Author Uses DNA Record to Argue Evolution

Can the "fossil genes" found in DNA be used to prove evolution? Sean B. Carroll, author of The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution, argues that the DNA evidence can be used to convince people, beyond a reasonable doubt, that evolution is real.

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IRA FLATOW, host:

Up next this hour, the ultimate proof of evolution. DNA evidence is used in courtrooms around the country every day to prove the innocence or guilt of a suspect. DNA can also be used to show paternity. You know, a simple genetic test can tell you who a baby's father is. And we use it to test for genetic diseases.

In all of these scenarios the reliability of DNA evidence is never questioned. It's a given. We really know that it works very well.

But DNA contains more than just a record of paternity or diseases because hidden in the strands are fossil genes. These are evidence of how an organism evolved over time found in the DNA. And that evidence, my next guest argues, can be used to convince people beyond a reasonable doubt that evolution is real.

Sean B. Carroll is a professor of genetics at the University of Wisconsin in Madison. His new book is called, The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution. He joins us from member station KQED in San Francisco.

Welcome back to the program, Dr. Carroll.

Dr. SEAN B. CARROLL (Professor of Genetics, University of Wisconsin): Thanks for having me, Ira.

FLATOW: Why do you think that this DNA now can be used once and for all to convince people about evolution?

Dr. CARROLL: Well I think in the long run, as DNA evidence sort of pervades all these aspects of society that you talked about, people have to understand that the very same science that we rely on in matters of life and death is pointing to the three billion year history of life on earth and the process of natural selection in just as persuasive and powerful a way.

FLATOW: And people - but people don't accept it. They'll accept it on one but they won't accept it on the other.

Dr. CARROLL: That's right. So that's where we stand right now in 2006. But the DNA evidence is pouring in at an amazing clip. And I think that we're just going to have to confront this in the school room, probably in the court room as well some more, to get people to understand that there's overwhelming evidence for the process of evolution at all sorts of levels, from fossils right down to DNA.

FLATOW: And let's talk about the fossils, because your book lays out in very easy lay language - it's terrific to read - exactly how much of the fossil record is in our DNA. Where is it? How do we know it's there? What does it show us?

Dr. CARROLL: Well it's one of the - probably the thing that's sort of counter to our intuition that as life goes on, various pieces of genetic baggage still stick around. So we carry in ourselves, for example, humans carry about 900 genes that are no longer active but were active in our ancestors at some point.

Almost 70 of those became inactive just since the split from our last common ancestor with chimpanzees. This is the general feature in all species. There are genes still around in the genome no longer active but that were used in ancestors and in different lifestyles.

And when we look at the identity of those genes and what they used to do and what they do today in other related species, they tell us about how life has shifted. How, for example, fish have shifted from say shallow water to deep water lifestyles, or from warmer temperatures to cooler temperatures, or how birds have acquired ultraviolet vision or how we acquired full color vision.

FLATOW: Let's talk about one of those examples of the - one fascinating example, you talk about the ice fish.

Dr. CARROLL: I think this is about the most amazing animal I know of on the planet. So in the southern ocean near Antarctica discovered about 70 or 80 years ago was what turns out now to be a group of fish that their blood is utterly colorless. And it turns out the reason why it's colorless is that they have no red blood cells.

Now red blood cells have nurtured life on earth, invertebrates for over 500 million years. So somehow these fish figured out a way to live without red blood cells. And they had a reason to do so.

And the reason is that in the very cold water they live in, below freezing, around 30 degrees Fahrenheit, red blood cells would make their blood more viscous and harder to pump through their veins and capillaries.

And so they have this very dilute blood. The oxygen concentration is the same concentration as oxygen in the surrounding water, and they just pump a lot of it around using a bigger heart. But they don't have red blood cells.

And then when we look in their DNA, their DNA contains just a little chunk, a little fossil remnant of one of the genes for a crucial protein, a coating of crucial protein in red blood cells called hemoglobin. And whereas all animals with red blood cells and hemoglobin have intact genes, the ice fish has just the fossil gene, just a remnant that's eroding away in its DNA.

