cameron stuff the disciples of Mike Lynch, and the like. I'm going to talk entirely about adaptive evolution but you shouldn't forget that in a general sense evolution just refers to changes in
15:05:20 the frequencies of genes and their linkage to each other in population. and that doesn't have to be driven by selection, it can be driven entirely by stochastic, but it's just, typically that sort of change is slow and adaptive change is often quite fast.
15:05:39 We have trouble understanding evolution.
15:05:43 Because it's all if certainly if you're interested in how things evolved to be the way they are now because it's already happened. so we don't get watch it.
15:05:51 It's dominated by a succession of very rare events.
15:05:57 If you want to compare different trajectories. The very rare events.
15:06:02 It is typically the relative probability of those trajectories determines the evolutionary path. And those relative probabilities are difficult to assess.
15:06:14 And last but not least again in terms of worrying about evolution that's already happened. We have tools for historical inference.
15:06:21 We have fossils.
15:06:23 And in the modern world we have the sequence of proteins, and the DNA that encodes them.
15:06:28 But the influences that are made from those sequences are imperfect. So for example, you can reconstruct ancestral proteins.
15:06:37 As far as I can tell, it is guaranteed that any ancestral protein reconstruct is not the actual ancestral protein, was there because it's a probabilistic exercise, and there are enough sequences that have high scores in this landscape that none of them
15:06:52 is going to actually be the one that was there at the time. The hope is, if you make several of them will sort of average across that space and make a reasonable facsimile of what was there.
15:07:12 I'm going to argue that there are three sort of modes of evolution. And one is continuous gradual change, and examples from the real world or antigenic drifting influence our antibody maturation in the human immune system.
15:07:27 And in terms of experimental evolution faster growth, water, local standard environments and many different people, including some people from have evolved east to grow.
15:07:47 Okay, and it grows a little bit faster. When you.
15:07:52 Bunting he sacrificed service UI to grow faster in the standard environment in which geneticists have been growing it for low the last 50.
15:07:52 The second is the appearance of novel trait.
15:07:55 So in the real world, things like photosynthesis the circadian clock cancer which is an unfortunate form of novelty experimentally in my lab we've evolved multicellular clarity we've evolved a circadian oscillator, things that at least the bark restraint,
15:08:14 strain, we started with did not have and these are qualitatively, I would argue rather than qualitatively different properties.
15:08:21 And last but not least, there's a thing called evolutionary repair.
15:08:27 In the real world, this means that you can look at some class of organisms like you can't read it.
15:08:32 And you can argue by sequencing genomes that they have certain universal features.
15:08:38 One of those for example is this device called the interface promoting complex, the tags proteins for destruction at the end of mitosis.
15:08:47 Initially when you carry it through a sequence, everyone had this.
15:08:50 But when people sequence God aligned Leah, which is a unicellular produce some reason why if you go hiking, you have to filter your water so it's not to get unpleasant diarrhea.
15:09:02 When the genome with this organism was sequence, there is no interface promoting complex. It's a multi subunit complex, none of the sub units are there.
15:09:12 When the people who sequence that tried to publish their paper they were told they had sequence poorly. And if they look more carefully they would find these things and they look much more careful.
15:09:21 They're just not there. and that's true and sisters.
15:09:32 And there's an experimental version of that that we've done a fair amount of, which is we take a gene which is important, but not essential.
15:09:42 And in the budding East turns out you can make the interface promoting complex important but not essential by making.
15:09:49 We haven't done it for that but we've done it for things involved in self clarity and DNA replication chromosome segregation cells grow worse.
15:09:59 And now you can involve them and ask them to grow better basically recover, to the evolutionary fitness of their wild type ancestors and then track down what is changed.
15:10:10 And what's interesting is, at least in our hand, it's this class of experiment that is the easiest to understand from cell biological point of view that the mutations yet, or in things we know about and when we do reconstructions.
15:10:23 Not only can we explain quantitatively fitness increases but we sort of understanding cell biological sense why things work.
15:10:32 Hey, and so this is just a sort of cartoon version of gradual evolution.
15:10:40 So, Here's your micro organism of choice.
15:10:44 And so these are experiments where you allow them to proliferate you hope interesting mutations rise.
15:10:53 You hope they survive the next evolution.
15:10:57 And gradually increasing frequency.
15:11:02 And so this preeminent example of this 70,000 generations of eco I adapting to a substantially lower glucose concentration and its present standard medium so this is rich links these long term experiment.
15:11:18 Evolutionary novelty is acquiring qualitatively new fitness increasing property.
15:11:26 It's extremely hard to make a rigorous definition of this.
15:11:30 So I wrote a piece about this recently an appeal to the Supreme. It's not a Supreme Court it's a state court opinion about the definition of pornography where learning justice, a pint they knew it when they saw it.
15:11:45 And that's a, that's an extremely inadequate definition but it's a little hard to come up with something that is either rigorous quantitative, but I'm just representing it here.
15:11:57 But now the new, square rather than circular.
15:12:03 And in evolution, this is the thing in a sense, this is the ammunition for the Intelligent Design crowd, because there are things that they are you like clocks, like motors like photosynthesis, that they are you could not have been produced by a small
15:12:21 series of successively improving.
15:12:25 I don't buy that argument for a second.
15:12:29 So the last thing
15:12:33 I will say, it's not quite the last thing about general thing is is that rates matter, in terms of how you get to improved fitness especially mercury depends on the different ways that you can get there so the fastest way of getting there.
15:12:50 And when you talked about this yesterday in, in her experiment is you can lose or gain a chromosome.
15:12:57 This happens to the frequency of about one in the mean,
15:13:02 the example on the slide isn't winnings but it, it's an experiment done by Lee and her collaborators, where they asked him to recover from the deletion of the type to myosin principal myosin periodic cells.
15:13:17 And what happened is that they duplicated chromosome 16 and by doing molecular genetics they showed that it's really only the duplication of these two genes that produces this thing.
15:13:32 The second most common way of fixing things is to have strong loss of function mutation.
15:13:40 So roughly speaking, if you do experiments. About 20% of nucleotides substitutions in the average gene so we averaged over two genes that's not very rich course strong loss of function mutation that actually means a neutral mutations, more common and
15:13:57 deleterious ones.
15:13:59 ones. And the rate is about 10 to the minus seven.
15:14:10 And so a classical example is resistance to a compound called cavity. By mutations in can one which is the Argentine transporter can have some analog, Argentina jack.
15:14:17 And the least frequent thing is specific gain of function mutations. So for example, our Pl 28 is the large is protein 28 and the large right assemble subunit.
15:14:32 It is the target of cycle hex I made an inhibitor of eukaryotic protein synthesis. There's a single amino acid that can be mutated to give rise to strong resistance to cycle hex my.
15:14:44 And so this occurs about 200 times less often.
15:14:49 And this sort of mutation just because the target for mutation so much.
15:14:54 Yes.
15:15:02 This is an estimate estimates of the mean rates of these.
15:15:17 These events right Do we have estimates also of the variance in these in these rates are they fairly similar to the due to the variances scale in some way with the mean rates. So what I would say for this rate, my guess is that the fraction of nucleotides
15:15:24 substitutions that destroy the function of protein. Maybe it varies between 10 and 40%, it's, it's not an order of magnitude.
15:15:33 Right. And so then the target size is that fraction or sorry, rate is that fraction multiplied by the length of the gene and nucleotides times the rate which we make individual nucleotides substitution.
15:15:48 This right there is presumably variability, because there are different sorts of gain of function mutations so that in particular.
15:15:56 You can have a protein that is capable of inhibiting itself. So the way that it's normally activated, something binds to, this is the inhibitory part, something binds that and freeze it.
