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Originally broadcast: 2007
Length: 50:40

The DNA Files:
Unraveling the Mysteries of Genetics

As heard on National Public Radio

Beyond Human

Hosted by John Hockenberry

Transcript

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JOHN HOCKENBERRY: This is The DNA Files. I'm John Hockenberry. What does it mean to be human? Philosophers have asked that question for hundreds of years. Now scientists consider the question by comparing the DNA of humans to other species.

SEAN CARROLL: The more you look at the genetics, the less unique we are. You know, we don't even have more genes than a puffer fish. So you know, you're just going to have to get over that.

JOHN HOCKENBERRY: We share most of our DNA with chimps, a lot with mice, and even a good bit with animals that seem quite remote like sea urchins and sea slugs.

ROSS HARDISON: There's no reason to think that every nucleotide or every base pair in the human genome is important in making you human. It is possible, maybe way more than half of the DNA in our genomes is doing nothing.

JOHN HOCKENBERRY: Coming up in this hour of The DNA Files, "Beyond Human." We'll be right back after the news.
...
JOHN HOCKENBERRY: All right. Let's talk for a minute about gorillas and chimpanzees. How different do you think they are from us? How different do they seem?

GIRL 1: This sounds kind of cheesy, but when we were at the gorilla exhibit, and the little baby gorilla looked you right in the eye, you could just tell that they were making connections with you, and that you were similar to them, really like making judgments about you.

JOHN HOCKENBERRY: This is The DNA Files. I'm John Hockenberry, and this program is "Beyond Human."

GIRL 2: I guess we're more advanced, like our world, but I doubt a lot of us would be able to survive in the wild, how they do.

JOHN HOCKENBERRY: About 10 feet away, there's a family of Western Lowland gorillas walking through the woods. Well, 10 feet plus some pretty thick glass that we're looking through. Welcome to the world famous Bronx Zoo in New York. I'm here with some 8th graders from Owego, New York in the Congo Gorilla Forest.

GIRL 3: There's a lot of similarities that you can see, but there's also a lot of differences, just structural, like their brain case is smaller.

JOHN HOCKENBERRY: Half a century ago, biologists compared species by looking at body parts and brain size, behavior. Now we have something else to look at, the entire DNA sequence inside our cells, our genomes that help make us us and chimps chimps, aardvarks aardvarks, and algae algae.

JOHN HOCKENBERRY: What percentage of similarity do you think, just guessing between chimps and humans, if you're looking at DNA?

GIRL 4: Probably like 80 or 90?

JOHN HOCKENBERRY: 80 or 90? So that would be like a 10% difference?

GIRL 4: Yeah.

JOHN HOCKENBERRY: What do you think?

GIRL 5: 75, 80%.

JOHN HOCKENBERRY: 75, 80%? Do you know what it really is? Are you ready? Are you sitting down? [laughter]

GIRL 6: Yes, we are sitting down.

JOHN HOCKENBERRY: 99%.

GIRLS: Oh, my gosh. I would have never guessed.

JOHN HOCKENBERRY: I mean, probably there are people in your class that you don't even think are 99% similar to you, right? [laughter] Ooh, touched a nerve.

GIRL 8: Ouch.

JOHN HOCKENBERRY: Okay. Thanks. We'll go down to this end of the table now.

ROSS HARDISON: We have a wonderful resource of many, many new genome sequences that are being determined. Of course, the sequence of the human genome was a revolutionary event for our field.

JOHN HOCKENBERRY: Comparative genomics is a relatively new science. Researchers line up and compare the genetic sequences of different species.

ROSS HARDISON: For comparisons, you need at least two, but we are putting together with our collaborators our alignments among 28 different vertebrate species -- that'd be human and mouse, chimpanzee and macaque and other monkeys --

JOHN HOCKENBERRY: Ross Hardison is director of the Center for Comparative Genomics at Penn State University. The Center analyzes patterns in genomes that contain millions, sometimes billions of bits of information.

ROSS HARDISON: The dog genome is in very good shape, and has been a spectacular resource for study. The cat genome is catching up, and the horse is quite similar to the human genome. We can move over to another continent, Africa, the elephant sequence --

JOHN HOCKENBERRY: As they compare these genomes, scientists are finding subtle differences and surprising similarities in everything from birds to baboons to bacteria.

ROSS HARDISON: And then happily, we're getting several other vertebrate species that are great for certain types of comparisons. Chicken has been published for about two years now. I see a lizard that's coming along that's going to be very useful, and frog -- the frog genome sequence is available, and I think five different fish.

SEAN CARROLL: So we can decode a bacterium. We can decode a virus. We can decode a -- a redwood. We can decode a human using all the same genetic code, and that's just terrific.

JOHN HOCKENBERRY: In the next hour, we'll cross the country visiting the labs and people who are pioneering this new way to look at ancient patterns in DNA. Sean Carroll is a molecular biologist at the University of Wisconsin in Madison.

SEAN CARROLL: So comparative genomics. What do we see when we gaze into genomes, and especially about evolution?

JOHN HOCKENBERRY: Carroll studies how various species evolved to have particular shapes, and what DNA can tell us about how that happened. He's the author of popular books, Endless Forms, Most Beautiful and the Making of the Fittest.

