S1: (xx) could i have your attention please? Dr Hammerman do we have any announcements about the exam online or anything like that?
S2: uhuh
S1: uhuh
S2: yeah so practice exam two is on the web and i will put the answers on um, i guess this Friday or Saturday. uh and you know that the, your next exam is Monday from six to eight and it will be in the same room as it was before which i think was fourteen hundred Chem or, wherever it was i'll i'll take a look and, know for sure. and i am trying to get a room for a review session which will be six to eight P-M Sunday evening. um that_ so essentially twenty-four hours before the exam. it will either be here or somewhere else in Chemistry i just don't have that room yet so, just try and keep Sunday evening open for review and Monday evening open for the exam. and try your hand at the practice exam.
S1: okay. um also remember that, yesterday's set of lectures are the last ones that are going to be on this second exam. so starting today everything is, else is on the last exam. i also just want to explain what this set-up over here is. i'm i'm not exactly sure how to explain it. i'm being recorded as part of a research project, it has nothing to do with what i'm saying it's because i'm a female and, a lecturer
R1: in the, in the sciences.
S1: in the sciences. and they collect spoken word. the spoken word. so, it has nothing to do with our class you don't have to worry about it they're not, trying to take your names and addresses or they're_ it's part of a research project it's science. so um, and actually this, this group um recorded a lot of my biochemistry students as they were giving (their) presentations this year so that's how (we) came to be part of this. um i think we, finished up everything yesterday that i wanted to talk about about Mendelian genetics. i did have a couple of questions at the end of class and, one person asked me about eye color genes and i can't remember exactly, who that was but i have some stuff for you, that i can give you later. okay but i didn't know the answer completely and this is what i've got for you. um and i think with that we're gonna go on and we're gonna start talking about, evolution and we're gonna start talking about it in a historical context we're gonna talk about, Darwin and how he came to the ideas that became known as the theory of, evolution by natural selection. and so, the first part of today's two lectures is kind of a historical story about how these ideas all came together. and once again, like when we were talking about Mendel you have to give these guys credit they didn't know any of the stuff that we now know about how genes work. and so all the things that they came up with were quite amazing, in terms of, the complexity and the thoroughness of their ideas. and so, appreciate them from the historical context if you can. um i just s- started out with some pictures here, to just remind you, of the incredible diversity of life, on this planet and, the diversity, of life that has since disappeared. all the things that have gone extinct. i just wanted to give you just a real, quick view and i'll go back to some of those pictures of all the different organisms and, and how, how can we make sense about all these incredibly different organisms? the ones that we've seen the ones that we can't see because they're too small, the ones that we haven't seen yet because we haven't traveled to Australia yet. things like that i i just want you to get, to think about that. because it is as the organizing concept of biology that evolution is so important. nothing in biology makes sense except in the light of evolution one famous evolutionary biologist said. because without this idea of how things change over time and how everything is descended, from, an original organism essentially, without that concept you can't possibly begin to figure out how all this diversity came about. so that's one of the big things about, why evolution is such an important concept and why, it's, it's taught wherever they let us teach it. um, it's also a wonderful illustration of the scientific method, um Darwin's Origin of the Species his book, represented the, one of the first consistent uses of, the standard scientific method. i talked yesterday about how Mendel was also using it as well and Darwin and Mendel were going on about the same time. and so, the question being asked after a pattern is seen, observations made data collected, experiments done, a revision of the original hypothesis, that whole, method of making the hypothesis and then looking, with experiments at what happens and then making new hypotheses all that, was something that Darwin rigidly used in order to come up with his ideas. and as an intellectual revolution, it was also incredibly important and, i do have to preface this by saying that, most of this history i'm gonna be talking to you about is Western histo- history. because it were it was Western ideas that influenced Darwin. um but, coming to the idea of common descent with modification which i'll get to in a minute, was a replacement of all sorts of other ideas that had been going on. and what it means is that we're all part an- of an immense evolutionary tree. we're all part of the same biological story and that was a brand new idea. and it also means that our world is not fixed it is changing all the time and therefore we fit into that world because we are changing all the time and all other organisms are changing. so, those three things about evolution is, is why it's just such a big deal and why you really need to understand it. i'm gonna really briefly touch on some evolutionary thinking before Darwin, um starting very early on. there was a fellow named Thales, and he said that, things had a cause and things had an effect. and that we should be able to explain natural phenomena, things going on in the natural world, um by natural causes. he said there was no need to bring up_ into the story, um sup- supernatural causes, that there were natural causes and natural effects. and, his ideas should have led to Darwin's ideas of, natural selection, but um he was overridden by a much more powerful and popular philosopher at the time, Plato. and Plato is one of these two guys, the other one's Aristotle and i can't remember which one is which. but, you can see them talking about heavy things. and Plato was a huge impediment to the idea, to the development of ideas about natural selection. he was the most influential philosopher of his time and his idea was that every individual thing has an essence, an ethos. and that, that was the pure characterization of every individual thing. so we each had our own individual essence, and as thinking beings we're supposed to try to understand this essence. and therefore variation, from this pure essence is uninteresting and not useful and we should ignore it. and so since variation is undesiril- undesirable, just ignore it. if you see things that are a little bit different in nature, just ignore it. it's the essence of the thing that matters. and this, was called essentialism. and, you, the extreme result of believing in Plato's ideas of essentialism is that you don't even see the variation in nature. you look outside and you see trees next to each other and you say they are all the same thing they all have the same ethos the same essential essence. and so you could see how this would get in the way to understanding anything to do with natural selection. if you can't see variation between things you're not going to see that there's any way of choosing between, these things that have variation. and... a single event creation, and and, pretty much all religions have creation myths that are are meant to explain how things came about, but um, especially in Western ideas this single event creation meant that everything was put on this earth at one time and it could not change afterwards. so between single event creation and essentialism, there was no room in Western philosophy for looking for variation and looking for change. um essentialism and creationism together, combined led to what was called natural theology. and natural theology essentially describes nature in order to show how good the creator is. um, there was a lot of very good descriptive biology done in the name of natural theology. but what it was essentially saying is, it is there and we should describe it we should learn about it but only, to bring higher praise to the creator. um i just want to mention da Vinci at this point. he was of course later on than Plato but, he was a troublemaker he found fossils and he, noticed, that they had variation, he saw younger fossils on top of