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Science Talk

The Making of the Fittest: A Conversation with Evolutionary Biologist Sean Carroll

In this episode, evolutionary biologist Sean Carroll talks about his new book, "The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution." Even without fossils or comparative anatomy, vast amounts of evidence for evolution and its mechanisms exist in the genomes of the organisms alive today. Carroll discusses immortal genes, fossil genes and repetition in evolution, as well as environmental issues in light of evolutionary understanding. Plus we'll test your knowledge of some recent science in the news. Websites mentioned on this episode include www.seanbcarroll.com; www.egrandslam.com; www.pbs.org/wgbh/amex/babies; www.sciam.com/news; www.sciam.com/podcast

Welcome to Science Talk the weekly podcast of Scientific American for the seven days starting October 25th. I am Steve Mirsky. This week on the podcast, scientist and writer Sean Carroll, after which we will test your knowledge about some recent science in the news. Actually, there are two prominent scientist authors named Sean Carroll. Sean M. Carroll is a physicist; Sean B. Carroll is an evolutionary biologist. He is our guest this week. Sean B. Carroll is a professor of molecular biology and genetics at the University of Wisconsin. He is the pre-eminent writer on evolution who is also doing first-rate evolutionary lab research. Carroll's new book, which came out just a couple of weeks ago, is called, The Making of the Fittest, and it looks at the genetic record for evolution. I called Carroll at his home in Fitchburg, Wisconsin.

Steve: Professor Carroll, good to talk to you.

Carroll: Thanks for having me, Steve.

Steve: Sure. Why did you write the book?

Carroll: I wrote the book because of [the] massive increase in the information we have about how evolution works, particularly in just the last few years, and I thought that most of that information was not in the general public's hands, wasn't really even in biology teachers' hands. So, I then [started] mining a whole new record of evolution and stitching it together in story form.

Steve: What do you find to be the general public's ideas about evolution?

Carroll: I think that the most common trope is the difference between mutation and selection and that the thought that something... evolution does depend upon a process that has a random component and that's often misinterpreted and misconstrued to mean that what's going out there is entirely a set of random luck. Not at all! The process of mutation generates random variation, but selection is not blind at all. Selection is definitely about the relative performance between individuals, and that's what drives the process forward.

Steve: The book talks about the fact that even without fossils and without comparative anatomy, there is in fact plenty of evidence for evolution and that evidence can be found in the genomes of every organism that's alive today.

Carroll: That's right! And then there has been an incredible quantity of that evidence. The DNA has a documented history of [that is] extremely rich and so, in any species' DNA there are thousands of stories in there – the stories about how that species came to be, about who it's related to, and about how it's different from its ancestors.

Steve: There are three major themes in the book. Why don't we talk about each one of those? The three major themes being: some genes are immortal, they are so important they are unchanged for hundreds of millions of years; some genes, however, stop getting used and those begin to decay and you have actual fossils of those genes still lying around in various organisms' genomes; and the third being that evolution in fact does repeat itself from time to time. So, let's talk about it one by one. Some genes are immortal.

Carroll: Right! So, if we look in any living organism– so this could be bacteria, this could be the archaea that live in the hot springs of Yellowstone, plants, fungi, animals – there is a set of genes, maybe on the order of just a few hundred, that are found in every domain of life. And these genes encode functions pretty much devoted to the decoding of genetic material. that [These] must be very ancient functions in terms of cellular life, and what I mean by those genes being immortal is that over really 3 billion years, while others genes have been changing to the point where really their record gets erased over that period of time, these genes have been preserved by natural selection so faithfully that we can see that shared code among all these organisms. So, the reason why they are being preserved is, they are so essential for function that really the organism can't move forward without them. They have to be protected, essentially, from major change, but most other genes do not have this [the] role for this. This set of immortal genes is a tremendous way we can trace the history of life.

Steve: Now give me an example of one of those.

Carroll: Well! One of the most fundamental jobs that goes on in a cell is [the] making of proteins. All organisms have some steps they do in common and the genes that encodes the proteins that are involved in carrying out those steps are very highly conserved, this set of immortal genes. So, things, for example, that are involved in decoding RNA using tRNAs, that's such a fundamental step; the genetic code is universal. The components involved are shared among all organisms and the genes are immortal.