15:16:09 So in principle mutations anywhere in this part can activate the protein and so this writer, gain a function mutations, could be substantially higher.
15:16:18 Right, so I don't have a quantitative answer to your question but the qualitative answer is the variants of this is low.
15:16:27 And it's understandable, primarily in terms of the length of jeans and the variants of this is higher, and that has to do with idiosyncratic features about how politics work.
15:16:43 And so cancer is a form of evolutionary novelty.
15:16:48 So here's your normal cell prim proper Victorian lives is is born lives and dies in sort of the same region of the body unless it's part of your circle circulatory system.
15:17:01 It will commit suicide rather than doing socially the wrong thing.
15:17:08 And bunch of mutations are capable of turning it into a Rebel Without a Cause you come up. If you haven't seen this slide before and you come up afterwards, and you can name both people I'll give you 20.
15:17:22 Okay.
15:17:24 And this hate on order five mutations and what's interesting is it's a mixture in the typical cancer of loss and gain and loss of function mutations gain a function mutations in proteins that are normally involved in increasing cell proliferation, so
15:17:41 they become more active, quote unquote, they should be.
15:17:44 And its loss of function mutations and proteins that are either normally involved in restraining cell proliferation or doing things like repairing damage to DNA.
15:17:56 And so, one of the questions. So this is an example this is you like natural evolution.
15:18:06 It's a mixture of loss and gain a function of mutations and so one of the questions is, is it likely that loss of function mutations play an important role in evolution outside the law barfing in the lumbar curry selection pressure is often its timing
15:18:20 population sizes are limited population size is by money, space time by the length of PhDs.
15:18:29 And so what about the real world. And so I'm just going to say a word about that.
15:18:34 Oh, here is an evolutionary rebar tree,
15:18:39 the Hawaiian archipelago.
15:18:41 There's a hot spot in the mantle every so often lava comes up, it makes islands and they gradually get washed away so this goes all the way over to the tracker Peninsula, Russia, New Island roughly every mean here's everything that lives there got blown
15:19:00 or drifted from here. So long way.
15:19:05 And so there are spectacular examples of what is called evolutionary radiation so this is a California car we schools in the plant.
15:19:14 You can look them up on Wikipedia they're roughly 20 species that are endemic North and South America. If you're not a botanist they all look about the same.
15:19:25 This is the Hawaiian silver Sword Alliance so this is a question plan.
15:19:32 This is a tree.
15:19:34 This is the spiky shrub. These are all descendants of one of these species. Okay.
15:19:41 And the presumption is that relatively few plants, made it to Hawaii. And so they and their descendants got to explore niches that other people hadn't been to.
15:19:55 And so this leads to the following model for the evolution of novelty, and perhaps it's also nation Beijing.
15:20:05 So here is your classical fitness diagram up. So here's the phenotype This is nucleotide one ABS AGC D this is tied to, etc.
15:20:18 In the real world, this is a very multi dimensional diagram, because there's more than two nucleotides in the genome.
15:20:27 And that probably has important effects for what the extra dimension of fitness looks like but since we have three dimensional visualization I'm just doing it this way.
15:20:43 So here we are an environment one fitness peak organisms balanced deleterious and beneficial mutations has the near the top of this peak.
15:21:01 And only small me effect mutations can take them up hill here as a second fitness peak somewhere else, Gina type space, large effect mutations can take you there and by the sort of Fisher geometric argument you're more likely you hit this peak of told
15:21:08 end up near the bottom because it has a larger areas on the top.
15:21:14 But it could be the case that these mutations, allow you to migrate and survive in a second week.
15:21:22 Right. You will also not be very far up the fitness peak but this is a bigger peak in these two. And these guys cannot invade each time they have zero fitness.
15:21:35 And the argument would be that in a crowded ecosystem.
15:21:36 So you need this mutation.
15:21:41 If this sequence of events, large effect mutation followed by migration happens niche tues occupied.
15:21:49 And you compete poorly.
15:21:53 So you're out competed.
15:21:56 And you are a hopeless monster.
15:21:58 If, by contrast, you are in a virgin ecosystem, like Hawaii.
15:22:06 Then maybe there's no one here.
15:22:10 You can ascend this p by having mutations the geneticists might call them suppressor meditation.
15:22:16 And you can end up at the top of this peak, you end up there,
15:22:21 you've survived and reproduces, and you're and you're a hope for monster and the interesting question is what determines who wins. So one possibility is its first to the post.
15:22:35 Like a British elections.
15:22:36 Right.
15:22:38 And the people who get their fastest are the guys who are going to survive, and then the argument is if you get there by making loss of effect loss function notation, because their frequency is so much higher, and especially if you require more than one
15:22:54 if you square that increasing frequency.
15:22:57 It is likely to be loss of function mutations that get you there.
15:23:01 Okay.
15:23:02 If what determines who wins is who independent when they arrive, where they end up on the peak, then it's possible that you need gain a function.
15:23:14 There's one instructive thing which is you can look at the history of domestication in human agriculture, and people who are plant scientists there things like TSNT, which is the ancestral form of maize, that you can interbreed with modern maze and you
15:23:28 can do quantitative genetics and you can find the mutations that have been inadvertently fixed by humans in the domestication roughly a third of those are obvious loss of function mutations.
15:23:41 By that I don't mean the substitution.
15:23:46 At a conservative conserved amino acid of a radically different amino acid I mean things like transpose ons are nonsense mutations things that are my killer geneticists just by looking at the sequence would say this is.
15:23:57 And because most of domestication was done before Mendel.
15:24:01 This wasn't done by careful breeding and it was done in a semi naturalistic environment and it seems like it's quite a strong argument that in something that is intermediate between the Barbary based experimental evolution and evolution without human
15:24:17 intervention, sort of exactly halfway between the loss of function mutations played an important role and interesting that you said you were being quantitative.
15:24:26 There's also the size of the population.
15:24:28 So that what is for breeding a big things versus for microbes might be very different.
15:24:35 Yes. Daniels absolutely right. So it depends enormously on the size of population, if you make populations big enough, all single base permutations will occur in every single generation.
15:24:47 And I guess the interesting question is, even for microbial population, if you're trying to bait novel niches and the population that's exposed to those nominations is sufficiently small do you reach that limit or not.
15:25:01 But I totally agree that population population size is a sort of crucial ingredient in the arguments I make three
15:25:17 in the crop based naturalist argument, presumably the selection was four years old or something that is useful to us. Absolutely. OK, but so I guess like the argument would be then that you assume that there is roughly also some selection for just growth
15:25:33 or what you would consider a sort of natural fitness. What I think I guess what I'm saying is that the selection for yield was sort of a in CO it, in the sense that you know is primitive hunter gatherer I mean farmers farmers.
15:25:47 And secondly, it also included selection for things like pest resistance right because I, you know, it's not just yield in an invite in an idealized protective environment it's like in someone's feel.
15:25:58 Okay.
15:25:59 All right, so that's enough introduction.
15:26:01 So now we're going to talk about you Carrie. Can I follow up on that real quick. Yeah, so I read this book by Jerry folder where he goes on like a 200 page analytic rant on the difference between artificial or natural selection this what Darwin got wrong
15:26:17 wrong book.
15:26:18 And so I would like you to expand on this a little bit more because that book pretty much convinced me, you can't equate the two but you're saying this, that you can maybe maybe it's a continual maybe it's a spectrum.
15:26:32 So I guess I here's what I would say
15:26:37 what my lab does is to do artificial experimental evolution in the laboratory.
15:26:45 It seems to me that there. When we really understand. I would like to claim we are at least beginning to understand something about that.