older fossils and he could see connections between them, um, but he didn't tell anybody, really about this because he was already in big enough trouble, at the time. and so he i- did not mention the fossil record and what he thought he saw, which others later did talk about. um, and actually, lots of natural theologians were looking at the fossil record and they were unable to, figure out what was going on on the basis of their natural theology so they just ignored it. let's go to a little bit, closer, to, Darwin in terms of time... and talk about some of his almost contemporaries. um first of all Hutton and Lyell were both geologists, and they came up with not together but sequentially a couple of really important ideas. important eventually to Darwin. the first one is called uniformitarianism. and that means that there are uniform processes that occurred a long time ago and are still occurring and will continue to occur. in other words geology is operating by the same mechanisms in the past as it does today and will continue to. and so those same geological processes that molded and shaped the earth originally and gave us things like, canyons here, are still going on. we might not see these things going on because they're slow relative to our lifetime. but, under this view the earth was not put into its final form at the moment of its creation, but it was undergoing change steadily. and so this was, kind of an out there idea. that the earth was changing, and that was important for later ideas. and the other idea that these two fellows came up with is called gradualism. and that's that change, can be very small, incremental, over small pieces of time, but in the end you can see very large and profound changes. they just happened gradually and slowly. and one of the pieces of evidence that they had for this, um included, the laying down of sediments in rivers, and this is a figure from your textbook, and, the geologist looked and saw how sediments covered up organisms, right now, and then they looked deeper down into sediments and saw that older organisms fossils had been covered up in the same way. and so you could go from a very deep valley up to a filled up, rift or you can go the other way you can go from, a very shallow valley and as water, goes down through it you can get a deeper and deeper valley, but the idea here was that slow steady incremental changes in the end can build up to very large things happening. and, so these two ideas uniformitarianism and gradualism, led to an idea that i think was it was working this way anyway. so if you can have the cliffs along the beach and they are, undergoing, this slow steady gradual change, why not organisms as well? why can't the organisms that are living on this earth undergo changes as well...? so somebody had come up with this, this idea, and you've probably all heard of Lamarck, he was a French paleobiologist, and he saw lines of descent in fossils, so he was keeping track of these and watching them, this is, Lamarck. <P :04> and, he could see a line of descent. he could see older fossils and more recent fossils, and, so he said alright living things can change through time. and then his his big leap, was that, the changes were adaptive. as living things changed over long periods of time from older more ancient organisms to newer ones, there was an increase in adaptive ability. the newer organisms were better fitted to their environment, so he essentially saw um, what Darwin later talked about. unfortunately Lamarck came up with the wrong mechanism for how to describe what was going on here. he said that these changes that were adaptive, occurred through what he called inheritance of acquired characteristics. and probably the example you heard about in relationship to Lamarck when you learned in high school was um, the giraffe. stretching its neck to reach higher and higher, um leaves. and eventually it got a longer neck and then it was able to pass on those changes in its longer neck to its offspring. um this is not correct you know that, certainly that you can't make a change in, your body that isn't part of your gametes and see a change in your offspring. but, um, it was the right idea just the wrong mechanism. um if you wanna think about it in a different way, he um he talked about it in terms of something called environmental induction <P :09> and um he said that there's something_ if there's a need in the organism for something, it will, change in order to meet that need. um, he talked about how ducks did not originally have webbed feet, but in the act of swimming everyday they stretched their toes apart until a membrane grew between them, the toes on their feet and so they got webbed feet which made it much more efficient for swimming. since they were using it everyday, and they needed it, they stretched their toes the membrane grew and they became webbed footed. and then this webbing was passed on to the offspring. um a similar idea in relationship to humans would be, if you go to the gym everyday to work out, you become very very, big. very buff. and then you marry Maria Schriver, and your kids all come out, looking like that. right? it's not based on what's, in your genes because Lamarck didn't know about that it's based on what you did to yourself to make yourself better during your lifetime and then you pass it on to your offspring. um, again this is, this is not correct but it was, it was a_ an interesting idea. so he did figure out two really important things. he said organisms can evolve. <P :08> and he also said, that one organism, is ancestral... to another. and these are both, these were both at the time, um, really against the norm and he was adamantly denounced by his scientific peers. <P :05> our next person in this historical story <P :04> is a guy named Cuvier... and he actually provided, more new information, that supported the fact of evolution than anybody else, but he was adamantly anti-evolutionary. he came up with all these great pieces of data but he, refused to look at them in that way. he was the founder of paleontology and stratigraphy and he, established the fact of extinction. which was once again a really big idea. but he was a catastrophist, um, he believed that there had been a series of catastrophes like floods, and that the creator had carried out new acts of creation after each flood. and that's why you saw layers of fossils because the lowest layer of fossils represented organisms that had been wiped out by the first flood. and then, there was a whole new act of creation. and then those organisms were wiped out by the next flood and that's what you saw in the next layer of fossils, and so on. so that's how he explained the layers of, um, of fossils. but he did bring about the idea of extinction. which was a big one and one that most of his contemporaries didn't believe in. um, he didn't believe that man was continuous with animals so he, refused to believe in any, continuity between organisms, but extinction and he did really good work on fossils and that that makes up for something. um Cuvier and Lamarck had many debates about their ideas they were contemporaries. and Cuvier always won because he was the best speaker. so that didn't really help in terms of moving towards the idea of evolution, but that's how it goes. <P :04> so... other things that were going on at this time included a lot of travel, um a lot of natural, theology natural history sorts of things. so people were writing up new species as they found them, they were going to places they had never been before, they were finding lots and lots of fossils. um, mircoorganisms were detected under a microscope primitive microscope and those things all together led to this building, of, thought and ideas kind of all bubbling around at the same time. so that's, that's where, we get to our hero... Rob- Charles Robert Darwin. and i have, a few pictures of him, this is one relatively young at least still looks, kind of old. i couldn't find any real young pictures of him. and the reason why i wanted to show you a young picture of him is because, he started doing things when he was twenty-two. okay he was, um, he was beginning his scientific career at about the same age that you guys, are. um just a few things about him, he um, was born in Shrewsbury England to a well known and wealthy English family of physicians and they just expected that he would go to medical school and, continue in the family way, but he dropped at_ out after only two years of medical school because he couldn't stomach, the crude surgical practices that were, going on at the time like surgery on children without anesthesia, he just couldn't