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ANDREA SEABROOK, host:

Every Saturday, we like to tackle a basic question about how the world works in our segment called Science Out of the Box.

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SEABROOK: This week, we go to the very basics of biology - taxonomy, or the way scientists classify life forms. If you are of a certain age, you probably learned in school about the three kingdoms of life - animals, plants and fungi. If you're a bit younger, you were shown two more kingdoms on the map of life - protista and monera. But that familiar map has been completely redrawn now to reflect what molecular biology has taught us about the incredible diversity of life on Earth.

Our guide for us through this geography is science writer Carl Zimmer.

Welcome.

Mr. CARL ZIMMER (Science Writer; Fellow, College Morse, Yale University): Hi. Thanks for having me.

SEABROOK: First question, Carl Zimmer. Going back to the father of taxonomy, also your namesake Carl Linnaeus, he classified life by looking at the structures that life forms have, you know, arms, arm bones, all through the animal kingdom and so on. But that was 300 years ago. Nowadays, we can observe living things on the molecular level. How has this changed our taxonomy?

Mr. ZIMMER: Well, it changes it pretty radically because back when all you could do is look at things with your naked eye, there were a lot of things that you couldn't see. So bacteria all just looked like little rods or spheres or something, and they kind of all looked alike. But if you can actually get in and look at their DNA, you can see that there's this huge amount of genetic diversity on the planet that we just didn't appreciate existed.

SEABROOK: Hmm. So now, you're saying it's how much DNA organisms have in common, like how close we are to apes as opposed to the potato, for example, rather than…

Mr. ZIMMER: Right.

SEABROOK: …the fact that apes have arms and potatoes don't.

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Mr. ZIMMER: Exactly. So you can see our kinship with other mammals because of our arms and legs, our hair, our warm-bloodedness, and things like that, but it's kind of hard to say whether we're more closely related to yeast or to E. coli if all you can do is just kind of look at them because, obviously, they don't have hair or arms or anything like that. But you can look at their DNA and you can see how different they are from ours, so we actually share a much more recent, common ancestor with the yeast than we do with E. coli.

SEABROOK: Hmm. I read that, in fact, humans and potatoes are more closely related than the tuberculosis bacteria is to the cholera bacteria.

Mr. ZIMMER: Yeah. So this diversity of bacteria is so huge that it's kind of hard to fathom. And part of the problem is that over on our side of the tree of life, things look really different, so you've got potatoes and you've got mushrooms and you've got whales and so on, but we're all pretty closely related. And meanwhile, bacteria and these other microbes take up a huge portion of the tree of life that's just vast compared to our own.

SEABROOK: Yeah. I'm actually looking here at this tree of life that's called the three-domain tree of life - the modern tree of life - and you're right, it's this sort of sprawling kind of God(ph) bifurcations all over the place. Three main branches: Archaea, Bacteria and then Eukarya, and then what we used to think were the three main kingdoms - animals, plants, fungi - is this tiny little thing way, I mean, at the end of one of the branches. It's like there's so much more than just animal and plants and mushrooms that we see around us.

Mr. ZIMMER: Yeah, kingdoms used to really mean something. Carl Linnaeus said that there were two kingdoms, and, basically, he was just trying to just draw a map of the world and nature, and he split it into these two kingdoms - animals and plants - and it seemed pretty obvious. You had animals that could move around and eat things, and then you had plants that didn't, and that stuck around for a long time. It was a pretty useful classification.

And then there started to appear these kind of weird organisms that people didn't quite know what to do with, so they made a new kingdom for protists which are single-celled organisms that aren't really clearly animals or plants. And then after a while, people kind of recognized that fungi really deserved a kingdom of their own because they're really different than us or plants. You know, plants make their own food from sunlight and a mushroom doesn't. We eat food and then digest it, and fungi actually do it the other way around - they release enzymes, so they digest their food first and then they eat it. So the fungi got a kingdom of their own. But then once people started looking at DNA - and, really, it was with the work of Carl Woese at the University of Illinois in the 1970s that just blew this whole convenient system wide open.

SEABROOK: Yeah. I think the map that I'm looking at is the Carl Woese map of life. Can you outline for us what Bacteria, Archaea and Eukarya are?

Mr. ZIMMER: Sure. So, Eukarya we can start with because that's us. So, Eukarya include all the species that keep their DNA tucked in a nucleus - this little sac in the cell. And if you look at our DNA, it shows that all Eukariotes are closely related compared to other things. And so, Eukarya includes animals and plants and mushrooms and other fungi and then a whole, whole bunch of little single-celled organisms - Amoebae, what are sometimes called protozoans - it's these things that give us malaria or Giardia, which makes us sick, too, little critters that live in the soil or in the ocean, so those are all Eukariotes.

So then the other two big branches of life are known as Archaea and Bacteria and if you look at them, they look totally identical, but one of the things that Carl Woese did was to look at their genes and say, wait a minute, there -a group of what we call bacteria, they're actually no more closely related to other bacteria than they are to us. So he called these microbes Archaea and that then leaves the so-called true bacteria as the other major branch of life - what Carl Woese called a domain of life.

SEABROOK: It took a while to gain acceptance in the scientific community. Does everyone accept it now?

Mr. ZIMMER: When Carl Woese first suggested that there were these three domains to the tree of life, it was very controversial and it stayed controversial for quite a while. Part of the problem was that it was the '70s, and sequencing DNA in the '70s was hard. And so it would, you know, take years in some cases to figure out what a single gene looked like. So Carl Woese was making this argument based on what looks today like very little data. So what changed was technology, so people were able to sequence DNA really fast. So once that happened, it started to really become clear that this idea that there were three domains to life and that the animal kingdom was just a pretty small branch on the tree of life really started to gain some momentum, and now I think it's generally agreed upon.

SEABROOK: Carl Zimmer, were you named after Carl Linnaeus or Carl Woese? Maybe you're…

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SEABROOK: You're not old enough to be named after Carl Woese or are you too old for that?

Mr. ZIMMER: I was born before the three domains of life, I will say that - not that I'm 4 billion years old. Well…

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SEABROOK: Carl Zimmer is a science writer who has studied Carl Linnaeus and Carl Woese, and his latest book is called "Evolution: The Triumph of an Idea." Thank you very much for talking with us.

Mr. ZIMMER: Thank you.

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SEABROOK: In the coming weeks, we'll be looking more closely at the tree of life, exploring how our new insights on DNA deepen our understanding of evolution. We'll also hear about the new and growing field of epigenetics. And is the so-called junk DNA really all junk?

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