15:26:55 When we understand how evolution works outside laboratory over a longer time scale. I think one of two things it's going to be true.
15:27:04 There are obviously some differences between what happens in the lab what happens in nature, but they're important commonalities and lessons learned from studying evolution in the laboratory will help people do better dissection of evolution outside the
15:27:19 laboratory and understand. To what extent, things that people see inside the low bar for you also are important in nature.
15:27:28 Right.
15:27:29 The other possibility is that the 200 pages of ranting are entirely correct and there's no commonality between.
15:27:38 If the second thing is true I will have had fun playing and evolution will be unbelievably difficult to understand. And so, I'm an optimist.
15:27:48 And so, I would like to think that we learn, useful things that will help us think better about what happens outside and so I'll say this.
15:27:58 I will claim that all the work we do is a form of rigorous, in terms of its relationship to the world outside the laboratory is rigorous speculation.
15:28:07 We do experiments, we make conclusions we reconstruct things. We make sort of molecular geneticist I conclude excellent blah blah blah. And then we speculate about how this is, is relevant to the outside world.
15:28:21 Some of the things like the research on domestication where people could be in an unbiased way just track down the mutations responsible.
15:28:31 It is sort of shocking be, how larger Frank, those patients for loss of function, patients, and the vast majority of those were were fixed before they were sophisticated.
15:28:44 And, you know, to me, it was sort of semi it's sort of it's in this gray zone between the two.
15:28:51 But it could be.
15:28:53 It's.
15:28:54 The problem is if it's in the gray zone you don't know which of the two ends it's closer to maybe it's super close to the bad end of the lumbar train it's not relevant.
15:29:02 Right. I mean it's certainly true that the evolution in the real world is much more complicated, because there are many more interaction.
15:29:11 And there's all sorts of interesting stuff about.
15:29:15 Okay.
15:29:16 Alright so we're going to talk about you carry it.
15:29:19 They are perhaps the ultimate novelty so I'm just going to remind you about what I said this on the very first day.
15:29:27 Here is something that we believe happened, and Archean and Gulf, a bacterium, it made an end sim violent.
15:29:36 That in those symbiotic became the mitochondria most of the genes ended up in the eukaryotic cell nucleus, very very roughly speaking, the genes for metabolism came more from the bacterial parent than they are here one, the genes for the central dogma
15:29:54 protein synthesis DNA synthesis RNA synthesis membranes, etc. Came more from Marciel parent but that's a big big generalization.
15:30:03 Okay.
15:30:05 My just said that.
15:30:08 So it's hard to dissect how this all happened.
15:30:11 Is it only happened once.
15:30:14 Now, actually it's an important thing to say we don't know that it only happened once we know that only one of those events has given rise to all of you carriers, because there's this thing called leak of the last eukaryotic common ancestor who have been
15:30:40 can roughly be inferred, maybe something like this happened thousands of times but if that was true. There was just one winner.
15:30:40 And it happened a long time ago.
15:30:46 And it's a net because it happened a long time ago we are uncertain of, who today's closest living relatives are of the ancestors when it happened, those closest living relatives, even if we could unambiguously identify them are not the same as the ancestors
15:31:04 there a billion years descend from the ancestors.
15:31:10 And so here's this showing in in. Oh and actually there's a super important thing to say essentially everything I'm going to say from here on out except from describing to new shoes PhD project is going to be about the work of my current scientific hero
15:31:27 john the couch. And I'm giving this talk, partly because if I was finishing my PhD and looking for a postdoc john would be the person I would be looking at.
15:31:34 Okay, so here is the origin of life 3.7 billion years ago there's a separation of work yeah bacteria.
15:31:46 There's no symbiosis occurred, it gave rise to all the eukaryotes.
15:31:52 There was a second mo symbiosis of a cyanobacteria which gave rise to the photosynthetic, you can increase the oxygen content.
15:32:03 And so here are three approaches that trying to figure out what went on. so one is to find and study the ancestors.
15:32:11 There inaccessible.
15:32:14 The second is to experimentally recreate this process, which I'll talk about in a second and the third which is the McCutcheon angle is the discovery, a contemporary analog that can we see something like this happening in front of our eyes and study.
15:32:31 Okay. So as I said, we're experimental speculators.
15:32:36 So we do experiments from engineering to reveal and test putative, there should be a word here putative evolutionary trajectories.
15:32:47 And I guess I said this to, they do not just white, red, bold and caps show how evolution happened that side.
15:32:59 So here is Mission Impossible which are to mimic the original fusion, or here is bigotry Richard Fineman slide and quotation what I cannot create I do not understand.
15:33:12 And here's the new shoe sitting in the back.
15:33:17 And he wants to try and see if he can make this happen inside the lab so here is the idea. And we would be super happy for people to tell us like why this one work how it's more likely to work if we do X, Y or Z.
15:33:30 Okay, because we're in the early stages. This is an Archean Halo fireworks Mediterranean UI, which grows in high salt.
15:33:38 This is our friend and co I who does not.
15:33:54 What has been so far to try and persuade these guys to get this guy to grow in higher salt this guy to grow and lower salt so we can at least find conditions where they will both proliferate. Then we would like to engineer them so they growth depends
15:33:59 on each other for example by one of them, making an exporting one amino acid and the other doing the opposite.
15:34:10 And then we would like to do magic. Okay, and so the simplest way of imagining this is you remove the cell wall which is called the escalator from these guys and you treat them with something that will stimulate the fusion of cells.
15:34:25 So you hope that you will persuade a lot of these cells to fuse and surround one of the cells.
15:34:34 So here's our event, somebody on these guys can be killed, very effectively by bacteriophage public enemy number one which stories can talk about next week.
15:34:47 I'm sorry, in principle, you could take this horrible mixture that you've produced sterilize it with age. And so the only case.
15:34:56 That will survive have to at least be transiently inside.
15:34:59 Perhaps if you do this often enough, you can make this a stable Association, and tenacious ultimate ambition which will certainly extend long beyond his PhD is having produced such a thing with more magic in time to see if the index and by on can take
15:35:17 on mitochondrial white properties, I will be perfectly happy, we got here.
15:35:23 Okay.
15:35:28 So that's the crazy approach.
15:35:31 Oh, just because if you need something that's phonetically tractable and it just turns out that this guy is reasonably genetically tractable so yes you could have.
15:35:39 I mean, the problem is our key are generally not that accessible to that your modern asked molecular geneticist, so it's just trying to take. And it turns out
15:35:52 it's relatively easy to get things to work and lower so.
15:36:00 And that's the of the cultural archaea that's the closest living ancestor. Sorry, descendant of the ancestor.
15:36:08 Right. Sorry, so it looks a bit like what the ancestor might have looked like.
15:36:13 Whether you should place any way on interesting question.
15:36:25 Do you have a question.
15:36:28 Go for it.
15:36:40 Have a really nice question. You mentioned a couple of slides ago about how, in principle, we could also, if you, if you had a time machine had access to the ancestor, to the ends to do the ancestor.
15:36:43 What I'm just wondering what could we learn if say we did have access to this endless symbiotic ancestor.
15:36:54 What would we know that we don't well we would know more about its property, right, we still wouldn't know how the fusion happened or anything like that we would just, we would know more about the ingredients of the cake.
15:37:09 Would that And would that how much would that help us.
15:37:12 Yeah, I can I'm totally happy with the argument, it wouldn't help us very much and so we should try these other two approaches. Yeah, that's what I was wondering, it wasn't obvious to me how I could help us.
15:37:22 So it would in many ways and so for instance you know if you think about the origin of nucleus, right.