watch it he decided he wasn't, wasn't built to be a physician. um so he went to divinity school, and he, um came out as a clergyman by eighteen thirty-one, but mostly what he was doing during this time, when he wasn't in classes was he was walking around and collecting specimens and, pressing plants, and, talking to animals and he just was a naturalist at heart. he just wanted to be outside looking at things and collecting things. that's all he ever really wanted to do, not be a physician and not be a clergyman. but, then he got outta college and he got this great job offer. he got this job offer, to join the crew of this survey ship called the H-M-S Beagle. and he was hired on as the crew's naturalist_ this is, this is the only picture of the Beagle i could find. this is actually a picture of a model of the Beagle. um so, but this is sort of what it looked like. it was an old gunship that had been refitted for going out on this, this um expedition. and um, just imagine being twenty-two and s- having somebody say to you do you want this job? do you want to travel around, the world essentially, on a boat for five years doing what you've always wanted to do collecting things writing about things, tasting and smelling and eating these things? and he said sure. i think, i would have gone too. um, he was already a really good naturalist. he wasn't just this baby going out he had been working on his craft and his desire for several years at this point, and his knowledge of natural history and geology probably surpassed most of his contemporaries even though he was just twenty-two. and, they set off on a five year voyage. um, his life on the Beagle itself wasn't that great. it was, this cramped little boat and he had about as much room as, i don't know maybe, like from here to here. and he was always seasick he was just one of those people that never got over being seasick. so you know he was always throwing up and he never could really sleep well and, you can just imagine how hard it is if you're seasick trying to read as you're in your hammock as the boat's going through, stormy areas and so, he had not the easiest time of it but he really accomplished a huge amount. he worked very hard everywhere they went he collected things and wrote about things, and every once in a while his notes and collections were sent back to England when they came across another boat that was going in the right direction they would send things back. and so by the time he did get back to England he was already pretty famous. um some of the things that he saw as he went on this route, really stuck with him, um some of the diversity, of organisms that he saw. especially in Brazil that's when it really first hit him and then of course in the Galapagos Islands. but, things that just, blew him away when he saw them (say,) this is so beautiful and it's so odd and it's so different from anything i've ever seen. how, how did it all happen? <P :05> so, in five years, he got back. and i have an older picture of him. <P :05> i think this is probably not at age twenty-seven but it's just an older picture. um, he got married and he moved to London, and then he moved to a smaller town, south of London. and he sorted his collections and he wrote about them. and he h- he was never healthy after that um, for a long time historians thought that he picked up some tropical disease on his trips. but um, since then they've figured out that probably he had some kind of nervous disorder, um he had headaches and nausea and fatigue, and after about the age of thirty he couldn't work more than two or three hours at a time. he just was too tired all the time. and um as i said they think that maybe he had some kind of nervous disorder, due to his extreme ambition and intelligence and driving himself all the time. but in any case he was very, sickly and he never left England again. and he never taught in universities and he never participated in scientific societies except to occasionally give a lecture. so he really, didn't do much except sit at home and work whenever he could and think about the collections that he'd made. so let's look at his ideas. let's look at how, he thought about the theory of evolution. he had taken with him on the, on the, boat ride, the long boat ride, um Lyell's book on principles of geology which had a big effect on him. it was actually the only book he took with him, he had all of the things that he was working on but this was his only book. and so, he had very strong understanding and belief in uniformitarianism, and in gradualism, so that made a big effect on him. he also had learned a lot about the fossil record both before he went on his trip and during his trip, and, he put that together in this story he was building up in his head. specifically on some of his travels he had seen what he called graded variation in nature. in other words variability, across things that are are pretty similar but there's there's variation between them this is, <POINTS TO OVERHEAD> um these are four different types of orchids that he saw during his, well the types that he saw when he was traveling. and they all have similarities but they all are very different. and he called this graded variation in nature. <P :04> during his trip one of the biggest deals one of the biggest most important places that they stopped were the collection of islands called the Galapagos Islands. and they're up there on the left side of the old map. and, um, he saw very unusual organisms there, and he saw organisms that were only there and nowhere else, and, they had a lot to do with him thinking about how things can change over time. this is, one of the iguanas one of the land iguanas seen on the Galapagos Islands and there are several different types of them on the different islands. and this is the Galapagos tortoise... um another thing that he saw, during this time, and also when he came back, had to do with the way that breeders of domestic animals um farmers and so on, could carry out artificial selection by choosing which organisms were allowed to breed. so for example dogs you know h- i don't know how many different types of dogs there are but they've all been brought about by humans artificially selecting, which, parents, can have, puppies. so, in order to get from the wolf which is the beginning point of all dogs to, the Great Dane they, artificially breeders would choose the biggest, the smoothest, the ones with the most drool ability, i don't know what you get to get a Great Dane. and you slowly work over, not very many hundreds of years to get incredible differences in artificial selection, artificially bred dogs. i mean you can go from this little puffy thing to, the Great Dane, to Buster who you met yesterday who was not, chosen to look that way but who looks great anyway. um but this was done over not very many hundreds of years and you can get such change with artificial selection, and if you start thinking about how old the earth is and how long, evolution has had a chance to work naturally, then the kind of diversity that you see across the world is completely understandable. i mean four hundred years versus, billions of years? and we can do this in four hundred years? so he saw that, and then finally, um, one of the last things that really pushed him into the idea, had to do with a guy named Thomas Malthus. and um Malthus was a clergyman and more importantly he was an economist at the time, and he wrote a paper called the Essay on the Principle of Population. and, these were the things that he said in it. <WRITING ON OVERHEAD NEXT 1:40> first of all that human populations, increase geometrically. <P :06> and he said that food production... increases arithmetically. now, you can com- you can fight against those, ideas but he's essentially saying that populations go up, and food production is not going up as fast. and so his next idea following that, was that human population size... would eventually increase to the point, where there would be, limited resources <P :04> and overcrowding... war, famine, disease <P :05> essentially a struggle for existence between members of the human race, to get the limited resources because there were too many of them and not enough of those resources. so Malthus's idea was based on the idea of, humans, but throw in this idea Darwin came up with the idea of a struggle for existence as applied to species other than humans. so this was Malthus's idea and Darwin took it along with the other ones, and it came together in his head. <P :11> so that's perceiving common descent with modification. so starting with some particular organism and seeing change over time to make other