FLATOW: Wow. We're talking about fossil genes this hour on TALK OF THE NATION: SCIENCE FRIDAY from NPR News. Sean B. Carroll, who is author of, The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution.

So that shows that the fish at one time had the…

Dr. CARROLL: That's right.

FLATOW: …the hemoglobin and the red blood cells.

Dr. CARROLL: Yeah. Their ancestors did. They lived in warmer waters. And what happened was with the breaking away of Antarctica from South America, that isolated the waters around Antarctica and changed the direction of the current, and that led to a dramatic drop in water temperatures in the ocean around Antarctica.

And most fish couldn't adapt. But the ice fish adapted. And the most striking and to biologists surprising way they adapted was by dumping red blood cells and all that physiology which is, as I said, had been around for half a billion years.

FLATOW: Right. Do we have these examples of fossil genes in humans.

Dr. CARROLL: Yup. There's almost 900 of them in you and I. And about 70 of those are recent events since we split off with chimpanzees.

One example - or I can give you a couple examples. We have a lot of fossil genes for - that would normally be detecting odors. So in other mammals, think of a mouse or any type of animals that are making its way in the world using its sense of smell, they have - it's most abundant gene family in any mammal genome. A mouse has about 1,200 of these genes used for detecting odors.

Well about half of those genes in our genome have gone to pot. They're no longer functional. And the reason why we think this has happened is that in just our distant primate ancestors evolved full-color vision. This didn't happen in other mammals. It only happened in old world primates.

And once you start seeing your way in the world in color, spotting mates, spotting food, detecting danger using your sense of vision, then essentially the pressure has relaxed off your sense of smell and the genes that equip that sense of smell. And the net effect is that those genes accumulate mutations and eventually become inactive.

FLATOW: Why do we still keep them around then?

Dr. CARROLL: It's just a matter of time. It's been still so recent that they haven't been erased completely from the DNA record. There's a pretty steady rate of mutation.

And while these genes can accumulate one or two or three mutations in the course of a few million years, it still would take a much longer period of time for them to disappear from the DNA all together.

So they're there as sort of very informative relics that tell us about ancestral lifestyles.

FLATOW: So if we don't use it, we lose it eventually.

Dr. CARROLL: That's the simplest rule. That's the rule of natural selection. It can't - it can only act in the present. There's no planning for the future. So if genetic information is there but not being used in mutations and it has no effect on the organism's performance, then that information's eventually lost.

FLATOW: Talking with Sean B. Carroll, professor of genetics at the University of Wisconsin in Madison, his new book, The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution.

He's going to stay with us for the rest of the hour. Hope you will, too. We're going to take a short break. Don't go away. We'll be right back.

I'm Ira Flatow. This is TALK OF THE NATION: SCIENCE FRIDAY from NPR News.

(Soundbite of music)

FLATOW: You're listening to TALK OF THE NATION: SCIENCE FRIDAY. I am Ira Flatow. We're talking for the rest of the hour with Sean B. Carroll, professor of genetics, University of Wisconsin in Madison, about his new book, The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution. Our number 1-800-989-8255.

One of the - so many fascinating things in this book, I'd like to talk about and one of them is your explanation. I think you put it in great perspective, the best explanation I've seen written about how a trait that has such high odds against it being developed, one in millions and millions of years, how over time that becomes much more probable. Explain that for us.

Dr. CARROLL: Well, it involves really sort of everyday math. I think one of the hardest things sort of to get your head around with evolution is there is this random component.

Somebody asked me the other day about evolution's sort of trial and error. And no it's actually the reverse. It's error and trial. And the error we're referring to is these errors made in copying DNA. And every new individual that's born carries new mutations that didn't exist in its parents.

