How A Humble Microbe Shook The Evolutionary Tree

IRA FLATOW: The world of biology was upended in 1977 with the announcement of the classification of a new form of life, tiny single-celled archaea. Archaea look like bacteria in size and shape. They originally thought they might be. But it turns out they weren’t. And they didn’t fit anywhere into the plant or animal kingdoms.

Archaea were classified as a third domain, classified by Carl Woese and George Fox in research they published 41 years ago. As George Fox told me on NPR’S All Things Considered in November of 1977, he believed these archaea may be signposts toward discovering the earliest forms of life on Earth.

GEORGE FOX: We’ll been looking primarily for commonalities between these organisms, the regular bacteria, and higher forms since these things which are in common are probably going to turn out to be properties of the earliest forms of life.

IRA FLATOW: And then, you can extrapolate backwards to see how early it started.

GEORGE FOX: Right– we would like to try to determine what the major properties of the first living forms– or nearly living forms, if you will– were.

IRA FLATOW: Thank you, George Fox at the University of Houston in 1977. And I bring all of this up now, because the discovery of archaea as well as the trials and tribulations of biologists trying to decipher early life on Earth is a story wonderfully told in the new book The Tangled Tree: A Radical New History of Life, written by science writer David Quammen. David, welcome back to Science Friday.

DAVID QUAMMEN: Thanks, Ira. It’s great to be back with you. And it’s dizzying and wonderful to hear you talking to George Fox back then.

IRA FLATOW: Yeah– he’s still around, isn’t he?

DAVID QUAMMEN: Oh, he is. I interviewed him for the book. I get e-mails from him a couple of times a week. Yep, he’s in Houston still.

IRA FLATOW: And I wanted to tell our audience that we have an excerpt of your book at sciencefriday.com/tangledtree. And I remember, when I was talking to George Fox, I remember how excited and how shocking that discovery was back in 1977.

DAVID QUAMMEN: It was shocking. It was shocking enough to get Carl Woese on the front page of the New York Times on November 3 of that year, including a picture of him. Typical Karl Woese– tousled white hair, sports shirt, and his feet up on his desk wearing Adidas.

IRA FLATOW: And so what was so shocking about that?

DAVID QUAMMEN: Well there were supposedly only two major forms of life, as you were saying. The tree of life– and by that, I mean sort of the classic Darwinian picture of the shape of the history of life– had two major limbs at that point. Fancy names for those were prokaryotes and eukaryotes. Less fancy names were bacteria constituting the one limb. And everything else, including animals, plants, people, fungi constituting the other.

And then, Woese and George Fox came along and said– wait a minute. There’s this third group. They look like bacteria. But if you look at their DNA and their RNA, they are not bacteria. They’re not only very different from bacteria. They’re more similar to us. They’re more similar to eukaryotes. And that was the big news.

IRA FLATOW: So what exactly makes them different from bacteria?

DAVID QUAMMEN: Well, what Woese and Fox detected was differences in one particular very fundamental molecule that they were looking at using as essentially the Rosetta stone for comparing different forms of life. As George said, back at the earliest stages of the history of life. And those molecules differ drastically between the bacteria and the archaea.

But then, the biochemists came in. And they started, particularly German biochemists, and they said– yeah, well, we’ve been noticing weird things about those so-called bacteria too. They have different kinds of cell walls. There’s no peptidoglycan– fancy name for a fancy molecule– in their cell walls. They have different kinds of membranes, different kinds of linkages in the lipids– the fatty molecules– in their membranes. They are really different at the biochemical level too. And eventually, they were classified as– as you said– as a separate domain of life.

IRA FLATOW: Number 844-724-8255 is our number. We’re talking with David Quammen on Science Friday from WNYC Studio. And when they were first discovered, and as I said in my report, they were sort of the biological weirdos. They preferred these really extreme environments, right?

DAVID QUAMMEN: Exactly, yeah– they call them extremophiles, extremity lovers. They preferred really salty environments or acidic environments or hot springs. Some of them were found in the hot springs of Yellowstone Park. Some of them, more recently, have been found around thermal vents at the bottom of the North Atlantic between Greenland and Norway.