organisms. but let's look at how he perceived natural selection the other big part of his idea. <P :06> and this is um, this is usually presented as a series of facts and inferences, several facts leading to a particular inference, several other facts leading to, other inferences. um the first fact, has to do with, something that Malthus said and also what Darwin had seen in various places, and that's that all species have the potential for exponential growth of population size. if you put no limits on the resources for a population, the population can keep growing as long as there's enough food and space for everybody, the population will increase. however... mostly what you see is population size remaining stable. on the islands where Darwin was, was working he saw, you know certain sizes of populations. when he left England and then came back he saw certain populations of deer and so on and butterflies. and they were still about the same. even though there's this, potential for huge population growth generally populations remain stable. the third fact is that resources available to a population are limited so, there's a limitation in resources there's, unlimited potential for growth, but the population remains stable so what's going on here? and what's considered to be the first inference in looking at natural selection, has to do, with this set of three facts. and that's that since more individuals are produced, than can be sustained by available resources the resources remain steady, population starts to go up but it bumps up against this, lack of resources, so there's got to be an intense struggle for existence. organisms are going to eat, other organisms. they're going to try to have more space than anybody else, there's going to be a struggle for existence among the individuals of a population and you're only gonna have survival of a small portion, of each generation. now the critical insight here, in his focusing on the competition for limited resources was that he was looking at, the competition <P :04> among individuals... of the same species. not between peregrines and salmon, that's not the kind of competition he was looking at he was looking at the competition between one salmon and another salmon. or one peregrine and its neighbor. this is, usually called the development of the population concept, and it's_ was an insight, that Darwin had that others had not. others who had had similar ideas had looked for competition between individuals of the same_ of different species as opposed to of the same species. those are the first three facts and the first inference, that he came up with. the next fact that led him on this, development of this idea was that no two individuals are exactly the same. and this was easy for him to see everywhere he looked he could see it. he could see it in something as small as beetles and he saw it in as large as humans. [SU-F: whoa ] i know isn't that? <SU-M LAUGH> but, so he saw that, first of all, he said nobody's, alike. and he said most of this individual variation is heritable. and so he did have this idea. um he didn't know about genes he didn't know what Mendel knew, he didn't know what you know, but he said this variation that i see is passed on to the next generation. and from those two facts that he came up with two more inferences. he said that some of the individuals_ the individuals are competing with each other. they're different and they're competing. some are winning and some are losing, based on their variation. and, some are just better at winning than others, and so survival is not random. it's not just, the pink beetle versus the blue beetle. the pink beetle is better at surviving because it has longer pincers or something. it's not random there's a reason, underlying the variation that makes one better, at surviving and reproducing than another. and that variation that superiority, is carried somehow in the genes we know he didn't know that he said somehow how it's heritable. and therefore, he called this, differential survival, the process of natural selection. some were winning and some were reproducing more. and those that won were more fit for their current environment and they were selected for, in this struggle. and his final inferences to do with the development of the idea of natural selection is that over many generations natural selection will cause gradual changes in populations. the next generation will more resemble, the best adapted previous generation. because the best adapted of the previous generation had more offspring. <P :04> so that's where he got his ideas. there's um one more story here, about another person that was crucial to it, and it's most interesting just because he was so different from Darwin Alfred Russel Wallace was this really poor uneducated guy, who, earned his living by going to the tropics and collecting things. um, he started doing things like this when he was thirteen he left school so no college education for him. he just had a very bright mind a very open mind, um when he was twenty he went down to the Amazon, because he wanted to look at the differences in organisms he wanted to look at spatial diversity, um, because he had read some of Darwin's journals and he thought, ah this is great i just wanna see more if it, this is so cool. um he came back to England and he was going to do some stuff with his collection but his boat burned up, and everything was lost. he just really was kind of a hard luck guy, but, he, sent, an essay a story, um, explaining what he thought to Darwin and Darwin had already come up with all of the ideas i've just talked about. he had written his theory but hadn't published it. he gets this letter in the mail from this guy Wallace who says, essentially the same thing. and he's_ well i- if you've, if you've ever published something you know that it's critical to publish it first or you don't get credit for it. so Darwin, was a really nice guy but he_ you know he worked years on this. and so, the compromise that came out of this is that both he and Wallace, presented their essays at the same meeting at the same time on the same date and they got joint equal credit for conceiving this idea of evolution by natural selection. um, and then, Wallace didn't write the book but Darwin did. these are, all the different covers you can find on various editions of the Origin of the Species from Amazon-dot-com. i'm sure that Darwin would hate all of them, cuz none of them really represent what he was thinking. but, that's what, um the Origin of the Species, by means of natural selection or the preservation of favored races in the struggle for life. um, even though there was a lot of controversy about some of the things in the Origin of the Species, in general, most scientists_ most biologists period, read it and they were, it's_ it was sort of like rereading a mystery story, you've read the book once and you get to the end and you say oh god i never would have figured out who killed him. but the second time you read it you can go back and you can say ah there's, there's something telling me that this is going to happen and that and that's going to happen and then that's going to happen. and biologists who were reading this at about this time were like ah, how come i didn't see this before? this is so right. this is so perfect. and again there were some, people who disagreed with it but was more on the basis of theology than it had anything to do with the data presented or the ideas as they evolved. so to summarize, Wallace and Darwin's theory of evolution is really a group of related ideas, the first, idea is descent with modification. and that's that every species is descendent from a common ancestral species with ultimately a single origin. and a species is made up of individuals which vary from each other, and those differences may influence the ability to acquire resources. these populations change over time, and some of these changes are adaptive, and those, adaptive changes will increase an organism's chance of passing those genes on. so that's descent with modification, and then natural selection is the mechanism by which evolution proceeds. so again Lamarck had the idea about this descent with modification but he didn't have the right mechanism. the mechanism of natural selection. so that you see differences in reproduction, and survival, due to genetically inherited traits. and finally the idea of gradualism is that, species are evolving slowly over time through the steady accumulation of changes. so that is pretty much, the story of Darwin. and we'll take a ten minute break and come back and talk about, the mechanism (in) micro-evolution.