And those mutations, while very few, occasionally changed the property of that organism, whether that's how it sees or how it appears or how it digests food. And given the large numbers of individuals that are born, if you think about certain animal populations, whether that's, you know, mosquitoes or sea gulls or whatever, there are so many individuals born per year that the probability is very much on the side of new useful variants arising in a reasonable amount of time, whether that would be a year or a decade or a century.

And once those new variants arise that are better performing at some task, whatever that might be, evading predators or capturing food, those individuals' offspring will be more successful and those individuals' offspring will be more successful, et cetera.

And evolution sort of works like compounding interest. Small differences really add up when compounded over the time of decades to centuries to millennia. And that's how really changes sweep through species and they acquire new traits.

So it's this combination of the mathematics of a random change and then the mathematics of compounding interest to sweep that change through the population through reproduction and survival.

FLATOW: Darwin wasn't the first to think of evolution. Other people were sort of thinking or tinkering about the idea, with the idea before him. What did he add to the story that no one else had thought of before him? Or what advantage did he have, you know?

Dr. CARROLL: He had - well, one - a key advantage Darwin had, he had great grounding in geology. He used to be referred to on the Cambridge campus as the one who walks with Henslow. And Henslow was the ordained minister who taught Darwin geology firsthand.

And he traveled all over England. And Darwin also started to read the works of Sir Charles Lyell, who's really the dean of modern geology. And it was Lyell who sort of opened the world's eyes to the gradual and great changes that took place on earth in land forms, in the oceans, mountain building, all those sort of things.

And that gave Darwin a real advantage to understand that the earth was very old and processes occurred very slowly. But then he just simply connected and said, well, if this is true of the earth then why not the life that's on earth?

And so a grasp of the immensity of time I think is what gave Darwin the keenest advantage over other naturalists of his day in being able to conceive of the idea of dramatic changes in species, essentially that sort of thing we see documented in the fossil record, over the vast time scale of earth's history.

So people sort of forget that, you know, he just suddenly wasn't studying finches on the Galapagos. He had great geological training and orientation. He paid careful attention to coral reefs and to earthquakes and things like that.

And he was really just thinking about life in the same context he was thinking about land.

FLATOW: You know, let's talk about the genetic, the toolbox genes. You have a section in your book called Looks Are Deceiving. All animals share a tool kit of organ and bodybuilding genes. And you go on to describe, using I think the eyes as an example - talk about how - and to me, if I read the book correctly, it explains how humans can only have 20,000 genes and still make up all these different body parts.

Dr. CARROLL: That's right. So this is perhaps the most stunning series of discoveries that emerged in genetics, say, beginning in the 1980s and through the ‘90s, and that was the understanding that no matter how different in appearance, for example, animals are - let's say fruit flies, butterflies, earthworms, humans - they share a set of genes involved in building their general outlines of their body and their body parts, including things like eyes.

So while for a century and a half or so naturalists and biologists thought that, you know, we were so different from certainly things like fruit flies, and we were significantly different from other members of the animal kingdom, even, you know, other primates, the reality in the DNA record is that no in fact our genomes are virtually super-imposable on that of a chimpanzee, very, very similar to that of a mouse. And the content of those genomes contain a really similar set of body-building genes with all other animals.

FLATOW: Even the fruit fly.

Dr. CARROLL: Even the fruit fly. And that's in fact where the first discoveries really, sort of where the revolution started was some - a line of work that probably people weren't paying very close attention to at first of studying the genes that build fruit fly bodies. And then suddenly discovering that we have those very same genes doing very similar roles in our development.

And that runs totally counter to our intuition that if, you know, we look so different and we see ourselves as so complicated, you know, why would we share any genetic recipe with something as simple as a fruit fly? But the truth is that we do share tremendous amounts of that recipe and we just use these genes in different ways to build our bodies that are so distinct.

FLATOW: It's been said many years, as I've been covering science, that if we were to, you know, a species that would disappear or many species disappear, if we would start all over again, we would never wind up with the same-looking things. But you seem to sort of - don't agree with that, if I read you correctly. That we sort of are - animals sort of all go back and then have these toolkits make us the same sorts of stuff?