15:37:28 If you think about the under symbolic event. Do you think the nucleus, first emerged in the ancestor, and then the endless embedding given happened, or do you think the nucleus came after like it's one of the defining aspects of eukaryotes, and it probably
15:37:40 plays an important role in what is hilarity etc. We don't really understand how it evolved and. So, if you had the actual ancestor that would be quite amazing because you know, I think, Okay, so, so I gave you the pessimistic to escape the optimistic
15:37:55 right sort of depends a lot on what the ancestors look like.
15:37:58 sort of depends a lot on what the ancestors looked like. If they look like to single cell organisms with not much of what you can look like now. We're so well.
15:38:05 If he just said there was an RPM that already had a nucleus.
15:38:21 I was just wondering, first of all, quick technical question as to. Couldn't you find somebody other than equal I who's better suited to the high salt.
15:38:28 We wouldn't know quite a lot that we didn't previously know before. And since we don't really know who it was, where r plus we don't have access.
15:38:29 I couldn't use which we, yes, we, we, we could have done, but he just, you know, where you slap. When we genetically try and manipulate other organisms.
15:38:43 We've done a couple of times, we really stuck.
15:38:46 There's an E coli lab, and a facility, or Rico I slash bacillus lab down the hole we just do better when we have experts, we can talk. It's that simple.
15:38:55 Got it. Yeah. And then just use it quickly that would the when you're trying to detect the end dose and beyond. You would just be blasting it with a page and then, and then what and then as you saw, anything that survived you would also understand how
15:39:08 you would actually know that there was this sharp, so you blast it with faith.
15:39:14 And then you take whatever is left and you put it a very low cell density in medium life both of these amino acids right so at high density the Salesforce secrete enough so they don't have to touch each other to feed each other, and very low density that
15:39:28 won't be true.
15:39:29 be true.
15:39:31 Right. So now you propagate that culture.
15:39:34 Maybe.
15:39:36 Initially there was an eco ly inside some bag of stuff, they get spat out. And if that's true if you read dilute it the very low density, it should fail.
15:39:49 And if it's a stable Association, it should survive.
15:39:56 Rs.
15:40:06 The Magic the magic that will make the association stable is some sort of mutation in the two partners and we don't know what what that would be. I guess.
15:40:15 The idea is put.
15:40:17 Sure.
15:40:52 pressure.
15:40:55 We can try that too. I mean, we've talked about all sorts of things. So one of the things you can do in principle is to take these guys and make them so they can only ferment make these guys so they can both for men are aspiring after a page, or whatever
15:41:13 whatever is left medium can only be required. So they depend, you know survival ends on the side.
15:41:22 And my friend who's sitting in the back three has, has done in trial sterilization experiment for us. And if you use three different page and very high tide hours.
15:41:32 You can do a very good job of showing very logical like popular.
15:42:03 Bye.
15:42:03 Bye.
15:42:05 It's this with great admiration to to new. This is new. This project is the new shoes idea not mine. My job is to see everything I can do to make it more likely to work.
15:42:18 And we're trying in here has a, there is a project be that is guaranteed work so he will get a PhD, come hell or high water, Andrew have a quick question.
15:42:30 Yes.
15:42:31 Me.
15:42:34 There's some work from Peter Schultz's group where I think they get e coli living inside yeast I'm sure you guys are experts, give me the Redux what why is that system not not useful, or do you just not.
15:42:48 I am I am not convinced that the results that have been published, are a stable association that will last in the absence of selection is the simplest way.
15:43:20 Yeah, so I want to finish this set is in the papers I've forgotten the name of the person whose name because the person went to Champaign Urbana Right, right.
15:43:32 That, that so far what they've published this to show that this association can be maintained for something like five transfers but not beyond that. And also, it's a you carry at the pre exists injecting ingesting bacteria.
15:43:48 Andrew.
15:43:48 Andrew I was gonna maybe jump on your comment before about the rates mattering, it's kind of falling Boris's comment so it seems like it really matters what the rate is of escape in this family I'm wondering like let's say you don't allow them to touch
15:44:06 each other then you're definitely not going to get it into Symbian.
15:44:10 Maybe this was like the triple phase experiment, but is this a tight system where you will not see anything if they're not in, I think, I think it can be made.
15:44:21 I think it can be made tight enough. So the population sizes that are practical inside the lab. This is a very strong reflection and, you know, the experimental evolution we've done we are always on the lookout for cheating.
15:44:36 And sometimes we see cheating and sometimes the cheating is sufficiently interesting that we publish on the cheating is a real thing to work. And sometimes we just have to figure out ways to start again and eliminate.
15:44:49 Okay. Well, let's let me go on with McCutcheon because McCutcheon is less Mission Impossible.
15:44:59 Alright, so here's john McCutcheon, um, it's his folder. This is the picture because this is on his Twitter.
15:45:04 Okay.
15:45:05 And so he works on how plants and insects live with each other. So this is an eighth so if you garden roses, or have a parent garden roses aphids or pest number one.
15:45:20 And they suck a flow of the stuff that goes down from the leaves to the roots in a plan, and live on that.
15:45:27 Now the plants are smart, because they use like carbon dioxide, nitrogen to make glucose and 20 amino acids.
15:45:37 For us, we have nine essential amino acid stuff that we have to eat, we can't make insects have 10.
15:45:48 And
15:45:53 these were in the wrong order sorry. So plants have eliminated all 10 essential amino acids from the sap.
15:45:59 Right. These are there one letter code yesterday nice Lucy exactly right.
15:46:05 But insects has to turn the plant slap on glue SAP and glucose into the 20 amino acids, they're not getting 10 of them so they need help.
15:46:17 And they host bacteria to make the essential amino acid so this is a symbiosis but it is an unusual symbiosis. In the sense that the bacteria that have been doing this for aphids have been living inside the aphids for 150 million years.
15:46:33 Here's an aphid.
15:46:35 And they're the cells here that make up something called the bacterium an individual sales record bacteria site. and these cells are full of bacteria.
15:46:46 OK, so the bacteria inside the eukaryotic cells picture.
15:46:51 This is one back curious like for there's one boundary there there's another there. This is its nucleus, all these little circles are bacteria.
15:47:05 And what's interesting about these bacteria so this is the CO it has about the lumbar tree strings have about 4000 genes they have more than 30 different sensory pathways button or a fit a cola which is this bacteria here has about 600 genes and very
15:47:22 few sensory possibly so it's sort of down to the bare essentials of what's needed for one bacterial cell to reproduce inside an extremely constant and protected environment because they're transmitted vertically from generation to generation aphids.
15:47:37 And the demonstration that is that this is the phylogenetic the aphids.
15:47:49 And this is the phylogenetic of the bacteria inside them and with the exception of this one cross here, these two are perfectly congruent. So this argues that these bacteria, not been outside 450.
15:48:04 So you can ask.
15:48:06 You can make a plot of things with their number of protein coding genes against their genome size.
15:48:16 And these guys up here and whatever this color is white, black, or bacteria so this is mycoplasma genitalium, which is the smallest bacterial genome. These are plastic so chloroplasts and their friends.
15:48:30 And these are mitochondria, which have a sort of wide dispersion of genome sizes but they don't have that many genes.
15:48:39 And there's a clear sort of burying gap.
15:48:46 Right.
15:48:46 And just since I was talking about Buckner physical is down here with mycoplasma.
15:48:55 And so this is john slide. And it says that the sack feeding insects have been made by bacteria going inside insects. In the case of the aphids This is a stable Association, the bacteria have most of the genes perhaps all the genes needed to make a bacterium.
15:49:15 But what he studies
15:49:19 are other classes of insects, where they have endless symbionts they typically have two different bacteria, unless bacteria collaborate between them to make the 10 amino acids, the insects need.