Not all of them, we know now, prefer extreme environments. But that’s how they were first detected. Also, some of them in environments with little or no oxygen. So they metabolize carbon dioxide and produce methane.

IRA FLATOW: Now, as you mentioned, it was big news at that time– front page of the New York Times. But it was sort of that the newspapers were getting it a bit wrong, weren’t they?

DAVID QUAMMEN: Oh yeah, they were saying– martian-like bugs, the bugs that predate the earliest known forms of life. The newspapers– the New York Times did a pretty good job. The Chicago Tribune did not do so well. And a lot of other papers got it very confused.

And the fact that Carl Woese had allowed this discovery to be announced in a press release. His funding came from NASA. And NASA issued a press release. And the newspapers got a hold of it. And so people, including scientists– respected scientists like Salvador Luria– heard about it, read about it from garbled newspaper accounts before they saw the journal article.

And that was one of the causes of it being largely rejected by the scientific community at the time. There was a lot of resistance. People thought this was junk science. Because it had been announced in the newspapers confusedly before they saw the scientific paper– saw the Woese and Fox 1977– and saw that it was very solid science.

IRA FLATOW: We go to the phones to Walter in West Columbia, North Carolina. Hi, Walter.

WALTER: It’s South Carolina, but that’s all right. Fascinating topic and a very fine speaker. I’m honored to participate in your show. My question is– among the archaea, are there to date any known pathogens of humans or animals or plants?

DAVID QUAMMEN: That’s a good question, Walter, yeah. And as far as I know, the latest answer to that question is no. But nobody knows exactly why. We have all these bacteria that are pathogens of humans. And now, we know these other things that look like bacteria and have the same sort of appearance do not infect humans, do not cause disease. As far as we know– at least as far as I’ve heard so far. But the question remains– why not?

IRA FLATOW: When I was talking to Dr. Fox in that little cut, he said– there might be three, four, or five more of these undiscovered branches out there. Could there still be?

DAVID QUAMMEN: Well, I don’t think so. Because the Woese and Fox work, the methodology of it, became in a sense even more important than the discovery of the archaea. And a lot of other scientists started using that methodology– using this one Rosetta stone molecule– to compare different forms of life, to sketch new versions of the tree of life.

But also, a wonderful scientist named Norman pace– now at the University of Colorado in Boulder– who was essentially Carl Woese’s scientific son, his protege. Norm Pace pioneered the use of that methodology for identifying and characterizing creatures that couldn’t be grown in the laboratory, that couldn’t be cultured and grown in a lab.

And they call that sort of environmental discovery of organisms. So there has been a lot of that done. You don’t have to grow a bug in the lab anymore to identify it. And if there were completely different non-archaea, non-bacterial microbes out there, the Norm Pace methodology probably would have detected it by now.

IRA FLATOW: All right, talking with David Quammen, author of The Tangled Tree. We’ll get into that tree a little bit more in great detail after the break. 844-724-8255 is our number. You can also tweet us @SciFri. We’ll be right back. Stay with us.

This is Science Friday. I’m Ira Flatow. We’re talking about the origins of life and how we divide and classify the living world with science writer David Quammen, author of the new book The Tangled Tree: A Radical New History Of Life. Our number 844-724-8255 if you would like to comment. We also have an excerpt up on our website, sciencefriday.com/tangledtree.

Let’s go to the phones. Interesting calls on this. Let’s go to Cleveland and Renee. Hi, welcome to Science Friday.

RENEE: Hi, thank you so much for taking my call. I’m a biology teacher, high school biology. And when you say tree of life to students, they immediately get an image of a straight stalk with a bunch of branches. And obviously, that’s not exactly how it works. So I was wondering if you have a better analogy that you use to describe that. Thank you.

DAVID QUAMMEN: Good question.

IRA FLATOW: That’s what your book is all about.