Dr. CARROLL: Yeah. I think to a greater degree than we realized, evolution is pretty reproducible. Given similar selective conditions, a lot of different types of animals, for example, will happen upon similar solutions. We see this in the DNA record now, especially this very recent record. I have to emphasize how much the data has exploded in quantity in just the last few years. It's absolutely colossal growth. And now that we have this DNA record in front of us, we're realizing hmm, the same things seem to happen multiple times; and just look at this species adapting to this condition and this species adapting to a similar condition at a different moment in time at a different place on earth.

And so that's why I think it's going too far to say really nothing would ever happen the same way again. To adapt to the water from land or to adapt to land from water, or to live in caves or to be more tolerant to, you know, high salt or low salt or greater temperature - that's really - those similar selective conditions will essentially select for similar genetic variance. And we're seeing this in the case of color patterns in birds and reptiles and mammals. And we see this in terms of vision in different sorts of animals that the same genetic changes have taken place tens to hundreds of million years apart in completely different types of species.

FLATOW: Totally separated and have the same genetic change.

Dr. CARROLL: Yes, completely separated, completely independent and, you know, at different times in earth's history.

FLATOW: Surprising to you?

Dr. CARROLL: Well, I think you've got to step back and figure out why that is. I spent some time on this in one of the chapters in the book about sort of working that everyday math of evolution to understand why it's in fact quite probable that individuals will be born with exactly the same genetic variation at different moments in time in different species. In fact, they'll be born in pretty significant numbers, given geologic periods of time.

And so it's - once you sort of sit down with just a little notepad, you can figure out from the mathematics that really evolution will repeat itself again and again and again and again. And we see now all sorts - and I document a lot of these in the book - several examples of the same event happening four or five times in different species.

FLATOW: Talking with Sean B. Carroll, author of The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution. 1-800-989-8255. Bruce(ph) in Colorado. Hi, Bruce.

BRUCE (Caller): Hi, Ira. Great show. I love listening to you. I catch you as much as I can. My question was regarding human evolution. Knowing what we do now about previous human evolution, where is the human species headed, assuming we survive?

Dr. CARROLL: I like the qualifier, Bruce, you put in there at the end.

BRUCE: Yeah.

Dr. CARROLL: Well, as a group, as 6 billion individuals on the planet, I'm not going to point to anything that we're - any direction we're headed collectively. But we have as populations in the last 10,000 years experienced a lot of evolution, and that's left a pretty strong mark on the DNA record of various populations. So if we just look back a little bit in time, some of the parasites and pathogens that humans have faced have had a huge impact on human evolution. I'll single out malaria, for example.

Malaria, the pressure from malaria has influenced genetic evolution in Africa and the Indian subcontinent to a great deal, and we see this for example in that one of the mutations that confers some degree of resistance to malaria is the sickle-cell mutation. Again, a change in a globin gene. That sickle-cell mutation has arisen at least five times in human history in the last 10,000 years and spread through populations.

So in recent history, humans are definitely under natural selection, and the most powerful form of that would be the diseases that we fight. And so any local human population is still under, you know, natural selection, and the most obvious form being the infectious diseases that it faces.

As an overall population, if you're thinking, you know, are we getting smarter or, you know, will we end up with 12 digits, or will we all be able to dunk a basketball, there's not really any pressure that's going to move all 6 billion of us in that same direction. But anywhere there's variation in the human population, and there's a lot of it, that process of evolution is taking place.

FLATOW: Okay, Bruce. Thanks for calling.

BRUCE: Thank you.

FLATOW: 1-800-989-8255 is our number. You know, I've read so many things in this book that I haven't read before in other places. Is that because you've never published it before, or it hasn't been published in other places?