15:49:32 And these are plots, their Genome Sciences.
15:49:36 And you will notice that they are now overlapping with the organelles.
15:49:43 And here's an example one of these three way symbiosis This is planet Kaka citrate, which is a citrus building bug.
15:49:53 It has a eukaryotic nucleus.
15:49:57 It has what is believed to be the initial bacterial symbiosis.
15:50:03 And then inside it is what is believed to be a later arrival, and I'll present some of the evidence supports the idea that later. Right.
15:50:15 And the two bankers I just said combined to meet the 10 essential amino acids.
15:50:20 So here's picture.
15:50:26 So here's the insect cell nucleus in the bacteria site, this great stuff is insect cytoplasm blue is the older bacteria, this is Trimble is this if you're interested in bacterial phylogenetic is a beta proto bacteria and read some more recent arrivals
15:50:48 or nella, which is a gamma proto bacteria.
15:50:53 So one thing you might be interested in is what are the genomes of these guys look like.
15:51:01 newer arrival.
15:51:03 Sorry, it has 400 coding sequences that are colored by things they do. This is fewer coding sequences than the smaller Buckner of cola genome and so you might wonder if this is really all the genes, you need to make it bacterium.
15:51:04 So this is a newer
15:51:21 And here's the older guy.
15:51:25 As 120 coding sequences.
15:51:28 Okay, and has a genome that is smaller than some bacterial plasmids.
15:51:35 And in particular, there are no genes for ATP synthesis.
15:51:39 There are no jeans to make fatty acids are listed there no trees membrane protein.
15:51:58 them. Right.
15:51:59 Okay.
15:52:15 Okay, so in some clear sense, these guys are making the descent being organelles.
15:52:25 And you can ask how various amino acids are made.
15:52:29 So here's the fan and fennel alanine.
15:52:33 These are just the names.
15:52:37 The standard bacterial genetics nomenclature of the genes that encode the enzymes.
15:52:43 But first of all make precursors of aromatic amino acids which is why they're called arrow so all the stuff up to here can either go to find a while and crypto fine but then this branch point, CA, which ends up making fennel alanine and trip defense more
15:52:59 more complicated so there's a whole bunch of stuff.
15:53:01 And you can now ask who encodes the various beans.
15:53:06 And it's color coded so if they are in red they're encoded by Mara nella if they're in purple daring coded by both Princess Leia and Mara and Ella blue they're included.
15:53:23 I trained by their greenery by the house.
15:53:24 So they're basically indulging in the cooperative synthesis.
15:53:29 Let me know in the same way.
15:53:31 The rest of ourselves in our mitochondria, collaborate to do metabolism, like elliptic precursors make NADH which is ultimately transferred to the mitochondria, to oxidative phosphorylation.
15:53:52 Even the compliance last trans membrane proteins are there.
15:53:56 It does it gain the ability to transport like precursors or amino acids like you mentioned aromatics so presumably they're easier, because they can get through like membranes but like some of the 10 are clearly not, they need ways to get past them yeah
15:54:11 so so so here's the problem about proselytizing for someone else. Okay, right, john McAfee knows much much more about this than I do. And so, so it is presumably the case that there are membrane right so there's an interesting question of how permeable
15:54:26 or otherwise, are these membranes. So the simplest possible model would be they just have holes.
15:54:34 And so that things can go back and forth freely. Right, that's not true for mitochondria because we have to maintain an electrochemical gradient across them to make ATP.
15:54:45 But maybe these cells that ATP is primarily made by the insect cells, and therefore you can just have holes, both between the membrane that separates insects cytoplasm from for him why and the second membrane that separates, or an elephant.
15:55:05 So, you know, interesting question.
15:55:10 If you took the insects.
15:55:13 And you injected large fluorescent molecule and cytoplasm of the cell, does it end up inside the intracellular bacteria or not if it does their holes.
15:55:29 If it doesn't, there. So, I guess. I don't know if john has done this, but in the developmental stages of the insect does the this thing, sort of like, get privileged early on, kinda like john cells are like is it unclear how the battery or get shuttled
15:55:41 around to where they need to end up an insect. So,
15:55:47 again, more is known about that than I know but it is believed to be the case that the bacteria have to migrate from the bacterium back to the germline to be transmitted vertically, and how that might happen is completely
15:56:09 right this is not a model system right this is the sort of glorious complexity of nature. Yes.
15:56:27 They have jeans for things like rabbits animal proteins.
15:56:37 Okay, things that you might think are good to make close to home.
15:56:37 That, that's a particular example.
15:56:41 Okay.
15:56:43 And so this is a diagram of a bacterium, this is the cytoplasm.
15:56:50 There's one foster liquid by layer there's peptidoglycan which is this cross link.
15:56:56 Make sure sugar and amino acids and there's an outer membrane.
15:57:00 So, one of these guys still has peptidoglycan and you can now ask again.
15:57:07 Who's responsible for making it.
15:57:09 Okay, so this is, again, just the gene names in succession but the different biking steps to make by can. And again, they're color coded by whether by who's genome there in this is barn hella.
15:57:26 This isn't the host genome. This is Dean that's been transferred from a different bacteria. This is the host gene, yet another bank theorem and so on.
15:57:37 So, Right.
15:57:41 And
15:57:46 perhaps the most interesting thing is that these and those sent by unlike those effects and the physical aware, or button or a physical where something happened 150 million years ago and in some ways of thinking about it not much has happened since.
15:58:01 For these insects argument is they started at getting trembler.
15:58:06 But then what has happened afterwards is diverse within the firewall and even.
15:58:14 So here is a guy who has a.
15:58:20 These guys Barnhill is part of a closet back here, where the free living relatives, of course, the Dallas. Okay, this one has a small genome.
15:58:38 This one has a difference Dallas allied in this environment with a large enough so maybe this is a more recent arrival and its genome has yet to be whittled down.
15:58:49 This may also be more recent.
15:58:55 And this is yet another one, and this is where the tiny genome and the argument is that this is a descendant of the original secondary and those symbiosis.
15:59:06 And so this guy came in here.
15:59:11 And somehow got itself inside the original bacterium took over parts of some of the amino acid by synthesis so we come down here and this symbiosis changed.
15:59:22 And these guys here this is a secondary invasion where this guy got kicked out.
15:59:28 And up here, there have been two successive invasions and the argument is, you can tell who's the more recent and the older invasion by how large the genome still is.
15:59:44 We're wiggling over time.
15:59:46 Yes.
15:59:51 I was just wondering if like the scientific question here is figuring out what the rate limiting step for establishing into symbiosis is, is it like the.
16:00:01 Is it the entry in the first place or is it the stability of this over time and can this kind of study answer that. Or is that the question here or.
16:00:13 So I guess what I would say is,
16:00:18 at some level, this is an observation that raises question, right, that in so
16:00:30 there's, I guess, I guess you can frame questions in many different ways you can say, This is an evolutionary question about how associations remain stable and what happens to them and household Michael or biology rewired.
16:00:50 You could argue, and it's what I would argue is that we are watching organisms become organelles. And the question is, what can you learn by intelligently studying this particular evolving in those symbiosis about the process by which.
16:01:11 What was once a Freeland being organism becomes an Oregon L and transfers jeans to the host genome and so on, so forth.
16:01:29 nature, if you just take some random arthropods. And second, what like which of these steps, is that rate limiting step for how frequently you expect new into symbiotic events to happen.
16:01:37 So I think that's a super interesting question and I guess there's sort of two versions of the question.
16:01:43 How often does this happen even transiently, which I think is extremely hard to answer.
16:01:51 And how often does this happen to give rise to interactions I have some evolutionary stability.