<BREAK IN RECORDING> 
S1: okay folks. i think i'm gonna, bring us back now. um, so i wanna talk now about micro-evolution, which is usually defined as the mechanism of evolution. um i first wanna make clear a couple of things. um first of all what is it exactly that evolves? i mean we've all talked about how our ideas are evolving or our, our um, our relationships evolve but as biological beings, we individuals, individual organisms do not evolve. in terms of the idea of biological evolution, populations of organisms, are the smallest units that evolve. and the definition of a population, for our use right now and we'll expand it a little when we talk about the ecology of populations but our definition for now of a population is members of a species which we're going to temporarily define a species as interbreeding individuals and their offspring. so members of a species that occupy the same geographic, area. so, a more simple way of putting it is that a population is the same species in the same place and at the same time. okay they have to be able to interbreed for us to talk about (a you know a) situation. so, organisms individual organisms do not evolve but populations do. and we need to think about the fact that while, natural selection works on phenotypes what we're really looking at in terms of the raw material of evolution are genes. <P :04> so, while we have a population of wild dogs here, what we have here is the actual raw material of evolution, the D-N-A, and just a quick, review of some of the definitions we've already talked about, um genotype is the genetic makeup of an organism, while the phenotype is the expressed physical traits or metabolism or behavior of an organism, all those outward things that you see or notice. and alleles are alternative forms of a gene and for example we were talking yesterday about Huntington's Disease and one allele is big-H which is dominant, which confers the disease on anybody who has it while small-H which is recessive, does not, so different versions. um the gene pool is all of the genes, all of the alleles in a population. and the allele frequency is the abundance of a given allele in a population. we'll talk a little bit more tomorrow about population genetics and about gene pools and allele frequencies, but i'm just going to use some of these terms today and so you'll need those definitions. but micro-evolution as opposed to macro-evolution which we will also talk about tomorrow, is defined as the small changes in allele frequencies in populations over time. so changes in a population's gene pool. and micro-evolution, essentially is going to tell us how, tiny incremental and easily understood changes over short periods of time, can over long periods of time geological time all add up, to the incredible diversity of life. um we're gonna talk about five agents of micro-evolution. we're gonna talk about mutation, gene flow, genetic drift, non-random mating and natural selection. and we're gonna talk about mutations first. <P :08> alright this is just a representation of, a transcription occurring just to remind you of, the things that occur with D-N-A and R-N-A and so on, um all of those things you already know about. mutation is simply an alteration in an organism's D-N-A, um, it has to be in order to be part of the story, of micro-evolution, it has to be in the sperm or egg cells. it has to be in the gametes, because if you have a mutation in your, skin cell for example, that's not passed on to your offspring. okay you can end up with a tumor, a skin s- cancer, but that's not something that's going to be passed on to your offspring because the alteration in the D-N-A has not occurred your gametes. so that's an important part of a mutation in terms of talking about it, in terms of micro-evolution. and you know that it, results in new or altered gene product or products so in the protein, and then that protein has some altered function and so on. um one of the things that i want to point out here is that mutations are random. they are not directed... by the organism itself, wanting to mutate or by the environment. environmental things can cause mutations i'm not saying that but i'm saying that, an organism doesn't say hm, there's more lactose there and i should be able to use lactose therefore i need a mutation that will allow me to use lactose. it's not pushed mutation is not pushed by the surroundings towards a goal. mutation is not goal directed it's random. and they're they're rare sort of. um let me talk about this in a couple of different ways. first of all um Dr Hammerman talked about, the repair mechanisms that are around in your cells to, reverse mutations that occur. so, they're rare in that, even though they occur, and Dr Hammerman talked about, approximately, the um frequency they occur but, they're most often, repaired. okay, cells have really good repair mechanisms, and so, most mistakes that are made, are reversed. so they are rare, but on the other hand, they're really common. lemme show this to you in a couple different ways... <WRITING ON OVERHEAD NEXT 3:10> um, let's see there we have, in our genome, about, three million, loci. that's the plural of locus. and, each of us have, about three unique mutations (that,) friends neighbors siblings don't have. so that's kinda common, if you think of it that way. that we each have three differences that have occurred over our lifetime. um, let's look at it in another way, let's look at a population... of gypsy moths... on Long Island. <P :04> and, let's say, that... there's ten million gypsy moths <P :05> so that's, ten-to-the-seventh, and gypsy moths have, ten-to-the-fourth, two times ten-to-the-fourth, loci, per moth... and they experience, over their lifetime, on the order of ten-to-the-minus-fifth mutations, per locus. so you put these numbers together we've got ten million organisms, with two times ten-to-the-fourth loci per organism and they have this mutation rate, and that leads to on the order of two times ten-to-the-sixth, mutations, per population... so that's not, that rare. that actually, leads to an awful lot of variability. um, it's, it's usually, considered to be the fact that the average heterozygosity... for ever- for, and that means how many loci are heterozygous therefore have two different alleles, is about twenty-five to thirty-five percent, in... most organisms. and this is based on diploid organisms <P :04> so that's, a lot of variation. that's a lot of heterozygosity, and those were all generated originally by individual mutations. so mutations are rare but mutations are really common as well. <P :16> the other thing that you need to remember about mutations, besides their rarity or commonality, is that, mutations are not all the same. they can be neutral they can be harmful or they can be beneficial. um if you remember, mutations can occur in a variety of different places. they can occur for example in <WRITING ON OVERHEAD NEXT 1:15> an intron... so you're not going to get any altered, gene product. <P :05> um, you could change the codon, with a single point mutation, but you actually don't change the amino acid... because, some amino acids have more than one codon. <P :05> and actually about twenty-four percent, of mutations, are silent like this. <P :08> a third possibility, is that the amino acid is changed, but the function of the protein is not. <P :06> if for example you change one hydrophilic amino acid for another hydrophilic amino acid of similar size you probably or maybe, maybe won't get any change in function of the protein. and this occurs all the time too. so these types of mutations don't lead to anything that natural selection can eventually work on because you're not seeing an alteration in function, and therefore you're not seeing anything that is better or worse and that can be selected for or against. so you can have bad mutations you can have, neutral mutations but, you can also have beneficial mutations that bring about an increase in function or something about the gene product makes the function of the organism better and that therefore will let it, be able to be selected for over evolutionary time. and so beneficial mutations are absolutely indispensable to the process of evolution, and mutation is the ultimate source of all new heritable variation. <P :07> so that's mutation that's the first, part of the story of micro-evolution. <P :11> next is something called gene flow. and this is simply changes in allele frequencies in a population, due to immigration into or emigration out of a population. it can occur when whole organisms go from one place to another like wolves will walk long distances, um between populations you can have the introduction of a whole new set of genes from one wolf coming from one part of Canada and coming down into Yellowstone for example. or you can lose genes out with whole organisms emigrating away from a population. um another mechanism would include what happens with seeds and pollen. if for example if you have like i do in my yard huge, um oak trees with lots of acorns... and you also have a huge population of squirrels and they come and they pick up... the acorns and move them (to different) places, an acorn that is buried by a squirrel, right underneath the shade of the original oak tree, is not gonna have a very good chance of growing, while an acorn that's taken out to a little open space in my yard and planted in the best little pot of earth there and the squirrel forgets it, come April and it actually begins to grow, that acorn, will have its genes passed on.