DAVID QUAMMEN: That’s what it’s about, yeah. And let me let me introduce a new term, a new idea here– horizontal gene transfer. These discoveries by Woese and others led to the awareness that genes move sideways across species boundaries sometimes, even across kingdom boundaries. Genes move horizontally.

It’s supposed to be impossible and was astonishing to me when I first read about it in 2013. But that is what complicates the tree of life. The tree image that goes back to Darwin is all about divergence. Limbs diverging into branches, branches diverging into twigs. Eventually, leaves making the canopy of the tree, representing the abundance of life’s diversity on Earth.

But now we know, thanks to these molecular researchers, that there are convergences as well as divergences of limbs. There are channels that go from one major limb to another. There are branches that go sideways from one to another, representing this horizontal gene transfer effect.

So if it’s not a tree, then what is it? Well, some people say it’s a web. You should talk about the web of life. Or it’s a network. One researcher talked about the circle of life. None of those really get it either. It’s a very complicated– somewhat but not entirely– treelike history. And that’s why I ended up with the title that I did– The Tangled Tree. At one point, I was thinking about calling this book The Tree of Life is Not a Tree.

IRA FLATOW: It’s interesting, because this sideward movement is fascinating to me also. Also is the idea that we carry in our genes a great history of our genetic background, right, the much simpler forms of life.

DAVID QUAMMEN: We do. We do. We carry, in our genomes, we carry this record. And in our bodies, we carry this record. There are a couple of different instances of that. But one of them that I discuss toward the end of the book is the fact that scientists now recognize that 8% of the human genome consists of viral DNA that has arrived by the capture of retroviruses in our genomes.

A retrovirus is retro because it moves backwards, inserts its genome into the genome of the cell that it infects. And if it’s HIV infecting immune cells, it inserts a genome into immune cells. But if a retrovirus infects reproductive cells, if it infects ovaries, testes, eggs, or sperm, then that viral DNA gets inserted into those cells. And it becomes hereditary.

And over the tens of millions of years of mammalian evolution, we now know there have been viruses captured by our genomes that way amounting to 8% of our genome– some of which are now still functioning genes that allow us to be what we are, that allow us to be mammals.

IRA FLATOW: So what kinds of viruses might we have? Could we have other species in our genome? Or are there some animals that do that?

DAVID QUAMMEN: Well, yes, there are other animals that have acquired DNA from other creatures– in some cases acquired from bacteria. There are some fascinating studies showing that certain insect genomes have acquired bacterial DNA from a kind of bacteria called wolbachia. It’s a cellular parasite that infects many, many, many species of insects. And it gets inside the cells. And when it gets inside reproductive cells, sometimes it inserts its DNA into the DNA of the insect.

IRA FLATOW: Let’s go to Judith in Chico, California. Hi, Judith. Let’s go to Frank first in Columbia, Missouri. Sorry, Frank.

FRANK: Hi there.

IRA FLATOW: Hi there.

FRANK: I haven’t read the book. But I’m looking forward to it. I was lucky enough to hear Carl Woese’s seminar very close to the time that he announced the archaea. And there are a couple of things that I hope your book brings out.

First of all, both horizontal gene transfer and the archaea– they were just known as funky bacteria the time– existed and were known and had been studied before the Fox and Woese paper. And the other one– in a time when people kind of say, well, evolution is kind of maybe not so important to biology– that I remember distinctly Carl Woese was going on at great length and emphasizing very strongly that he was trying to put the bacteria into the evolutionary framework.

And his first work actually did come up with a tree. It was much later that he emphasized the horizontal gene transfer. But it’s a fascinating history. And I knew a couple of the players. And I think it’s just a wonderful story of how science works. So congratulations for writing it.

DAVID QUAMMEN: Thank you, Frank. And yes, those aspects that you mentioned are in the book.

IRA FLATOW: What did you find– you’ve studied this carefully. What was the most surprising thing that you discovered?