SEAN CARROLL: So the genome is the complete DNA information of an individual, and in us, it contains about three billion bits of individual pieces of information. And what scientists are able to do now is inventory all that information for an individual species. Now this DNA record can tell us about species relationships. It can tell us about how species are different from their ancestors, and of course, it also tells us about the operating instructions for making new individuals. So the DNA record is written in a very simple alphabet, that of just four letters, A, C, G, and T, but it's almost the infinite permutations of those four letters that gives us all the complexity of the living world.

ROSS HARDISON: If you can imagine three billion characters -- and there are only four types of characters -- A, G, C, and T -- and it's the order that they are along these three billion positions that's important.

JOHN HOCKENBERRY: Again, Ross Hardison of Penn State's Center for Comparative Genomics.

ROSS HARDISON: If you line up the genomes of two species, and you find segments that are still quite similar, we say they are conserved. It's an inference that we're drawing.

JOHN HOCKENBERRY: These conserved DNA segments give us a glimpse into the past we share with other species. Researchers are finding similar DNA sequences doing similar tasks in very dissimilar animals.

ROSS HARDISON: That means that they were the same sequence and the last common ancestor, and they're still similar enough for us to line them up. Almost the entire genome has that property between humans and chimp. You go out to mouse and it's a lot less. So we can line up of the order of -- depending on how you do it, maybe 40%. So you can say that 40% of human is conserved with mouse. Then if you line up human with chicken, it's a very small percent of human that lines up with chicken.

So the fact that something is conserved in human and chimps doesn't mean much. It sure means a lot if you can find it conserved between humans and fish or humans and chickens. And in fact what we see, if we look at thousands of regulatory regions, you see that a small fraction of them, about 2% align all the way from humans out to chickens, and they have some very interesting properties. I mean, not only has selection been working on them really hard, so they don't change much, they regulate a certain category of genes. They are the genes that encode proteins that control the fundamental early stages of development.

SEAN CARROLL: How is it that the head is put at the right end of the animal, and you get the right number of digits, and you get this beautiful bilateral symmetry that exists in a lot of animals?

I don't think any biologist is sort of immune to that wonder at how a single fertilized egg becomes a complete complex individual with all of its body parts. And this process we refer to as development or embryonic development.

So only a small fraction of all the genes in our genome are devoted to body building and organ building and sort of the patterning of the way we look. You can sort of think of them, if you want, metaphorically speaking, as the sculptors and painters in our genome. And over the course of a couple of decades, developmental biologists have defined what we call a genetic tool kit for development. It's changes in this tool kit that underlie the diversity of everything we see. A lot of what's going on in evolution is we're just changing the number and identity of particular body parts.

So once sort of making vertebrae was figured out, it's just tinkering with the number of vertebrae or the identity of vertebrae or what's sort of erected on that sort of chassis, and that would be true, whether we're talking about snakes versus humans or even humans versus chimpanzees. You know, the anatomical resemblance between ourselves and the chimps is pretty obvious, but you know, we've got bigger brains, different facial shape, different arm length, and these are really perceived as minor tweaks of anatomy. We're just a remodeled ape, I think. That's what I boil it down to. And this process of remodeling involves using these genes in either slightly to dramatically different ways in the course of evolution.

So it's demystifying a lot of what we found mysterious about biology and about evolution by making lots more connections between the simple and the complex, and this is what we can do through genomes, and this what we can do through developmental biology. We can trace the origins of structures. We can trace the relationships among structures, and we can see all sorts of gradations from really very, very, very simple versions of some structures to what we think is, you know, the more complex grand versions that we carry. So we're finding much more in common with the whole animal kingdom than we ever thought before. And you know, humans wanted to hold themselves out as something unique. Well, the more you look at the genetics, the less unique we are. You know, we don't even have more genes than a puffer fish. So you know, you're just going to have to get over that.

JOHN HOCKENBERRY: So 99% similarity. What does that say to you?

BOY 1: Well, for how much we have, 1% is still a lot.

JOHN HOCKENBERRY: What do you think?

BOY 2: Chimps and their DNA, all of it, all of their chromosomes, it's 1% different. But you have to realize that not all of the DNA actually controls something. A lot of it's just left over from whatever. So in that 1% that's different could be a lot of stuff that controls traits and the brain size and the body hair and the body structure and --

ROSS HARDISON: [laughs] If you try to talk about a percentage human or a percentage chimpanzee, that's a hard thing to define. There's no reason to think that every nucleotide or every base pair in the human genome is important in making you human. It is possible, maybe way more than half of the DNA in our genomes is doing nothing. So what does it mean, if 98% of something that doesn't do anything [laughs] lines up? Right? That's not such an interesting question. The interesting question is: What's different?

JOHN HOCKENBERRY: One clue can be found in our genes. Researchers have found that chimps do share almost all their genes with humans, but they work differently.

ROSS HARDISON: When they see genes whose coding sequences are substantially more different than you would expect, we say, "Well, wow, maybe this has something to do with making humans uniquely human or making chimps uniquely chimp."