S3: um in a population where like let's say primates and one group disperses more than another would there be more genetic variation? in that population? 
S1: i i missed the last part i got as far as the primate groups 
S3: oh would there be more genetic variation in a pop- population that um, disperses more? (xx) 
S1: is there more variation in population's that disperse more? it depends on how large the group is that disperses and we'll get to that in just a minute. it depends on, what the variation was in the gene pool of the group that left. okay. but in any case where these acorns go is random. okay it it's not directed, and so flow from genes from one population to another is random in this case. you can lose some you can gain some, but the mechanisms don't allow for direction. <P :04> the next story is something called genetic drift. <P :06> and this is an elephant seal and i'll tell you why i've used this as an example in just a minute. um genetic drift, is, is chance at work. it's coin flipping at work. um, for example if you've got a coin and you flip it a thousand times, you're going to get pretty close to five hundred heads and five hundred tails. okay, you know that is true. but if you flip it only ten times, the chances are pretty good that you might get one head and nine tails, or eight and two or five and five, but the chance, probability of heads or tails only works out to equal amounts of heads and tails with a large sample size. if you have a small sample size your coin flipping, the randomness of coin flipping you can't count on getting an even distribution between the possibilities. so, this randomness this coin flipping effect has a disproportionately large effect on small sample sizes and that's what genetic drift is all about. it's the chance alteration of gene frequencies in a small population. how much it matters to the population depends on the population size smaller ones are much more susceptible to it, and it's usually in populations of a hundred or fewer individuals that it can have its biggest effect. um, let me give you some examples that will make this clearer. the f- there are two variations on drift the first is usually called the bottleneck effect, and this occurs when populations are reduced to very small numbers usually by some catastrophe. by some drastic event. um, and what you get is a severely reduced genetic variation, because you have only a few individuals contributing to the gene pool. and that's what this elephant seal is here as an example of, um in the eighteen nineties, they had a whole bunch of elephant seals but hunters, killed most of them, and brought it down to about twenty individuals. <P :04> and amazingly this population recovered, and there are now on the order of about thirty thousand, individuals. and these are really big animals and actually, i have a little, a little movie, of this really enormous elephant seal, running at you. <P :05> come on. <STARTS VIDEO> so he weighs about, i think he weighs about two thousand pounds. so just imagine if he's coming at you. <P :07> <STOPS VIDEO> um, but, all these thirty thousand elephant seals are essentially, genetically identical. scientists went and took, blood samples from a lot of them. thousands and thousands of them. and they looked at twenty four different genes, um they did R-F-L-P analysis, of the elephant seals, and they found almost, zero variation in their R-F-L-P analysis of all these different genes. these elephant seals had gone through this bottleneck, the population regrew from only twenty individuals, and so you've got very low variation. the elephant ge- seals' gene pools gene pool has lost alleles through this bottleneck. let me give you another example of bottlenecks. these are cheetahs and you've probably heard, that cheetahs are, not only endangered but in real genetic trouble. cheetahs actually have probably gone through two bottlenecks. <P :05> the first one was about, ten thousand years ago, and it's guessed that that's probably due to some kind of climate change. <:04 PAUSE WHILE WRITING> and so you had a large population funneling down to just a few, and they don't really know how many individuals were left after this first bottleneck. and then they recovered, to another large population, and then in the eighteen hundreds, guess what? humans hunted <:05 PAUSE WHILE WRITING> them almost to extinction again, and so we had very few cheetahs again, and now there may be on the order of about, twenty thousand cheetahs left. but the problem with these cheetahs that are left is that they have very low, genetic variation. uh there's all sorts of problems with cheetahs, um one of the very common alleles that almost all cheetahs have, now, is very bad in that, it decreases fertility, in males, this fertility decrease is brought about because only ab- because about seventy percent, of all cheetah sperm, is no good. <P :06> it just won't swim. okay. there is another very common allele which lowers, cheetahs' resistance <:06 PAUSE WHILE WRITING> to several very common diseases. so, lots of cheetahs aren't able to survive disease outbreaks that would otherwise not harm, less um, less bottlenecked cats. so they have a very low genetic variability, even though the numbers seem okay in terms of what you've got for the population, of genes the gene pool it's so limited that any small change in the cheetahs' environment puts them at great risk. so they have a reduced capacity to adapt to any change that may occur. so they're in trouble and in trouble that we can't actually, change at this point. um, any small population is in this same kind of trouble. um, animals that have low genetic variability and small numbers are, not only in danger of being wiped out because of extinction but because, their genes just aren't_ the gene pool is not broad enough. that was a panda obviously just before this is um, a Florida panther and its cub, and i think that there's less than a hundred of these left, and the cheetah of course. um let me give you of another example of a different type, of genetic drift. <P :05> this is called the founder effect. it's not that different, but it has to do with emigration which we were talking about before while the bottleneck effect has to do usually with catastrophe that s- makes the overall population very small. the founder effect occurs when you have just a few individuals leave to start a new colony. now it might be fine it might be, a fine group that leaves with very balanced groups of genes but it might not be representative of the broad gene pool of the original population. and so you have a few individuals moving away and then starting a new population based on just those few individuals, and you see an example of drift. um, the example i wanna give you here is something called Ellis-van Creveld syndrome and it's found in a group of people the Pennsylvania Amish. and what happened here_ now this is, a group of um, people in this is in Eastern Pennsylvania. and, this, group was descended, from about two hundred original settlers. <:06 PAUSE WHILE WRITING> and one, of the settlers... had, E-V-C. Ellis-van Creveld syndrome. and what that is is a rare type of dwarfism. <:09 PAUSE WHILE WRITING> and it's caused by a recessive allele <:13 PAUSE WHILE WRITING> so the frequency in the current population, of Amish <:05 PAUSE WHILE