DAVID QUAMMEN: I think the most surprising thing was one particular instance of that viral DNA getting into the human genome. I read about a scientist named Thierry Heidmann in Paris who– with his group– had done a series of papers, made a series of discoveries about one of these viral stretches of DNA acquired by the human genome that is still a functioning gene. It’s called Syncytin-2. Syncytin is not spelled like Cincinnati, my hometown, but like synonym.

And this gene Syncytin-2 was originally, in the retrovirus, an envelope gene. Meaning it made a sort of an envelope, a membrane around the viral particle. It got into the mammalian line. And now in humans, our version of this gene Syncytin-2 is absolutely essential for creating a different kind of envelope, a different kind of membrane. It’s a membrane between the placenta and the fetus in humans.

And without that membrane– which has a really fancy name– without that membrane between the placenta and the fetus, human pregnancy is impossible. So I read about that. And I emailed this fellow Thierry Heidmann and said– if I come to Paris from Bozeman, Montana, will you talk to me for an hour? And he said sure. So I went. And we talked for seven hours about this. And it’s in the book.

IRA FLATOW: Let’s go to Liz in Waco. Hi, Liz. Welcome to Science Friday.

LIZ: Hi, I’m so excited to ask this question. I’ve always wondered that it archaea has no pathogenic significance for humans or no agricultural significance where the research dollars are coming from. And possibly if biotech companies are really looking toward archaea to mine them for genes, especially since they’re thermophiles. So I’m just curious about research dollars and about a tech aspect of that.

DAVID QUAMMEN: That’s an interesting question, yeah. In terms of the second point– are biotech firms looking to mine these for particular genes that adapt to extreme environments? My answer is– probably so. I don’t know the specifics. But I would guess that you’ve put your finger on it there and that there are some that are doing that.

Earlier on, I mentioned Woese’s funding. Some of it came from Nasa. That was why they issued a press release. And they were funding him as part of their exobiology program. Which had been– I don’t know if it had been founded by Carl Sagan. But he was certainly part of it. So they were funding this. Because they thought– well, this stuff might tell us something about the conditions that are necessary for the arising and the evolving of life on other planets.

A more general answer to your question is that this gets funded mostly because it’s pure science. It tells us something about the history of life on this planet going back maybe four billion years. And we should want to know that.

IRA FLATOW: Well, isn’t it more though another reason also or should be? I mean, this is part of our lives. These archaea are living with us. They’re living in our gut. They’re living in sheep. They’re all over the place. They’re part of the microbiome, part of the soil microbiome.

DAVID QUAMMEN: That’s right.

IRA FLATOW: How do we know what we don’t know about them? I mean, there just seems to be, for example– do they have a CRISPR tool of their own that they use to battle one another or the other bacteria?

DAVID QUAMMEN: That’s a good question.

IRA FLATOW: Do they leave fossils behind when they die like bacteria do?

DAVID QUAMMEN: All these good questions.

IRA FLATOW: We used to think that there was just, that most of us were made out of junk DNA until we got to– I always thought that was a silly concept– until we knew, hey, there’s a lot of stuff that DNA is used for. Maybe we consider archaea to be too much junk DNA.

DAVID QUAMMEN: Yeah, yeah.

IRA FLATOW: It’s just surprising. The listener asked a great question. Why don’t we study them more?

DAVID QUAMMEN: Well, I think we do study them more. But you don’t hear that much about them. All of these the things that we’ve been discussing today, the scientific literature is is full of it. But it hasn’t penetrated much to the general public.

I mean, some of my colleagues and people you know have written about this. Carl Zimmer has written about some of this in short form. Ed Yong has written about some of this. I’m not the first person who wrote about this for the general public. I don’t know. I may be the first person who has written a book about it for the general public, about this particular constellation of discoveries.

IRA FLATOW: Let’s go to a Grand Junction, Colorado. Michael, welcome.

MICHAEL: Hi–

IRA FLATOW: Hi, go ahead.

MICHAEL: So I was just wondering– I’ve read quite a bit about extremophiles. Not that I’m an expert. I’ve just always found them interesting. But I’ve never seen anyone answer this question. I was wondering if extremophiles from our own planet could live on planets besides ours.