GIRL 1: Their eyes are like exactly the same as ours -- the same shape and the same flat face, and 10% of like communication is only words, like only 10%. So it's all about body language and how you act.

JOHN HOCKENBERRY: What do you think the chimps are thinking? Do you think if they knew that you'd actually pay money to watch them stand around? [laughter]

GIRL 2: They probably think we're weird. [laughter]

GIRL 3: And they're kind of like -- they're probably wondering, just like we are, like, "What are they doing?" and like "How do they live?" and stuff.

BOY 2: We're just a little bit more advanced with the speaking, but they can do sign language, which a lot of people can't do.

WILLIAM FIELDS: Here comes Liz. Come up here and talk on this keyboard, okay? Come tell the visitor what you said. So is there anything you would like after the Wasserman test, Panbanisha?

COMPUTER: Coffee.

WILLIAM FIELDS: You'd like some coffee? You would?

JOHN HOCKENBERRY: Coming up, we talk to the animals, and evolve an eye. You're listening to The DNA Files. We'll be back in a minute.

FIELDS: All right. So -- all right.

...
JOHN HOCKENBERRY: This is The DNA Files. I'm John Hockenberry. That's a bonobo, one of the chimpanzees genetically most similar to humans. As our bright young students mentioned, there are some pretty big differences between chimps and us. For example, my human DNA has given me the ability to talk, which is why I can host this program. [laughs] Digging around in genomes may one day help us explain how language works, but to get a better picture now, we first need to widen our view.

WILLIAM FIELDS: Come up here and talk on this keyboard, okay? Come tell the visitor what you said.

JOHN HOCKENBERRY: At the Great Ape Trust, just outside Des Moines, Iowa, researchers communicate with bonobos using symbols or lexigrams. The bonobo sits at a large touchscreen. When she presses a lexigram on the screen, the computer speaks its name.

COMPUTER: Coffee.

JOHN HOCKENBERRY: William Fields is director of research and co-author of the book, Kanzi's Primal Language. No one trained Kanzi and his sister, Panbanisha to use the keyboard. They just watched the older bonobos listen to the humans and learned on their own.

WILLIAM FIELDS: This is Panbanisha. She's the real life of genius.

LIZ: Here you go, Panbanisha.

WILLIAM FIELDS: Okay, it's ready. Come do it. Come do it. She's going to match to sample.

COMPUTER: Brush.

LIZ: Good. Do 15 of them.

COMPUITER: Sue, Sue.

WILLIAM FIELDS: The lexigram comes up, and there's spoken English, and then Panbanisha matches the lexigram and the spoken English to the photograph. She gets several selections of photographs there, and she's really good. The only time she's wrong is when she wants to make a point, and she'll just hit one to be wrong. She's never wrong without intention.

COMPUTER: Popsicle, Popsicle.

WILLIAM FIELDS: She learned just the way children learned language. She acquired it just by being exposed to it, and humans using the lexigrams around her.

COMPUTER: Marshmallow, marshmallow.

WILLIAM FIELDS: We're getting ready to test her receptive vocabulary for English. We know it has to be in the thousands of words, and we'll never really know. We'll just have an idea of the dimension, because it's unlimited. I mean, I know that she knows "microphone," because I've asked her to hand me the microphone before, and she's handed it to me. We don't have a lexigram for microphone. Or I can ask her to go over and see the visitor with blond hair. She knows blond hair. We don't have "blond" on the keyboard. She has all kinds of competencies that we're unable to measure at the moment, because of limitations of the keyboard.

LIZ: I know you're upset, but we're not going to do that.

WILLIAM FIELDS: There you go.

LIZ: This is "clippers."

COMPUTER: Clippers, clippers.

LIZ: Do you want me to come in?

WILLIAM FIELDS: Yeah, Panbanisha got mad at us. We got a little too involved in the whole human conversation thing, and like I told you earlier, they enforce the social rules. The best way she could express her frustration with us was to hit the wrong key for "clipper." I mean, we all know she knows "clipper," just like she knows her name. And she hit it twice for us, just so it would make that noise. [laughs]

COMPUTER: Coffee.

WILLIAM FIELDS: Okay, well, I'm going to get the coffee when you're through.

AL: The order's been placed. [laughs]

WILLIAM FIELDS: What are you hanging around for, Coffee Boy? [laughter] A decaf caramel macchiato is a favorite. Panbanisha and I have spent a lot of time in the forest together. We've made stone tools together. We've camped out. We've made fires, drank a lot of coffee together. She's a really good friend. You're doing good. But they're not human. They are persons, but they're not human. They're bonobos. They have identity. They have autobiographical memory. They have episodic memory. They can identify themselves in photographs. They identify themselves in the mirrors. It's not just that they identify themselves. If you have two of them in the mirror, they can point to themselves, and they can point to the other one in the mirror. They know who they are. They have a history, and they can tell you about it.

Humans are wonderful and special, but they're not any more wonderful and special than any of the other Great Apes or the biodiversity on this planet. Even though we have wonderful talents -- or I think that they're wonderful -- that may just be -- that's just a bias. I mean, I happen to like mathematics, but the bonobos don't seem to do mathematics, even though they can do quantity judgments, and they can do numerosity and ordinality. They're not interested in differential equations, but now that I think about it, neither is my mother.