WRITING> of this allele is, about zero-point-seven. while in, most populations... the frequency of this allele is about point-zero-zero-one. <:04 PAUSE WHILE WRITING> so within this small group, of culturally isolated people, these Amish settlers mostly married within their own population and that's something that continues to this day. so essentially over two hundred years of inbreeding has led to this high frequency of this particular allele. this high frequency is definitely not due to the fact that this allele confers any advantage. as a matter of fact it's quite disadvantageous but this is drift working on the allele frequencies in the populations. okay so it this high allele frequency occurred only because of the chance of that first settler having this allele and it being inbred within this population over time. <P :05> um both of these types of drift obviously lead to a reduction in genetic variation in a population. which generally is bad. and both lead to inbreeding, and mating among closely related individuals. um, so the panda and the Florida panthers and the cheetahs, are all in real genetic trouble. um when is genetic drift likely? we have problems again with rare species, if there are only a few individuals that's gonna be a problem. when we have colonizing species, essentially, the founder effect. um when we have fragmented populations, and that's why i put the wolves up here again because even though they're not, rare in numbers if you look at the number of wolves in different parts of Canada there's plenty there, but in the U-S and increasingly in Canada people are coming between small groups of wolves so that there's no longer gene flow between them, we have isolated populations and you begin to get drift within the isolated populations. and so inbreeding and drift, small populations rare species, um, endangered species are endangered in more than just in terms of their numbers but in terms of the numbers of their alleles. <P :07> okay next, mechanism of micro-evolution is called nonrandom mating. and, this occurs when one member of a population is not equally likely to mate with any other member. in other words, i am not equally likely to mate with any one of you in this room. <SS LAUGH> not only because i'm devoted to my husband but because i would probably choose among, the group here based on something. okay. i won't say what but based on something, and based on that i would probably choose Dr Hammerman because we have cultural, connections right? [S2: whatever you say Marcie. ] <SS LAUGH> so so the i we don't, we don't operate with nonrandom mating. okay that's really_ it doesn't usually occur. um, nonrandom mating is the rule in most populations there is some reason why one organism chooses another. okay to mate with. and there's several variations. um, the first one is called assortative mating. and it occurs when individuals tend to mate with each other, with individuals with the same genotype. um an example is that humans, tend to mate with, other humans that are approximately the same height. okay this is, um, this is true. um it seems kind of weird to me but you don't usually see extremely tall people marrying extremely short people. okay. um, nonrandom mating also can occur if organisms can't move around very easily and therefore the only thing right next to them to mate with would be their neighbor and that occurs a lot in plants that don't have ways to spread their pollen or seeds very widely. um it also can occur with slow moving animals like koalas. they move very slowly, they don't usually go from one tree to another over, sometimes their whole lifetime, and so who they're going to bump into is somebody that's probably fairly closely related to them on that same tree. um this also promotes inbreeding as you would guess. but the other thing that these two types of um nonrandom mating lead to, is an increased proportion, of homozygotes... in the population. and so that means a decrease, in heterozygotes overall. just in general homozygotes, usually means, lower fitness and, the accumulation of this increase, in homozygosity... has a specific name. and it's called inbreeding depression. and even more completely defined as <WRITING DURING NEXT :13> the reduction... in average fitness... due to increased... homozygosity. so that take home message there is, marry someone from Australia. <P :08> there's another type of nonrandom mating <P :06> it's kind of interesting, and it's due to sexual selection. <P :08> and nonrandom mating due to sexual selection occurs when, a mate choice is based on a particular phenotype. the look of the mate or the actions of the mate. and we'll talk more about this when we talk about um, behavior, next week. but, this favors the um, traits that the opposite sex prefers, and these traits don't always have selective advantage. um, except that they make, the individual more attractive. this is a frigate bird, and the male frigate bird has this big red throat pouch which normally you can't see very well at all it's just kind of tucked in, but this picture shows him with it inflated out like this because he's trying to attract a female, frigate bird. he's trying to get her to notice him above and beyond all the other frigate birds who maybe don't have as big and as red, a neck. very attractive, to a female frigate bird. mostly it's females that do the choosing, um, and since females have been choosing males with these big red throat patches, the big red throat patched males have more offspring, and so those with bigger and better red throat patches have more offspring, and so we get over generational time more and bigger throat patches on these frigate birds. and_ so the selective pressure has come from the females' choice, the female is making the choice. the problem_ so we first of all have usually, is female choice, and again we'll talk more about that next week. the other thing that happens though is that, um these traits, that are selected, by sexual selection, aren't always adaptive. for example if you are a, predator looking_ say a hawk flying above and you see this big red throat, it's like, eat me. okay? <SU-M LAUGH> they can find this organism better because it's so flamboyant. so it increases the probability of finding a mate but it also increases the probability of being eaten by a predator. so some of these sel- sexual selection traits are not actually, adaptive. i have a little movie for you, um this comes from_ this is an advertisement from France. it has to do with sexual selection but it also has to do with how they can really do the most incredible things in France that we are not allowed to do. <P :04> oh you know what, i forgot to plug in the uh, sound thing. you need the sound. this is it isn't it? [S2: yeah ] okay. <P :05> and i pl- hm. i think <P :12> is it this middle one, Marc? [S2: yeah ] okay. alright. <:20 PAUSE WHILE PLAYING VIDEO> <SS LAUGH> <P :10><STOPS VIDEO><SS LAUGH> so something about that scrub pad, was better. so that's sexual selection. alright, the final, choice for how micro-evolution works, is natural selection. and, this is what we've already talked about some individuals will be more successful than others in surviving and reproducing, and that's because they have some specific traits that make them better at what they do. and the alleles of those who reproduce will