Steve: Let's talk about the fossil genes that are found in genomes. These are like broken, decayed genes, but you can still identify them as formally being complete genes that had an important function.

Carroll: Right! This is sort of a flip side [of] talking about immortal genes. So, the mutation goes on all the time and if mutations are injurious, those mutations will not stick around in [a] population, so that in this competitive process of natural selection, those mutations get purged out of the population. But if those mutations have no negative consequences, they can stick around, they will be tolerated, and what happens is that species shift lifestyle. Let's say animals start living in caves, where their ancestors lived out in open air. That changes the selective conditions and certain traits – their body pigmentation or vision. They are no longer maintained because there is no selective pressure to maintain that and the genes encoding those traits for vision or for body pigmentation, those genes decay and we find them as the fossil genes. But, there are all sorts of examples for this. We humans are carrying almost 900 fossil genes and about 70 of those have evolved just since our evolution from our common ancestor with chimpanzees.

Steve: One of the great examples in the book is how when organisms' vision gets more acute, or their ability to discern colors gets better, they start to lose their ability to smell as well.

Carroll: Yeah! That's a big signature on our DNA, so we, other great apes and old world monkeys, have full color vision and that's unlike other mammals. So, if you think of dolphins and cows and dogs and cats etcetera, they don't have the range of color vision that we have and there's been a trade-off evidently in this mark in our DNA, which is, as we came to rely upon color vision to find foods, spot other members of the species, spot, of course, danger, we stopped relying on our sense of smell as much for all those functions. You know, we don't go along in the world sniffing everything to determine what we're going to do about it and the signature [for] that is that... one of the most abundant families of genes in all mammals are receptors for smell for detecting smell and you know, a mouse has about 1200 of these, but in our genome, half of the genes for detecting smell have become fossil genes, they are inactive and that means, really, our sense of smell has been in the process of decay for quite a period of time. I think that's just the trade-off of, again, a shifting lifestyle, [a] lifestyle which depends more on color vision.

Steve: And again, we know that those used to be genes for smell because they are still close enough to those genes that are for smell in those other species, right?

Carroll: Right! The way to picture this is, the average gene is about, say, 1200 letters of text and if you think of it as an analogy of text, this text has a few typos that essentially break up all of its meaning, but we can still see that if most of the letters are still there, that it bears the strong resemblance to an intact text in some other species. It's just the word carrying around these sort of defective, you know, word document that have accumulated over millions of years. So, they are identifiable, but they are clearly harboring changes that make them nonfunctional.

Steve: And presumably at some point, when, for example, the trichromatic vision was invented by evolution in various species, at some point they had both, but there was no selection pressure to keep the smell genes around, so they started kind of fluctuating it by mutation and eventually decay.

Carroll: Right! So, all genes are equally vulnerable to mutation and mutations will, if the gene is just carrying an essential function... most mutation[s] will not be carried on very successfully in future generations because they compromise the performance of that individual. But if the mutation is having no effect, then the mutations can pile up and so, that we are shifting lifestyles to a color-based vision, you know, vision-driven lifestyle, the disadvantages of having a weaker sense of smell were really outweighed by all those advantages of color vision and the genes went apart.

Steve: And that's just going to be statistical because you can have individuals that had good ability to smell and good ability to see, but they didn't survive any better than the ones that only had the good ability to see.

Carroll: That's right! That's absolutely right! So, and in the cumulative wear and tear of time, these functions are abandoned. And another easy example, I think, speaking of vision – I gave, I think, five cases of this in the book – when species shift, say, [to] deep water where there is very low light or to a strictly nocturnal lifestyle or, as mentioned, living in caves or living below ground, we see the same genes being fossilized. Those genes evolve, for example, in vision itself and so this theme of shifting lifestyles and abandoning former ways of life, and that, sort of broken pieces of DNA text left behind from that, we can see that all over the place.

Steve: And that brings us into the third area pretty neatly, actually, which is, the same adaptations seen in different organisms. And ordinarily if you see the same trait and the same genetic sequence in different organisms, the first assumption is, there is a common ancestor. But sometimes you will see, in cases of convergent evolution, where you get the same trait and the same exact genetic sequence but it happened millions of years apart and may be continents apart.