All right. After you do your Wasserman test, we'll have some coffee, okay?

COMPUTER: Coffee.

JOHN HOCKENBERRY: How would you prove to a chimp that you're more advanced or do you maybe think that you're not?

BOY 1: I think it's -- a lot of it that the main argument is language.

JOHN HOCKENBERRY: Language?

BOY 1: They probably do have vocal chords, but just like not --

BOY 2: They don't know how to use them yet.

BOY 1: Not -- it's being developed.

BOY 2: They're probably just not as developed yet.

JOHN HOCKENBERRY: For years, we've assumed that humans have language, because we've mastered abstract concepts like grammar, symbols, and syntax. But we also know that the human voice box, and brain, are built differently than in most other species. So how do we sort out what's happening in our heads and bodies that's different from other animals?

ERICH JARVIS: To actually answer that question, we have to take a comparative genomic approach.

JOHN HOCKENBERRY: Erich Jarvis studies that genes and brains of vocal learners at Duke University in North Carolina. These aren't animals that can talk, but they are animals that learn to make more than the growls and whistles they're born with, animals that communicate by complex vocalizations. You know some of these animals.

ERICH JARVIS: There are three vocal learning groups of mammals at least and three vocal learning groups of birds. Amongst the birds, these are parrots, hummingbirds, and songbirds, and what we discovered is that these vocal learning birds have very similar brain pathways to control their learned sounds. We argue that the bird brain pathways are similar to humans. The mammalian part of the story is similar. In humans, bats, and dolphins, these are all vocal learners, and yet they are separated by vast genetic differences, but yet you have a chimpanzee, a very close relative to the human, 98% identical in its sequence, is not a vocal learner. So we're also doing genomic comparisons on chicken and chimpanzee and bat to ask the question, "Will bats and humans have a similar type of mutation as you find in songbirds, parrots, and hummingbirds?"

DONALD KROODSMA: We're listening now to a song sparrow singing here, and there's a close relative, a swamp sparrow, both in the same genus.

JOHN HOCKENBERRY: Donald Kroodsma has been studying vocal communication in birds for over 30 years. He's one of the best guys on the planet to take us for a stroll in the woods. He likes to be there before sunrise, of course. That's when the birds sing the best, apparently. So imagine it's 5 AM. You're in the Quabbin Reservoir, a wilderness area in central Massachusetts, shh. Here we go.

DONALD KROODSMA: And what's so intriguing about these two -- they're members of a group called songbirds. And songbirds learn to sing like we learn to speak. And I can say that a thousand times, but wow, then I can show you a sequence of my daughter's babbling and how she babbled at a year and a half to two, and that's something that we've all done to get to where we are so we could speak. Then you compare that babbling of that child to the babbling of a baby bird, and it's exactly the same process, because these songbirds have to hear other adults in order to develop normal songs. If they didn't, they'd just sing absolute nonsense. It's like taking a human child and not ever letting it hear language -- why, it would not speak a language [laughs], recognizable a language either.

And then there's -- there's this bird over here. It's an oven bird, singing on the forest floor. And the mnemonic that we read in the field guides is, "Teacher, teacher, teacher, teacher." It's a crescendo. It's just shattering, and our ears just can't capture what these birds are doing. And these songbirds have ears that are a lot better than ours. They can resolve sounds in time far better than we can.

Any small songbird like the winter wren, once you start to slow it down, it develops this richness, because now we're starting to hear the individual elements, and we're lowering it to a frequency where our ears can pick it up. And you take a tiny little 10-gram wren, and slow it down far enough, it starts to sound like a humpback whale.

ERICH JARVIS: All the research that I've been doing in the past 10 years has been leading up to one conclusion for me, that language or vocal learning in general, what's unique about it in those species that have it -- humans, songbirds, parrots -- is the motor skill part of it.

JOHN HOCKENBERRY: Again, Erich Jarvis.

ERICH JARVIS: And the neurobiology of our results are suggesting that the vocal learning pathways, what's unique about them is they're coming out of a pre-existing motor pathway, not in a perceptual one, or one might call a conscious one or something else.

DONALD KROODSMA: Oh, getting these songs right is an extraordinary athletic endeavor. And a friend of mine published a paper many years ago entitled, "Vocal Gymnastics in Wood Thrush Songs," and that really captures it. If you watch a gymnast flipping and turning in the air, and you think, "What did it take to get her there?" Why, she had to practice and practice and practice, and drive that routine into the neurons and into the brains so that she could do it without thinking. That's what these songbirds do, too.

That wood thrush, when they sing, they actually have two voice boxes, and it really is precision breathing, because they open and close those voice boxes, change the tension, puff the air through one voice box or the other to create this beautiful harmony. And if you're out with them at the right time in August and September, you hear them practicing. You can hear the wavering quality to their songs as they're bringing their whole body back up into singing condition. Everything has to peak for the spring and summer season to create these -- these masterpieces that we're hearing now. So I like to look at each one of these animals out here -- each one of these birds and say to myself, "Each one of those birds has an equal claim to success as I do." This oven bird, he is every bit as much a success as we are, an extraordinary success in the world that he lives in.