increase in frequency in a population. and again that's what micro-evolution is all about is a change in the frequency of alleles of a population. um, some things to think about though in terms of natural selection. let's just say first of all that selection, acts upon phenotypes. phenotypes not only being appearance but behavior, biochemistry, okay? but, natural selection, does not cause genetic changes in individuals cuz natural selection can only work... at the level of the population. so how you look how you behave what your biochemistry is, is what makes you fitter or not so fit. and then natural selection can't change your genotype and it can't change your phenotype, but what natural selection does is wipe you out or allow you to live and reproduce. and so over time the changes in allele frequencies in a population, is evolution, and that's caused by the mechanism of natural selection. so, evolution acts on populations. natural selection acts on individuals in terms of, yes you live no you don't, yes you reproduce no you don't. <P :08> let's compare those five different, agents of micro-evolution. and you might have guessed since i was, making a big deal about it at the end. natural selection is the only one of those five that i've talked about that consistently acts to adapt organisms to their environment. not individual organisms but the populations of organisms as they change over time. um, mutations can be good can be bad can be neutral. um gene flow, is very random so it's not consistently adaptive. sometimes it is and sometimes it isn't. genetic drift again is also flipping a coin. sometimes drift is fine sometimes it's good sometimes it's neutral sometimes it's very bad. and nonrandom mating can be adaptive but as i showed you in the case of the frigate bird or many other, sexual, selective behaviors sometimes it actually makes, for a lot of extra danger or, others' types of nonrandom mating can lead to inbreeding as well which is not adaptive. so only natural selection results in consistent increase in adaptation in a population. but that kind of brings up the question, what actually is fitness? what makes something more fit? and that's not easy to determine. you can't talk about absolute fitness, because, you can be perfectly well adapted to your environment and then the environment changes. and i, i put up a picture of a loon, um because this is an example of an organism that is incredibly well adapted for its environment which is the edges of small quiet ponds or around ponds_ i don't know how many of you have been up, to the fourth floor of the museum, the bird collection is on the third or fourth floor, and looked at some of the birds there, um but if you do and you go up and you look at the loons notice that their, legs are not in the middle of their body where you would find ducks' legs for example or geese legs they're way way back, so they're really good for propelling them forward in the water and they're really good for diving. and you can look at that, that head and that beak and see how perfectly adapted it is for, diving. but you put a loon on, the ground and it can barely walk at all. it's really awkward because its legs are so far back that its center of gravity is off, and so it's really well adapted for its particular environment which is the edges and the center of quiet lakes. and they nest on the edges of quiet lakes and then when, things change like motorboats and jet skis go by, they'll swamp their nests and they can't change, overnight, they're adapted to, the environment that was. and so very well, very fit organisms in a certain environment, might become extremely unfit if that environment changes. so, you can't say something is absolutely fit. you can say it is relatively fit, and it's relative to the current environmental conditions. relative fitness is gonna change as the environmental conditions change. so, selection might not always work to the long term advantage of a population. um many organisms become extremely well specialized for a particular place and time and then that increases the probability that they'll go extinct if the environment suddenly changes. <P :05> so what exactly is an adaptation...? it's some feature of an organism that leads to an increase in performance, and therefore leads to greater reproductive success. and one thing that's important in the, definition of adaptation is that it has to be considered_ it is considered to be an adaptation only, if it's a result of evolution by natural selection and not a result of genetic drift. so in order to fit this definition, adaptations have to have these four characteristics... so we're just gonna look at a couple of examples here. and the first one is one that you've probably heard of over and over and over again, it has to do with industrial melanism in the Peppered Moth. um, i'm gonna walk through, each of those four characteristics for each of these, examples. so first of all the first defini- the first part is that there has to be variation in the trait, and it has to be correlated to some environmental feature. so, we have a variation in phenotype, in the Peppered Moth. <WRITING ON OVERHEAD NEXT 1:04> we can have, white, with kind of, peppered black spots. and i'll show you a little film in just a minute showing this. or you can have what's called the melanistic form... which is mostly black. <P :05> and so there's variation in phenotype and this is related to an environmental feature <P :06> and in this case the environmental feature has do to with, lichens which are mostly white, on trees, that became darkened <P :04> by industrial pollution. <P :09> let me show you this little movie, i don't think the sound on this works very well so you might not be able to hear it but i'll just point out to you the things that i want you to see. <:04 PAUSE WHILE PLAYING VIDEO> i don't think you can see them there too well <:52 PAUSE WHILE PLAYING VIDEO> so that's the Peppered Moth and we'll finish the story, about it and we'll call it a day. [SU-M: <LAUGH> (xx) ] um, it has to be heritable... <WRITING ON OVERHEAD NEXT :50> and, the um, black moths, the melanistic form have a genotype of C-C or C-T, and the peppered, lighter color, they are T-T... so it is, it is um based on, this particular genotype. next is it functional...? well in this case, the color of the moth, has to match, the color, of the background, in order to be cryptic in order for it to be hidden so that birds don't see it and pick it off. and when they were doing experiments with this, um they actually pinned white moths to black backgrounds and black moths to the white backgrounds and white moths to light backgrounds and so on and then counted how many the birds were picking off. and there is an increase in survivorship for the ones that match their background. okay so the ones that show up too well get picked off by the birds. and finally is there a change in time, in the frequency of alleles? yes. um, actually they were able to figure this out based on butterfly collections... kept by English gentlemen. and they looked at the frequency of melanistic moths versus the peppered moths, over the change in time over about a hundred and fifty years, and saw an increase in the preponderance of the dark colored morph. so we'll stop there today.
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