16:02:00 Right.
16:02:01 And so it's certainly happened independently.
16:02:26 With aphids and in this particular insect and they were bored SAP, consuming insects, were something similar but independently, that I can give you a number off the top of my head about how many times at tap.
16:02:26 You may have an answer. Next slide, but so do our care of bacterial diseases.
16:02:28 Earth.
16:02:33 Not as far as I know.
16:02:41 No other bacterial pathogens that in fact archaea. Yeah, we know that there are a viral pathogens that in fact, I never heard of it.
16:02:50 Yeah, not not as far as I know, but it's also not clear anyone's looked very carefully.
16:03:03 And when you see like,
16:03:13 if you're gonna, sorry, go ahead, a tiny fraction of, you know what's alive at the moment on Earth has been sampled So, excluding things by observations, sort of dangerous business.
16:03:27 It maybe I'll answer this as you go forward but it looks to me like you have a beautiful system for the study of the evolution of a microbial community because what's happening is that you know there's this sharing of resources to build these amino acid
16:03:40 so is that, are you headed in that direction. Oh wow okay so I super have to emphasize this is the work of john McAfee, this is this you get it, I get it.
16:03:51 I'll call that later, but well i think i mean I think the answer, I think, is.
16:04:00 I think I should be very careful about speaking for someone else, whether you're interested in.
16:04:17 microbial community business but you should ask him, but then can I ask you a question if you have some sort of story in your mind for why these pathways.
16:04:26 Getting stripped these, these endo symbiotic cooperate to construct.
16:04:31 Forgive me for using the word cooperate to construct the amino acids that are necessary for the host because I know that's a recurrent theme in endo symbiotic bacteria and insects.
16:04:42 So is there some sort of just so story at least why.
16:04:46 I don't know if it's just so story which is, if the insect that in its internal bacteria are going to survive. And they're, and they're going to live on SAP, they have to do this right, you, the insects can't make these 10 amino acids.
16:05:01 So anything that destroys that cooperation so you know maybe these guys who come in were originally parasitic.
16:05:08 Right.
16:05:12 If they destroy it you know if they successfully kill this bank here the insect insect dies.
16:05:17 Right.
16:05:18 And so if they get maintain, they have to keep this guy happy him.
16:05:26 You know, why any of those things survive is an interesting question.
16:05:32 But I'm asking why not just have one bacterial and a symbiotic does all right. No, I understand so and I think this is not an isolated incident from what I understand from you know i right it's not and so presumably.
16:05:45 This one's did all the work and then there were some secondary invasion. And, and what are the features that invasion that allows it to succeed.
16:05:55 So that this more complicated and seemingly bizarre arrangement is stable, right, that seems like an interesting question, sort of related, and you have a related question anyway so you have you showed example bacterium inside the back to your meeting
16:06:22 And why do you think it goes like this rather than just to bacterium inside insects or, like, I don't know all the bacteria can also be epi imbalance right.
16:06:22 What do you think the dry, what drives the organization of these systems.
16:06:36 I guess I should say two things.
16:06:39 Again, this is not an area which I directly work.
16:06:41 And there are other examples of to bacterial endo symbionts. I don't know that there aren't examples to bacteria separately inside the inside, so I guess one thing I would say is least in terms of transmission.
16:06:57 This makes things easier so you're only transmitting one object, big bank Karen has a brighter side, so that's a hand wavy explanation why this is a better way.
16:07:10 I guess a related question there is there an obvious region I should have in mind why the insect can't make all the amino acids, you know, since we're talking about rare events I would imagine like, Oh, interesting.
16:07:19 So, so, animals just lost a bunch of the gene. Right, so, you know, there's a whole series of metabolic enzymes required to make his study which e coli yeast have.
16:07:31 And you and I don't.
16:07:34 And so reasons that are sort of lost in time.
16:07:50 Was it modest and things went through population bottlenecks. But is there no sort of physiological, can, can they can you clone it back in and have them do it, or is it now interfere with other things going on.
16:08:04 So, That's a good question.
16:08:06 My guess is that you could totally genetically engineer.
16:08:13 Human sudden instead of getting their trip to fend for meeting turkeys Thanksgiving, you would put all the genes in and I don't think necessarily would have some terrible interference with something else I think it's a sort of use it or lose it.
16:08:27 Exact you know in exactly the sense that bicameral critic Hola, and more banking which is vertically transmitted insight parasitic bank here and basically.
16:08:39 They've just lost all sorts of things that they don't need.
16:08:45 Alright, So there's one more slide
16:08:48 Can I ask another question about that previous leg. Yeah, sure.
16:08:54 These cases when there are sort of tiny genomes and larger genomes inside this trembler, we know these genomes and nested which is to say that other tiny like I do the tiny genomes represent a version of the large you know versus a large room lost a bunch
16:09:10 of stuff.
16:09:12 So I will make a spec you, I will tell you what I think they will look like, but I do not know the answer.
16:09:21 Right.
16:09:21 But there are some things in these tiny genomes, which have been kept because they're important, like I said ribosome protein.
16:09:29 My guess is all these big guys have these genes to write.
16:09:34 But there are probably also some jeans here, which are just remnants haven't yet been gotten rid of. It's just the useless genes get lost gradually over time so there presumably you one or two still left.
16:09:48 And then it's going to be.
16:09:51 They're more likely to be absolutely this guy than they are in these bigger guys but they might even be absent and the bigger guys because genes are being my model is that genes get lost at random.
16:10:03 And this the simple version is, it's easier for these guys to delete DNA, than it is to insert DNA, as long as that's true the genomes will keep getting smaller.
16:10:14 And you will gradually lose all the genes that are not useful to.
16:10:22 And just follow up on that this cartoon on here where the way you have the tiny genome at the bottom you have many more of those genomes is that, is that true that the timing of the GMO copies of you, the more copies will have inside.
16:10:38 I have no idea. All right. Okay, thank you. Right. This slide is drawn that way whether that corresponds to reality I just can't even begin to tell you.
16:10:47 All right, so here's the last slide.
16:10:49 So obviously there's an interesting question about where these guys come from Can you find guys who look like them could use do this in the laboratory.
16:10:59 And so here is a paper, which there's a novel human infection derived bacterium provides insights into the evolutionary origins of mutualistic insight bacterial symbiosis.
16:11:13 So what happened is a gentleman fell and stuck their hand on a dead crab apple tree.
16:11:22 And it got infected.
16:11:25 And there was assessed and people at the hospital, drain and they played it in and there's a gram negative bacteria and some automated bank here or recognition software said with P was point nine eight e coli, and the microbiologist really I don't really
16:11:43 believe that. And so then they did 16 is our DNA sequencing and its closest relative.
16:12:02 So what john the cartoon has shown is that this Bactrian will affect in fact for soft tissue culture cells.
16:12:08 Right. And so the question is now can you start doing some of this stuff in Lamar curry. By seeing if you contain this guy to live inside inside cells.
16:12:19 Does it affect them and kill them or text them when they can still go and divide.
16:12:25 So, it, it's not clear that this states that john McAfee knows the answer to that question Daniel, and it's a super interesting question. Even if it kills them you can look for sort of benign versions of one killer.
16:12:45 That's it.
16:12:53 Yes.
16:12:57 Delightful.
16:13:08 It seems like a lot of the questions about you know rate limiting steps, it's sort of hard to answer because you're studying a sort of small number. It seems like if you go to the lichens you just have this extraordinary diversity of into symbiotic events
16:13:16 and seems like, you know, comparing and contrasting different likens could be a good way to, to figure some of this stuff out right so so the question is pointing out the lichen sort of symbiosis between cyanobacteria fungi.