JOHN HOCKENBERRY: It's nice to think we might share something as complicated as language with songbirds, and that chimps like Panbanisha try to communicate with us. It makes me feel one with the universe and all. But let's face it. Our tax dollars aren't being spent on science research to make us feel warm and fuzzy. No, all this sequencing and lining up is really big.

FRANCIS COLLINS: This is a landmark occasion. Here in the very month of the 50th anniversary of the discovery of DNA's double helix, I am pleased and honored -- perhaps I should say "exhilarated" to declare the goals of the Human Genome Project to be completed. [applause]

JOHN HOCKENBERRY: That's Francis Collins who helped lead the Human Genome Project, announcing the completed sequence in 2003.

FRANCIS COLLINS: But then the Chinese proverb comes to mind, "Behind one high mountain lies yet a higher one," and so tomorrow, we will be looking beyond the mountain called the Human Genome Project to the next phase of how it is that we can apply this to the betterment of humankind for advances in medicine, which were after all, always the point.

ANTON NEKRUTENKO: When the human genome was sequenced, I think CNN had these headlines that now we're going to solve all the problems. All the diseases will be cured and everything. But in fact, it's very difficult to decode this information. So the only way you can effectively do that is by comparison with something else. Only by comparison you can actually make sense of genomic sequences, and so I'm doing a lot of analysis related to mammals, and Steve is doing a lot of analysis related to flies.

JOHN HOCKENBERRY: Anton Nekrutenko and Steve Schaeffer are colleagues at Penn State's Center for Comparative Genomics. Even before the human genome sequence was finished, scientists started lining up what pieces they could get their hands on with other animals and insects. We've gotten hints about our immune system from the primate genome. From dogs, we're learning about the roots of cancer, diabetes, and epilepsy. Oh, and about Steve Schaeffer's flies.

STEVE SCHAEFFER: It turns out that a lot of the genes that you find in humans, albeit they're distantly related, are found in flies, things that are important for segmentation and the formation of our nervous system and the vertebral column are basically similar between flies and humans. And the beauty of a fly is its generation time is only about two weeks in length, and it turns out that many of the genes that actually are involved with cancer can be manipulated and studied in a fly and nobody really has – you know you don't see PETA coming in and releasing the fruit fly. So the Human Genome Project wasn't just about humans. It was about looking at diverse organisms, developing genomes for model systems that can be experimentally manipulated so that if there are human counterparts in those organisms that we can study them in a laboratory.

***

JOHN HOCKENBERRY: When you look into the eyes of a chimp, do you see anything even remotely human?

GIRL 1: Well, I think we have a lot of similarities, physical and emotional.

JOHN HOCKENBERRY: Emotional?

GIRL 1: Well, just in their eyes. You can just tell how they're feeling some of the time.

GIRL 2: It's more than that, though. Like if you look at their faces, even they have expressions like in the lines of their faces, too, like one of the gorillas we saw out there, he almost looked like he was sitting there thinking about all of us out looking at him, like it was in his eyes, too, but you could kind of see it in the contours of his face.

JOHN HOCKENBERRY: How about -- what do you think?

GIRL 3: I think that chimps like humans have different like intelligence levels. So some might look more intelligent through their eyes than others do.

SEAN CARROLL: For many, many decades, in fact, leading all the way back to Darwin, biologists have been contemplating the origin of eyes.

JOHN HOCKENBERRY: Remember Sean Carroll? He says it wasn't easy to see how evolution came up with something as sophisticated as the eye. That is, until comparative genomics came along with a whole new way to look at the question.

SEAN CARROLL: So one of the most spectacular discoveries I think that's emerged from comparative genomics and developmental biology is that body parts that initially seem so different can have a very similar genetic recipe. And let's take, for example, the eye. One of the most spectacular discoveries made a little over 10 years ago in a very unexpected way is that some medical scientists have been studying mutations that affected the development of the normal human eye, and the counterpart of that gene was known in the mouse. Well, biologists in Switzerland came upon a gene necessary for making the fly eye, and when they scrutinized its sequence, lo and behold, it's the same gene involved in making the human and the mouse eye.

So the fruit fly eye -- the compound eye that's sort of 800 little individual light sensing units and very different from our beautiful, you know, human eye, these are to anatomists entirely different types of eyes, and it's hard to see any connection between them. But yet their formation requires the same gene, and subsequently, several more genes were found that are common ingredients to all eyes. Well, what it's telling us is that a long time ago, when eyes first evolved, they had these genetic ingredients, and that has told us a lot about how evolution works with available materials. It rarely invents from scratch. It starts from something that works, and elaborates upon it. It works from a simple pair of cells, these light sensitive cells, and just makes a lot more of those cells, and arranges them in some pattern on the surface of the animal, and now you've got what looks like a more full-fledged eye.

JOHN HOCKENBERRY: So again the recipe for the eye, if you will, take some light sensitive cells, sort of mush them all together, and pour in lots and lots of time.