IRA FLATOW: OK, good question.

DAVID QUAMMEN: Well, I don’t know the answer to that question. It is an interesting question. And I certainly am not going to rattle off three reasons why they couldn’t. I mean, who knows, maybe. Maybe– if there is liquid water and forms of mud, maybe acidic mud, and just the right absence of oxygen, carbon dioxide. I’m not going to say it’s impossible.

IRA FLATOW: And that man is David Quammen, author of the new book The Tangled Tree: A Radical New History of Life on Science Friday from WNYC Studios. You know, it’s sort of a little bit of hubris to say– hey, none of this could ever happen.

DAVID QUAMMEN: Yeah, nobody wants– I’m not going to say that.

IRA FLATOW: I mean, when you think of the history of science, where none of anything could happen that eventually happens.

DAVID QUAMMEN: Right, right. And the other thing– unexpected, Ira– there’s another good reason for studying these creatures, these archaea that don’t infect us. It’s because the latest thinking on them, the latest research suggests that they in fact are our deepest ancestors. That when complex cells came to be with the acquisition of a cell nucleus, cell organelles, internal structures, and things– the host cell from which our complex cell lineage was assembled was not a bacterium but an archaean. That they are probably our deepest ancestors. And that’s a little head-spinning too.

IRA FLATOW: Let’s go to the phones. Because you have ignited some interest. Judith in Chico– now let’s see if I can get to Judith in Chico. Hi, welcome to Science Friday.

JUDITH: Yes– when I was studying microbiology and infectious disease, I learned about jumping genes that could be transferred from one species to another, like the shigella toxin to E. coli causing that horrible kidney killing disease. So how is this different than a horizontal transfer?

DAVID QUAMMEN: Well, I am talking about horizontal transfer. And as you say, and as someone else said– I think it was Frank– it had been known in bacteria going back before Carl Woese. Joshua Lederberg in the 1950s coined the phrase infective heredity. Because he saw this happening among bacteria– passage of genes from one bacterium to another. And even from one kind of bacterium to another.

And then in 1963, a Japanese scientist named Tsutomu Watanabe and his group showed that this problem that we now face of antibiotic-resistant bacteria, that it is transferred around the world from one kind of bacterium to another by horizontal gene transfer. That’s why we have multi-antibiotic-resistant bacteria turning up everywhere.

It’s not because they’re independently evolving resistance to all these different antibiotics. It’s because one kind of bacterium can evolve resistance the slow way. And then, a gene for that– or a package of genes for multiple drug resistance– can pass in an instant from shigella to salmonella, from salmonella to streptococcus, from streptococcus to staphylococcus. And it’s horizontal gene transfer.

IRA FLATOW: Last question on the phone from Thomas from Los Altos, California about horizontal gene transfer. Hi, welcome.

THOMAS: Thank you. As you are talking about head-spinning theories, is it possible that our human genome is getting mixed in with maybe lower level species as we speak as the journey of evolution continues?

DAVID QUAMMEN: Well, is it possible? Yes, but it happens very slowly, very infrequently. I mentioned the Syncytin genes acquired from retroviruses. Those have happened over the course of the last 80 million years in the course of mammal evolution.

Horizontal gene transfer, there are a lot of reasons why it shouldn’t happen at all. And it doesn’t happen very often. But it has happened enough over the long stretches of time to have been really consequential in terms of shaping us and in terms of shaping the tangled tree of life. So yes, it’s probably still going on. But we’re not going to see it popping like popcorn in a popper in terms of its frequency.

IRA FLATOW: I’m constantly reminded of Jeff Goldblum’s line– life will find a way. He didn’t write it, but he said it. Thank you, David.

DAVID QUAMMEN: Thank you, Ira. Great to talk with you.

IRA FLATOW: Great to have you on. It’s a great book. David Quammen is the author of The Tangled Tree: A Radical New History of Life. And you can find an excerpt of it on our website at sciencefriday.com/tangledtree.

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