Carroll: Right! I'll give you that. I think there may be two striking examples. Some birds can see in the ultraviolet, and in some cases that's used in hunting prey, and in some cases that's used in interactions and mating, where birds are seeing reflecting patterns in feathers that we can't see. There the feathers reflect in ultraviolet light and that's been invented at least four times in birds. Another example I gave in the book is that there is this remarkable fish down by the Antarctic in the southern ocean and that water is very cold – it can reach [a] few degrees below freezing – and they have invented a very peculiar family of proteins that is throughout their blood stream and their tissues that prevents them from freezing, instead of freez[ing] like fish. That's when they bump up against the ice, but they have these antifreeze proteins, which is absolutely remarkable. But now you go to the Arctic and you look in detail and those fish have invented their own antifreeze 10 million years apart at the opposite pole of the earth. The antifreezes actually look fairly similar, but we know from reconstructing their genetic history that these were completely independent inventions. So, evolution does repeat itself. It's repeated itself. I'll give you the third example. In humans, when there are stronger pressures on human populations of, say, the last 10,000 years, [there] have been parasites and other diseases such as malaria. And you may know that resistance to malaria is conveyed by having one mutant copy of a global gene in mutations called the sickle cell mutation. So, the one copy that is protected against malaria, in two copies that gives you full-blown sickle cell disease. But here the case was one copy is good, the two copies are very bad. Well, that mutation has arisen five different times in human history in different parts of Africa and the Indian subcontinent and we know and it's the exact same mutation, the exact same change of one letter of the DNA code in human population that gives you a sense that evolution is far more reproducible that even biologists had appreciated out in recent years.

Steve: And you can tell that those mutations came about separately because the genetic sequences around those sequences are different.

Carroll: Right! We can sort of do pedigrees on the population that carried those mutations and tell that they arose at a different place in terms of ethnic groups—well, you know, region—and we can tell that they arose at different times again from the DNA records. This DNA record is also a good timekeeper and it's a good pedigree record in terms of a relationship among populations.

Steve: Let me go back from it because some listeners might be thinking about when you said that the fish are in the water, the temperature of which is below freezing.

Carroll: Yeah!

Steve: You meant freezing for fresh water.

Carroll: Freezing for fresh water, right!

Steve: Right! Because if you have salt water you can actually go down degrees further without the water freezing it.

Carroll: Right!

Steve: At the end of the book, you get into some environmental issues. Why did you think that fit in with this theme?

Carroll: Well! I think when you understand that the fittest in this book is all about the making of the fittest, as we can see it in the DNA records. But I think there is a perception that somehow, you know, current species that are better than previous species and we're always ascending, sort of, in some progressive scale of evolution. That's not really the case. Current species are just different; they are not really better. And when you understand the dynamics: that natural selection can only act in the present, they can't plan for the future – though we understand that the fittest is a very transient, precarious data – it's not an absolute thing at all. And why that's most significant to us is, species change over long as the Earth changes, as oceans change, as continents move, as the climates change. The species are keeping up with it and that's what they are adapting to. Well, we are now the huge agent of change on Earth and all we have to appreciate is the resources we depend upon – let's say fisheries in various parts of world – we have to manage those intelligently by the rules really of selection and evolution for them to be sustained. And so in the last chapter I gave various examples where we can see that intense pressure from human activity, over-fishing for example, does directly affect the evolution of a population. And when too much pressure is put on that population, they really can't keep up; we're outstripping the ability of evolutionary mechanism to keep up and these populations crash.

Steve: You talk in the book about how just the size of the holes in the nets has an evolutionary impact.

Carroll: Yeah! This is remarkable. Work done by some fish biologists understand that if you drag a net through the oceans, the little ones that get through the net may actually flourish, so you will see larger numbers of those species, but the ones that get caught in the net disappear and so, species that aren't of any commercial interest but they escape, for example, that aren't important in terms of the economic value, you will find that the larger escapes have been pushed to virtual extinction and some smaller escapes are thriving. Well, you might feel is that's good, you know, (laughing) the smaller kids are thriving. Well, no. The whole ecosystem is upside-down and the very valuable animals are gone. So, we have to understand that, you know, just something like a net with a certain mesh size on it is a very powerful force of selection when you drag it across the ocean.