16:13:34 Different types of funky and a billion different types of right as many, many, many, many different types of of both guys, and a postdoc who work with me Eric home, tried to build and successfully created an expert cellular fungal algal symbiosis.
16:13:55 Okay, to be honest and somewhat contrived way
16:14:00 and and so I think the answer is yes that's, that's an alternative way of looking at it similar things and it would be an interesting question to have the sequence of Xena of like in, and to try and understand something about how they do stuff I think
16:14:16 Right, but you know that they're specialists in growing on things like gravestones you know why I can go on someone's gravestone and got my teeth fall out but I'm not going to get any nutrition from it, whereas lichens can, but the cost of that is they
16:14:28 biggest problem with lichens is the problem about experiments, they grow really slow.
16:14:39 grow incredibly slowly so I think experimentally they're not. I mean, I guess what I would, I would agree with you in terms of the sort of, to the extent we can learn things just by genome comparisons, which I think is quite high.
16:14:51 There's a strong argument for sequencing as many lichens as possible.
16:14:58 How easy it's going to be making them into tractable organisms are sort of molecular genetics, especially molecular perturbations I think it's hard
16:15:22 Rs.
16:15:26 Easiest for us. Can you turn the mic on.
16:15:39 Boris Can you turn the mic on. So thinking in terms of this microbial pathogen getting inside the eukaryotic cell.
16:15:48 And then another one getting inside the worker eukaryotic felt, you can almost imagine that the business of one getting inside the other after the end the cell is
16:15:59 you know face segregation, especially by the time one of your bacteria there perhaps last it's a membrane altogether. So it's just membrane membrane lyst organelles, and then physics will possibly stick one inside data.
16:16:17 But, but, so the notion of it's not a membrane Lois Oregon out okay hasn't membrane has a membrane.
16:16:24 Right, so that there's, but the very fact there's, there's a while we don't know how permeable It is like the answer to this question is.
16:16:34 Okay, so what you would need to do is somehow find a way.
16:16:41 In a perfect world you'd make these organisms that genetically drank the bowl so you could put proteins that you could follow in their different membranes and you could isolate the membranes and you could do mass spectrometry could ask what the hell is
16:16:52 is in membrane.
16:17:02 Right.
16:17:03 As far as I know we don't know that but they.
16:17:07 So, the,
16:17:10 And are there training, you know, are there transporters for amino acids if there are whose genome do they come from and all that sort of stuff.
16:17:12 the mitochondria ought to have a triple membrane.
16:17:15 Right, because it ingested a gram negative bacteria, which had two membranes and inner membrane on the outer membrane and presumably, it was invested in eukaryotic in the sun, so then there should be a eukaryotic membrane surrounding that.
16:17:33 Right.
16:17:34 It only has to be inner mitochondrial membrane is clearly in some sense, the descendant of the inner membrane of the bacterium, and where the outer membrane of the bacterium is the descendant of the bacteria ladder membrane, or the animal or the deal,
16:17:56 membrane i think is unclear if it's clear it's not clear to me.
16:18:01 Right.
16:18:02 And guys like Buckner.
16:18:07 They have a double membrane.
16:18:09 So they're sort of like mitochondria, there should be three membranes, but they're right.
16:18:18 And the guy on the inside of the bank here I'm inside the bacterium has a double membrane.
16:18:30 And I think the guy on the outside has a double membrane.
16:18:33 Right, so there are membranes there so it's not no it's not just, you know, just a separate separation flavored mature of modern biology.
16:18:46 I'm curious. So, given like this less stories about a bacterium instead of bacterium.
16:18:53 And so is there a reason to try to reproduce the original and the symbiosis in our, you know, within our key on as opposed to try to bacteria. And do you think there is a, you know, maybe reasons that specific configuration was more successful, you know
16:19:11 there's obviously energetic thing but I'm curious. Yeah, I think, I mean.
16:19:19 So one of the reasons I'm sort of excited about this project is, if it works, and we can successfully get an Archean to inject ingest the bacterium and have that association, stable.
16:19:34 It will argue at least be that this is not nearly as hard as you might have thought, and therefore it is probably happened many many times, but only with, it's only the descendant of one of those events that survived.
16:19:49 And then if I haven't many many times it is presumably possible that it could have been, you know, there was bacterium investing bacteria menarche on injecting rk on it.
16:20:01 You know, someone just flipped the coin and we got the winner. Now unfortunately the converse isn't true. If the news companies project work it doesn't actually prove that this was incredibly difficult and possibly it just proves we can do it.
16:20:15 We enjoyed to just expand that point that a lot of people to ask things about rates and so on. And the difficulty with rates of our abilities, is the rather small set of things that we that we know have, we only have evidence for happened once as again
16:20:43 as one finds that things have happened several times then we can start talking sensibly about horrible recently, and it seemed just sort of generally one of the goals, was live experiments in the lab and goals of theory and rather different way is to
16:20:55 sort of decrease the things that one should be surprised by the way.
16:21:04 So you can increase the things you should be surprised by right so I would argue that, you know, one argument for trying this as an experiment is maybe it will decrease the number of things were surprised why, why one.
16:21:17 Yeah, absolutely.
16:21:18 But I think we need these ones what you were showing the examples of with these bacteria being absorbed by other bacteria which was the way that insects and so on, that there are so many things by now that one should you know could take the view well
16:21:30 you know you carry is unlikely to have been something that was a really a rate limiting process in getting from single celled life to us by different thinking about life on other planets and so on, and so it's asking you know which which sets of the processes.
16:21:46 There's one thing one really has to worry about being extremely rare things, and which things okay once you get single cells, sophisticated as a bacterium then everything's like very likely to happen.
16:21:59 Yeah, I think one possibility is that is that none of the events are individually that crazily rare. It's just that it's this, I mean one possibility is that there's a succession of events, all of which are slightly more probable than we used to think
16:22:14 they are. But the question is long enough so that if we multiply them together, it takes a long time for things to happen.
16:22:21 And the other possibility is.
16:22:24 It is a succession, but somehow we will be able to say that there is one event that must have been much slower as in, much less probable and all the others and I sort of personally have an open mind which of those two it will end up be
16:22:44 very simple question, trying to understand what is sort of a triple membrane. Why is it that I mean okay I understand that it was originally a double membrane and then the testicle how, like endo psychosis, but presumably like there must be some mechanism
16:22:58 for it to then reproduce inside and that mechanism is for double membranes so like why would it, copy the triple membrane.
16:23:08 I guess what I would say is it has it has to is, it has to escape from that membrane somehow and it could be that it replicated inside in Oregon L and the organelles subdivided right you know the license on sub the violence on it so I guess what else
16:23:24 I'll say is that
16:23:28 there are pathogens of humans like listeria, which originally going to ourselves.
16:23:35 And they have a triple membrane. So there's an industrial membrane around them and they break through that into several membrane and then they're in the cytoplasm rocketing right and so it's not, it's not wildly problem.
16:23:47 I'm just saying that that's what it must originally of look.
16:23:51 growing things in golfing thing that may be gross more quickly on its own but then it can be sort of tamed. Do you think that's sort of a crucial feature and the success of this.
16:24:12 Yeah, there you go. Yeah, they have to they have to grow.
16:24:17 So they have to grow at the same rate.
16:24:20 Yeah, right. Eventually, so there are two possibilities one is he started get lucky and somehow they both want to grow at the same rate and the other is some feature of how they talk to each other.
16:24:33 enables the slower one speed up. Sorry, the faster one to speed up the slower one, the slower one that slow down the faster one, so their growth rate three, but almost all of these you carry insect examples right or the sort of the opposite right the
16:24:48 host cells presumably are still dividing super slowly
16:24:54 turning off the bacterial division until yeah and so I right and so the interesting question is do we know anything about what regulates rate of bacterial cell division, inside the cells.