SEAN CARROLL: It does stretch the human mind's capacity to think about 1,000 years, 10,000 years. That's a whole history of civilization. A million years. I think that's actually -- humans can throw that number around, but it's inconceivable in human experience what a million years represents. But when I'm talking about the origin of eyes, I'm talking about something that probably got rolling about 600 million years ago. It's had a long time to wind up with compound eyes of flies and camera eyes of other animals, etcetera, and we can trace this by finding sort of the roots of the process in very simple organisms and in very simple organs, and what we're having to do is sort of take away so much bias that's been around in humans for centuries about we being more complex and about we requiring more special explanations, and understanding that our organs and our bodies are just an elaboration of a game that's been going on at least in the animal kingdom for 600 million years.

JOHN HOCKENBERRY: Coming up, my brother, the bacterium. That's in a minute on The DNA Files. I'm John Hockenberry, and this is "Beyond Human."
...
JOHN HOCKENBERRY: Welcome back to The DNA Files. I'm John Hockenberry. We're exploring comparative genomics. We line up our human DNA with the fruit flies, with the chimpanzees. Some stuff lines up. Some stuff doesn't. It's not like looking eye to eye.

They're so much the same and lots different. Let's go back to Erich Jarvis, the neurobiologist from Duke University. He compares genes to the brain pathways of vocal learners like parrots, songbirds, and bats, and me. I'm a vocal learner, but am I closer to a parrot or closer to my dog?

ERICH JARVIS: When you take this comparative approach, you start to realize, "Okay, what's really unique about language?" Spoken language is the ability to produce sequences of non-innate sounds, and yes, and have meaning to them. Well, there's something called auditory learning, the ability to make sound associations, and your dogs have it, your cats have it. So say, "Come here, boy" or "Fetch the newspaper" or "Sit" in English. "Osuwari" in Japanese also means "sit." These are not part of a dog's innate repertoire. Yet it has the ability to understand these human speech sounds and even some syntax, but those dogs cannot say it. But a parrot can and a human can, and the difference between a parrot and a human -- they're vast, but the difference between a parrot and a songbird is equally, if not more vast.

So to think that, okay, mammals are more advanced. So their brains are going to be more advanced. Well, whoever said mammals were more advanced? That kind of thinking led people to come up with these terminologies that had those definitions in it of lower to higher order and behavior complexity and intelligence. Pervasive throughout the field of science, even today, is the terms like lower vertebrates, higher vertebrates or lower primates, higher primates, and they look for brain structures or brain pathways that fit that kind of view. But when you really look, you can't find them.

JOHN HOCKENBERRY: When scientists start tearing down their assumptions, setting aside things they think they know and start asking questions in a new way like Jarvis is doing up there, well, [laughs] prepare to be surprised.

ERICH JARVIS: When we found that these brain pathways for vocal learning were so similar, more than we would have had expected, in these various different animals, we thought that it seems to be something simple that should drive this evolution of this brain pathway, but the answers that we're coming up with, it seems to maybe involve more than just the genetic change, but how an animal interacts with its environment. So we think that females of certain species or even the males like a male who produces a variable song with variable syntax, and the more variability you have, the more likely she's going to mate with you, like a jazz singer. Think about it in that way. And so that female selecting for that behavior then influences which genes get selected for in the next generation.

So with vocal learning behavior, these songs as our language is passed on culturally from one generation to the next. So here you have a non-genetic inheritance of a behavior. Well, how is that behavior actually then selecting upon the genes? And so I argue that there's a positive feedback loop. The behavior gets passed on in a learned way from one generation to the next without the direct influence of genes except the control of the behavior itself, but then that behavior then gets selected upon to become more and more variable through this cultural transition from one generation to the next.

JOHN HOCKENBERRY: Surprise. Maybe you thought only humans had culture, like table manners, poetry, symphonies. Jarvis says birds can pass songs down the generations. That's culture. Culture affects the way songbirds choose mates and evolve just like us. I wonder. Is lining up genomes really the best tool for identifying our similarities and our differences? I mean, where's the romance? Boy meets birds, bird meets song, chimp meets whatever.

BOY 1: No other animal really looks like -- at all like us, and chimps sort of do.

GIRL 2: Like we're their bald ancestor or something. [laughter] When you think about us, our only advantage is the fact that we're smart. I mean, you look at humans, we're like this scrawny, hairless, little thing, and almost any animal could overpower us physically. Our only advantage is intelligence. That's the main thing that sets us apart.

GIRL 3: But we're not sure of that.
DANIEL POVINELLI: Hey, how are you doing, huh? Huh? How's it going? How's it going?

JOHN HOCKENBERRY: Even without peering into anyone's DNA, it's pretty obvious that humans are not the same as chimps. I mean maybe as babies, we look an awful lot alike -- round head, flat foreheads, small jaw, but as we grow up, the paths diverge. We start thinking differently. At the University of Louisiana, cognitive researchers are trying to find out when that happens. They compare how children learn with how chimps learn. They asked, "When did children start to develop the kind of abstract concepts that chimps can't grasp?"

DANIEL POVINELLI: My name is Daniel Povinelli. I'm a professor at the University of Louisiana, and we're here at the Cognitive Evolution Group's chimp testing facilities n New Iberia, Louisiana.