Steve: That's about the most powerful selection force there is. That's life or death.

Carroll: That is absolute life or death and the escapers that get through, well that, you know, that's a very different changed ecosystem than what was there before, and those fish populations that we have depleted to an extensive degree may never recover no matter what we do. We could leave the ocean alone; they may still not make it back. We still change the balance in the local area.

Steve: Well, it's really a terrific book, The Making of the Fittest by Sean Carroll. The subhead is DNA and the Ultimate Forensic Record of Evolution. So you've got a little CSI in there, too.

Carroll: Yeah! It's a CSI (unclear).

Steve: Sounds good! Sean Carroll, thanks very much!

Carroll: Thank you, Steve!

Steve: For more info about Sean Carroll and the book check out his Web site www.seanbcarroll.com. That's S-e-a-n-b-C-a-r-r-o-l-l. An excerpt from the book is scheduled to be up at his Web site by the time you are hearing this podcast and in the coming months, Sean will start contributing to what's scheduled to be a series of featured articles for Scientific American magazine, so keep on the look out for those.

Now, it's time to play TOTALL.......Y BOGUS

Here are four science stories. Only three are true. See if you know which story is TOTALL.......Y BOGUS

Story number 1: A candidate for office suggested that all students be given thick textbooks to use as shields in case of a school shooting.

Story number 2: Microbes living deep underground in South Africa are dependent on chemical reactions driven by the energy given off by radioactive uranium rather than by photosynthesis.

Story number 3: A study finds that blue-eyed men prefer brown-eyed women, apparently because they are evolutionarily driven to enhance their offspring's genetic diversity.

Story number 4: They used to call the freshman 15 referring to the 15 pounds kids would allegedly gain during their first year of college. New research at one big college found that the weight gain was on average about half that.

Time's up!

Story number 1 is true. A guy running for superintendent of schools for the state of Oklahoma suggested that students be issued thick textbooks for use as shields in the event of a school shooting. He showed videos of a calculus textbook stopping a pistol bullet, but not stopping a rifle bullet. Nevertheless, he is sticking to the book as shield idea.

Story number 2 is true. A community of microbes has been found deep underground that depends on radiation from uranium as the foundation of local food web. For more, listen to the October 23rd daily podcast 60-Second Science at www.sciam.com/podcast.

Story number 4 is true. A study of over 900 students at a big Midwestern university found that the freshman 15 pounds is more like eight. The gain is probably due to stress and the availability of alcohol and high-fat foods. Just a thought, some kids might still be growing, too. For more, check out the story on our Web site's news section called, "Students Gain Wisdom and Weight in College."

All of which means that story number 3 about blue-eyed men preferring brown-eyed women is TOTALL.......Y BOGUS, because a new study shows that blue-eyed men prefer blue-eyed women, perhaps because eye color can reveal paternity and if a blue-eyed couple has a brown eyed baby, well, somebody's face is going to be red. Brown-eyed men cannot tell paternity by a child's eye color and the study found no eye color preference among brown-eyed men. For more, see the story at our Web site called, "Blue-eyed Men Prefer Blue-eyed Women" at www.sciam.com/news.

A couple of notes – our baseball mathematician from two weeks ago, Bruce Bukiet, had the Mets over the Cardinals, but a Met win wasn't in the cards, so Bukiet's probable winners are just 1 for 6 in this postseason. He has the Tigers with a 56 percent chance of winning the World Series over the Cardinals. That series stands at one game apiece as we go to press. Also, last week, Robin Marantz Henig discussed a PBS program on test tube babies, based in part on her book and Scientific American article, Pandora's Baby. The PBS Web site says that the entire program should be available online by the time you are hearing this podcast. That's at www.pbs.org.

For more Scientific American, check out our science video news at our Web site, sciam.com. You can sample the daily SciAm podcast, 60-Second Science, at the Web site and at iTunes. And you can write to us at podcast@sciam.com. For Science Talk, the weekly podcast of Scientific American, I'm Steve Mirsky. Thanks for clicking on us.

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