(Soundbite of laughter)

Dr. CARROLL: No, Ira. What it is, and I actually appreciate that comment most of all, I just went digging for some of the very recent gems. They're in the research literature, but these are not cases well known. For example, they're not in the textbooks yet. But I couldn't have written this book four or five years ago. This is really some of the gems that have emerged from studying the DNA record of all sorts of species that have interested us for mostly natural-history reasons or humans, for the obvious reason, and these are the emerging findings. And sort of when collected together, they start to tell some general stories about the way evolution works and the sorts of things we can find out by studying this record.

So yeah, my hope in writing this book was that I would even be surprising the experts in bringing to light some stories that haven't gotten much attention. And at the same time, because of that sort of intersection with natural history, that for people who are just generally interested in nature, that they'd appreciate, get a deeper understanding of us figuring out, you know, how do birds see in the ultraviolet or how do animals adapt to caves and things like that.

And that's really where a lot of action has been in the last few years. And it means that for the textbooks, whether that's, you know, high school or college, we just have a heck of a lot more very persuasive, very crystal-clear examples of how evolution works.

Probably the classic example everybody's been taught or seen is things like peppered moths and industrial pollution in England, et cetera. Well, we've now got dozens and dozens and dozens…

FLATOW: You've got better stuff.

Dr. CARROLL: And we can see the smoking guns of evolution. We know exactly how it happened.

FLATOW: Talking with Sean Carroll, author of The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution on TALK OF THE NATION: SCIENCE FRIDAY from NPR News.

What is fascinating about some of the things as you lay them out is to see just how one or two letter changes in that alphabet of the genome can make such an incredible difference in what results. You lay them out, comparing those little alphabets next to each other.

Dr. CARROLL: That's right. And I do give several examples in the book of where just a single change really is the difference between success and failure for individuals within a species. And they're adapting to whatever it might be - a predator living on a lava rock flow, being able to see their prey in, as I said, in things like ultraviolet light. And some of these changes are very simple. A single letter change in the code, and those single-letter changes of course are happening all the time. So those are very easy evolutionary adaptations to occur.

FLATOW: Do you give any credit to the intelligent design movement for re-invigorating biologists wanting to…?

Dr. CARROLL: Well, maybe in terms of us saying something. Yeah, maybe that's the silver lining in all this is that at no point in my career has evolution been discussed so much, and it just happens to coincide with probably a new golden era in evolutionary science.

This DNA record is so immense - the DNA record is so information-rich that biologists are fully occupied mining this. And so we're going to come out of this with so much more to talk about, so many crystal-clear examples that, you know, in this current climate, it's going to puncture a lot of the objections, or certainly a lot of the rhetoric, that has been floated that somehow evolution is a weak theory in crisis. You know, far from it. It's a strong science that's absolutely in its heyday.

FLATOW: But how many minds will it actually change?

Dr. CARROLL: Well, I don't think it changes many adult minds. I go to a lot of campuses, and I ask kids who are sort of 18 to 22, and I say, you know, how many of you think people's minds are still open at this age? And I'll get a few hands. I think it's going to have to trickle down to when kids first get exposed to the scientific method and to biology in high school. And I do have a lot of interactions with high-school teachers, and I think, you know, the important role that - you know, my day job is as a researcher. The important role we can play is equipping teachers with better and better material so that it's crystal-clear exactly how this works and that it's exciting and inspiring to understand the actual history of life on earth, that this is not taking anything away from other things held dear to people. It's actually, you know, using our talents as humans to understand the history of our species and the history of life on earth. It's a very inspiring story. It's much more enriching I think than just making up ad-hoc explanations.

FLATOW: Well, Sean Carroll, I want to thank you for taking time to talk with us. Your book is exciting to read, and I recommend it to everybody who wants to understand more, because it is written in such simple yet detailed language, and it's quite a pleasure to read it. Thank you for taking time to be with us.

Dr. CARROLL: Thank you, Ira.

FLATOW: Sean B. Carroll is professor of genetics at University of Wisconsin in Madison, and his new book is called The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution.

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