JOHN HOCKENBERRY: Povinelli has been testing a group of chimpanzees since 1991. Many of these chimps were born and raised right here in this indoor/outdoor facility. Outside, they're free to swing and spit and be their chimp selves. Inside, researchers test the chimps' cognitive skills. Can they put round objects in round holes? Can they separate heavy objects from light ones? Young human children at the nearby Center for Child Studies take the same tests. The kids quickly master general concepts like shape or weight. Yes. The chimps can, too, but might have to learn them all over again the next day. [laughs] Povinelli wrote a book about his work called Folk Physics for Apes: The Chimpanzee's Theory of How The World Works.

DANIEL POVINELLI: I think the problem we have as human beings in getting our mind around, "Well, how can we be so similar to apes in our DNA profile, in our bodies, in the way we move through space and our gestures, etcetera -- how can we be so similar to them and at the same time apparently so radically different?" And so it tempts us into this zone of saying, "Well, maybe we've just sort of souped up the basic ape mind, and we're just quantitatively, massively better than chimps at all of these areas." But you know, when you really look hard at the experimental data that scientists have been struggling to accumulate about the similarities and the differences between humans and chimps, it really looks as if there's a qualitative, fundamental difference in this abstract, symbolic level of thought.

JOHN HOCKENBERRY: But what causes that fundamental difference? All our human bravado about being more intelligent, knowing mathematics, knowing architecture are just symptoms of something deeper. Is it even possible to find the source of this difference between humans and chimps?

DANIEL POVINELLI: So a lot of people want to know, "Well, if there is this qualitative difference, where is it encoded? Is it in the genes? Can we identify a particular segment of the genome or regions of the genome? Can we identify the brain areas that are different that support this level of abstract thinking?" And they really want something that concrete. But of course, biologists know better, that these are complex developmental systems that don't necessarily code one for one in a simple fashion, but rather set up a brain system, a mind system that can, depending on the environment it's raised in, can form different kinds of abstract thoughts. But it's all nested within this potential, this developmental potential to become a part of the human species.

You know, a lot of people engage in debates back and forth about, "Well, should we start with the supposition that they're similar, or should we start with the supposition that they're different?"Well, I just think that that's fundamentally the wrong way of looking at it. Let's just start with the supposition that we don't know, and let's develop the best possible tests -- and admittedly, they're crude at this point in our understanding of the mind -- but the best possible tests for elucidating what the similarities are and what the differences are. Because let's face it, the human mind is incredibly powerful. It wants to go out and reshape the world in its own image. But is that really what we want to hinge our understanding of chimps on, is the way in which our minds work? I don't think so.

I think we want to create a space, an intellectual space, which gives them the opportunity to say, "Yeah, we're very much like you here. No, we have no idea how you think here." And it's that intellectual space in science that's ultimately going to allow us to understand our place on this planet -- what makes us similar and grounded to the other species on this planet, and also the obvious radical ways in which we've departed from the natural world.

JOHN HOCKENBERRY: Maybe we're asking the wrong questions of our DNA, or maybe our DNA doesn't have all the answers. What are we really trying to find out anyway? We want to understand evolution. We want to know why we're here, why birds sing, how chimps think. We know we're all related, descended from one ancient ancestor, and that random genetic differences are handed down through generations -- that is, if they turn out to be useful for that population. So why are we the ones that survived? Why us? Evolution, a struggle to survive, a competition to adapt. Is that really what's written in our genes? Maybe we should be thinking of evolution in a different way. I kind of like the idea that I'm cousin to a chimpanzee, choir mate to a chickadee, yeah. That's nice. But nephew to a mold? Have you ever thought about all the species that live in our guts and on our skin and alongside our eyeballs? Yeast and E. Coli were some of the first species to be sequenced. Am I a bacterium's brother?

MARK MCMENAMIN: We represent a bacterial community on foot, [laughs] so to speak, all bacteria.

LYNN MARGULIS: The fundamental unit of life is bacteria, absolutely. The bacteria got together into communities, and made all kinds of things, but one of them is the ancestor to all the nucleated organisms.

MARK MCMENAMIN: Yes.

JOHN HOCKENBERRY: Lynn Margulis and Mark McMenamin see the world in terms of relationships, of cooperation, a web, not an ancestral tree. These two worry that scientists will get stuck looking at genomes, comparing one to another like life is lined up on a ladder, and then they might miss what's right in front of their faces, like moss on trees, bacteria in our guts.

LYNN MARGULIS: So the basic idea is that what we think is an individual is in fact a community of many individuals in a coordinated way. It's an evolution.

MARK MCMENAMIN: Yeah, it's an evolution. So what we're walking around now is our corporeal bodies, which are microbial communities that are inside of us. They represent an ancient ecology that has become fixed in place, so to speak.

JOHN HOCKENBERRY: Lynn Margulis is an important contributor to what's called "GaiaTheory." The concept that sediment, air, water, and living beings form one vast interdependent system. She says life is one big bundle of symbiosis -- organisms working together. Paleobiologist Mark McMenamin looks at life that way, too. What's more, according to these two scientists, we don't just live together, we move in together. We cohabitate, and we become something altogether new. Together. That's what they call “symbiogenesis.”