16:25:07 Right. Or do you need to make sure you start with a super slow growing Archean, rather than one that maybe is more rapidly growing in the lab, like is that the way it's going to work the best
16:25:24 guess what I would.
16:25:30 So I think
16:25:33 he's if you maintain selection on things. And they grow at different rates.
16:25:39 If the guy in the inside is growing too fast and may pop the guy on the outside.
16:25:45 Everyone dies.
16:25:46 Right.
16:25:47 The guy in the inside grows too slowly you make guys who like the guy on the inside as long as you kill both of those things in guys who have bacteria on the inside.
16:25:59 And guys who have bacteria on the inside. Ever reproductive rate greater than one.
16:26:03 You can get proliferation.
16:26:05 That presumably in would select quite strongly for things that would try and regulate their relative growth rates, so neither of the bad things
16:26:19 have a quick follow up question.
16:26:21 I'm concerned about the outcome you've articulated which was that it will decrease to the things you're surprised about by one
16:26:29 in my I guess my concern is that even if you succeed. How do you know that you're not studying the idiosyncrasies and, you know, I know you already sort of address that question in the introduction but to go to Alex's point.
16:26:42 Why not look in a system in nature where, you know, you see these recurrent symbiosis arising the example that comes to my mind is Ciliates analogy, which I realize are not necessarily as genetically trackable as these guys, look at the regular properties
16:26:57 of those things and then study a model instantiate none of that.
16:27:04 To avoid what I would see as kind of a worrisome outcome.
16:27:10 I guess.
16:27:13 So, I mean you gave the answer to the question that why I don't know how to work with Ciliates and algae.
16:27:22 Right. I like to ancient learn.
16:27:32 Roughly speaking, and I guess what, I guess what I would say is if this can be made to work
16:27:37 in a way it was surprising, like given you know there's a bunch of twerps running around in Hobart you're trying to make things happen.
16:27:47 And it would certainly suggest that at least in principle establishing something like this and making it stable is not that hard.
16:27:55 That's all it says right to be.
16:28:01 And I and I guess I'm, you know we're cell biologists and molecular genetics so so then our approach would be like okay How the hell did this happen you know which means got mutated what is happening, how does this work.
16:28:19 And
16:28:19 at some level.
16:28:22 I'm perhaps more interested in that question than I am interested in this sort of deep ecological relevance question because if I was more interested in the second question I would be working on Ciliates an algae that they just which I think is super
16:28:37 cool and interesting.
16:28:40 and interesting. I just think it's, it's going to be much harder to figure out what's going on and molecular science exactly the same as the answer to the question about like, like I would encourage other people to pound on those things like there is
16:28:52 no tomorrow. And I'll be super interested in what they find.
16:28:57 It's just not what I wanted to
16:29:06 wanting to add and maybe this might not be a good point as, for me at least, the question is also about the origin of eukaryotes. And I agree that you can learn probably a lot more about indo symbiosis in general by studying different systems, but I can
16:29:20 see trying that and spending probably a whole lifetime studying that, but not necessarily learning too much about how the archaea bacterial fusion actually led to carry Genesis and.
16:29:36 And I feel like looking at this and prokaryotes seems to be important to really think about that more deeply.
16:29:41 I was just curious if there's kind of a clear delineation in your mind between the end of symbiosis that we're seeing with these bacteria, and when they become organelles like is there is there some really clear definition, or that distinction.
16:29:56 No, no, I think, I think, Well, okay, maybe I can.
16:30:01 So what I would say is,
16:30:06 in principle, yes, but I don't know how to do the experiment same principle.
16:30:11 The question is if you take back your ethical one, which seems to have mostly its own.
16:30:19 And you could produce a bat of insect cytoplasm.
16:30:24 Right. Can you get it to grow and proliferate in it's like cytoplasm Can you then Frank need insect cytoplasm until you finally get to the point where you're not adding any proteins on the outside, and you have a bank.
16:30:40 That's reproducing in a test.
16:30:40 Right. That means, the Knights in tact organism with its own genome able to do everything.
16:30:48 Once you've transferred genes that you need to survive.
16:30:58 Sorry. Let me try and say this.
16:30:58 Once you've lost games that you need to survive even within the insect cider plans.
16:31:04 And those genes now reside in the insects chromosome.
16:31:10 Whether they came from you, or from different bacteria.
16:31:17 Then, in Bali mind.
16:31:19 You've started the descent into work and help them.
16:31:22 Because you're no longer capable of autonomous replication right now.
16:31:28 No one's ever as far as I know, going to do that experiment.
16:31:32 You know, producing innovative in tech side of plans, and, you know, watching these guys divided because they divide quite slowly because that keeping pace with the inside sales and so on, so forth.
16:31:42 And it's sort of a nightmare experimental system but it's at least a thought experiment that you could do.
16:31:48 Right. And so I would say, you know, when you lose that first thing that you need to be capable of independent survive.
16:32:01 Okay, again, I'll try and say careful if you've just lost one you could, in principle, get it back from someone else, but there will be a certain stage where you've lost enough, I don't know what, three or four is very unlikely you're going to get an
16:32:15 especially if they come from different parts of your genome, it's very unlikely you're going to get them all back.
16:32:21 And now you're sort of on this descent, and what it looks like from a cultural work is that the longer you've been there.
16:32:28 The more things you've lost and in particular these two bacteria are sort of somehow genetically acting, mostly as a single bacterium but they've already sent quite a lot of genes.
16:32:40 So the host chromosome, and there's an interesting question of why that looks like it's been less common.
16:32:48 In the aphids and they're in the same by on, even though it's been there for roughly as well.
16:33:07 Have you thought of the idea of trying to use library of mutants of both the rk and the CO like to sort of increase the probability that you may be made a kind of sick Archean that is more likely to take up the COLA and vice versa.
16:33:24 cola
16:33:28 tried this The simple answer is, it would make sense for both partners to really increase their mutation rate so that when you do this, you're mixing together a bunch of genome that have, you know, you certainly won't make all combinations of a from the
16:33:46 Archaean be from the pro carry the bacterium but why you might as well, you're going to need mutations to make it work so you might as well make some before you start trying to get them to eat each other.
16:34:03 We haven't gotten, we're not nearly that far.
16:34:07 In option for the call a but Hello ferrets and most archaea don't have mutant libraries. so like Andrew said, like you said they were genetically tractable right there.
16:34:18 So for archaea let me say genetically tractable, it means like yeah but early days of E. coli, you know where you can maybe get something into the cell.
16:34:31 Maybe do homologous recombination here in the library I would make just, you know, random collection point mutations by having our print DNA polymerase, like, yeah, that's already Yeah, but that's the idea.
16:34:39 Here we can increase the mutation rate but for equally we do have the luxury of picking from a huge collection of stuff, or just making the whole library and trying to push it in right.
16:34:54 So I think this, I think this question of the stability is really interesting but actually you know coming from the cell biology side. The just initial investigation seems both a challenge and, but maybe like an opportunity to be studying what those conditions
16:35:11 might be. I guess I'm like the first place my brain goes is to get rid of barriers like the cell wall, and the escalator and I guess you guys have thought about trying to you know do things with L forms and other other cell Wallace states.
16:35:30 Yeah, I mean by version is that the first thing to do is to just remove the our keel.
16:35:38 So war NC persuade a bunch of them diffuse themselves random bacterium and see what happens. So with that in mind, I'm really curious with the rate how high the rate you could get of just imagination of a random particle like 100 nanometer be there so