MARK MCMENAMIN: Symbiogenesis is when a sea anemone picks up some kind of photosynthetic microbe, and the photosynthetic microbe lives inside of its tissues and starts creating sugar. Suddenly the sea anemone has so much energy, it doesn't know what to do with it all, and it forms a coral reef.

LYNN MARGULIS: Exactly, but what he didn't tell you is sea anemone is not an anemone like a flower. It's an animal. So what he's talking about is the evolution of a green animal. An animal can be photosynthesized. It's as if we shaved your head, and we took little algae, little plant things or plants, and put them under your scalp, and you sat in the lights, and you didn't have to go running around, looking for food.

JOHN HOCKENBERRY: You might call that brain salad surgery. You know, I think I have that album somewhere in my basement still. I'm not sure I'd like that, but it could be handy. Evolution is all about adapting like this to an environment, and cooperation can be as important as competition. While walking through Harvard Forest in western Massachusetts, Mark McMenamin with his daughter, Jenny, and Lynn Margulis talked about the evolutionary effects of cooperation. Species don't just help each other; they share their operating systems, their genomes.

MARK MCMENAMIN: Instead of evolution being a process of one organism saying to another, "You're in my space. I'm going to kill you," it's about a group of organisms wanting to perpetuate an ecology.

LYNN MARGULIS: Look at this tree.

MARK MCMENAMIN: You see how this dead tree is just --

JENNY MCMENAMIN: Ew, it feels weird.

MARK MCMENAMIN: Covered with shelf fungi.

JENNY MCMENAMIN: Oh, it feels really weird.

MARK MCMENAMIN: We're looking at a dead tree that has white shelf fungus all over it, coming out of the bark, and this is not a situation in which a spore of the fungus has floated through the air and landed on the tree and started growing, but rather this is fungus that was inside of the tree that is now coming out, because a tree cannot live on land without its fungi. It is creating an environment for the fungus, but the fungus is sustaining the tree as well. The connection here is totally symbiotic. You can't have life on land without it.

JENNY MCMENAMIN: It needs the fungus to live?

MARK MCMENAMIN: It needs the fungus to live, yes. 90% of all trees --

JENNY MCMENAMIN: That's weird. I thought it just needed like sunlight and water.

MARK MCMENAMIN: No, it needs more. It needs the mineral nutrients. Once it gets them, it can produce so much sugar that it passes this down to the fungus, and so sugars are being pumped into this fungal ,bodies in the soil, and in exchange, the fungus is pumping mineral nutrients into the trees, and so there's a two-way flow. Minerals going up, sugars going down.

JENNY MCMENAMIN: Daddy, look at the inside.

MARK MCMENAMIN: Yeah, there's the inside of the shelf fungus.

JENNY MCMENAMIN: What's that called?

MARK MCMENAMIN: Those are the spores, yeah.

JENNY MCMENAMIN: Weird.

MARK MCMENAMIN: Yeah.

JENNY MCMENAMIN: It feels weird. It feels like a bone.

MARK MCMENAMIN: You -- you can't really distinguish the individual in the plant fungus situation. It's the -- the extension of the marine bio to coming on to deadly, dry land habitat and terraforming it, transforming it, and it can only happen with the symbiosis.

JOHN HOCKENBERRY: If Lynn Margulis and Mark McMenamin are right, comparative genomics might only be a starting point here. Stay with me now. Lining up genomes and checking for mutations, sorting out what's been added and what's been lost over the millennia, that can tell us a lot. I mean, we can see ancient similarities in our operating machinery, how an amazing structure like the eye developed, how the life forms we see today took shape, but to really understand evolution, we might need to throw out some old ideas, old ideas about the meaning of our differences, about competition. Maybe we're not just in this for ourselves. The story of life is written in our genes, but not just in our genes. DNA is only part of the story. Evolution and the way we think about it continues to evolve.

Thanks to Houghton Mifflin for allowing us to use the birdsong CD from Donald Kroodsma's book, The Singing Life of Birds. Thanks also to our students from Owego, New York, and thanks for listening to The DNA Files. I'm John Hockenberry.

To find out more about comparative genomics, visit our website at dnafiles.org where you can download a podcast of this program. This series, The DNA Files, was produced by SoundVision Productions with funding by the National Science Foundation, U.S. Department of Energy, National Institutes of Health, and the Alfred P. Sloan Foundation. This program, "Beyond Human" was produced by Barrett Golding. The DNA Files is managing editor, Loretta Williams, editor, Deborah George, science content editor, Sally Lehrman. Research director is Adi Gevins. Production support by Noah Miller, Julie Caine, and Jenn Jongsma. Office support provided by Steve Nuñez and Beverly Fitzgerald. Our web director is Ginna Allison. Technical engineer and music director is Robin Wise. Our host is John Hockenberry. Our theme music was composed and performed by Steve White. Additional music by Jeff Arntsen, Conrad Praetzel, and Robert Powell. Marketing of The DNA Files is by Schardt Media. Legal services by Cooper, White and Cooper and Spencer Weisbroth. Special thanks to Murray Street Productions. Send your responses and letters to feedback@dnafiles.org. For CDs and transcripts, call 888-303-0022. That's 888-303-0022. The executive producer is Bari Scott. This has been a SoundVision production, distributed by NPR, National Public Radio.