Darwin, Linnaeus, and One Sleepy Guy

[Update: You can listen to my talk here.]

I’ve just spent the past 30 hours at the Chautauqua Institution, the lovely village of ideas out in western New York State. Each week they bring in people to talk about a theme, and this week is a celebration of Darwin and Linnaeus.

Many interesting things have transpired over the past 30 hours. I spent some time listening to one speaker, Ken Miller, talking about the amicable intersection of religion and science with a couple skeptical listeners. I had to get up to call my wife while Ken was talking about how God was an explanation for the intelligibility of the universe, and meeting fierce opposition. But when I got back the mysteries of the cosmos were apparently solved–Ken and his opponents had stopped the debate and were showing off their MacBook Pros and Airs, as well  as their cool Powerpoint/Keynote tricks. Church of Mac trumps all, I guess. I never did get the answer to the meaning of the universe.

Another speaker, Beth Shapiro, ancient DNA expert from Penn State, informed me that people in Siberia ride reindeer like horses, although she was thrown off one. Who knew?

The Chautauqua Institution is not immune from bloggers. I met Barbara King, an anthropologist and author of Evolving God, who blogged on some of the talks (and is talking herself later in the week). I also met Larry Moran, University of Toronto biochemist and blogger at  Sandwalk, who is far more cheerful than his stiletto-like blog posts would suggest. We parted ways after spending a while bickering on an empty street about the importance of genetic drift.

I hope–but do not know–that my own talk will be posted on line. In the meantime, let me cut and paste my prepared remarks below. I’d add links, except that I am very sleepy and have a plane to catch in the morning…

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I’d like to thank the Chautauqua Institution for inviting me to speak during this week’s series. I’m particularly grateful that the Chautauqua Institute saw fit to make this week’s theme Darwin *and* Linnaeus. We are now descending into a frenzy of Darwin celebrations, and you’re not going to escape it until the end of 2009. We’ve got his 200th birthday in February, and the 150th anniversary of the publication of the Origin of Species in November. The spotlight is going to be on Darwin, and Darwin alone.

I think this is a mistake. Darwin deserves celebrating, but that doesn’t mean we should fall prey to a cult of personality. Darwin did not invent biology. Darwin did not even find most of the evidence that he used to back up his theory of evolution. And he certainly did not discover all there was to know about evolution. Biologists have discovered many new things about  evolution since his time. In some cases, they’ve challenged some of his most important arguments. And that’s fine. That’s the great strength of science.

So today I’m going to take advantage of our dual celebration of Linnaeus and Darwin. I’m going to talk about the process of science, how great thinkers challenge the thinkers of the past, how their own great ideas are altered by future generations. I’m going to talk about why Linnaeus was so important, and how Darwin shattered some of Linnaeus’s most cherished claims. I’m also going to talk about modern biologists have done the same to Darwin.

The best way to convey how drastically biology has changed since Darwin’s day is to focus on one group of living things. It’s a group about which Darwin–and Linnaeus–had little to say. I’m going to talk about microbes.

Now, when we think about the magnificence of nature, the majesty of life that biologists seek to decipher, microbes may seem like minor stuff. What’s a bacterium next to a human being, or a blue whale, or a redwood? But if I’m successful today, you will leave here convinced that microbes are in fact a very big deal. They dominate the history of life, and dominate the planet right now. And they force us to rethink the ideas we’ve inherited from Linnaeus and Darwin.

Let me start off with Linnaeus. He was born in 1707 in southern Sweden. He started out studying medicine, but ended up studying botany. This wasn’t such a big jump as it sounds, since plants provided physicians with most of their medicines. Every doctor was, in effect, a botanist. Even today, scientists find many medically important molecules in plants. The breast cancer drug Taxol, for example, first came from a yew tree.

Linnaeus turned out to be a botanical prodigy. At age as 23 he was giving lectures about botany at Upssala. At 25, he journeyed to Lapland in northern Sweden. At the time, this was terra incognita. Linnaeus traveled 4600 miles, making his way by foot all the way to the Arctic Ocean and back. When he got back home, he went through the plants he collected and wrote a book called Flora Lapponica.

But writing a book about plants posed a profound puzzle–and in solving it, Linnaeus would become the most famous naturalist of his day. The puzzle was this: How was Linnaeus supposed to name his plants? There was no standard way to do this in the early 1700s. People gave all sorts of names to the same animals and plants, and if you read about a plant in a book from England, you had no idea if they were talking about the same plant you were looking at in Sweden.
And the names people did use could be hideously complicated. For example, when some naturalists referred to the wild geranium, they’d call it–

Geranium pedunculis bifloris caule dichotomo erecto foliis quinquepartitis incisis summis sessilibus

Linnaeus also realized that the puzzle of names actually hid a much more profound mystery. Naturalists could put species in groups. You don’t have to be an expert to see that geraniums and roses are more alike than either is to us, or to a mushroom. In the eighteenth century, naturalists generally believed that these groups were a glimpse at the divine order of the world. If they could discover a way to classify all species, they would, in effect, be reading the Book of Nature, written by God. But it was very hard to come up with a system that was consistent and that was also easy to use. How was a naturalist supposed to classify a whale, for instance? You couldn’t just look at all its traits to decide, because some traits would put it with fish, and others would put it with mammals.

It was Linnaeus’s great achievement to figure out the first good system.  He started out with plants, which he knew best. Rather than look at all their traits, he just picked out a few key ones. At the time, botanists had only just realized that flowers have sexual organs. The male organs, the stamens, hold the pollen, which fertilizes the pistils, the female organs. Since reproduction was central to life, Linnaeus used the number and size of stamens and pistils to organize species into larger groups, called genera. The genera would go into orders, and the orders into classes, and the classes would all go into the plant kingdom.

And once Linnaeus had a system for plants, he started expanding it to organize all nature. In 1735, when he was just 28, he published a pamphlet called Systema Naturae. He mapped out the animal kingdom, the plant kingdom, and even the mineral kingdom. Obviously animals and rocks don’t have pistils or stamens, so Linnaeus came up with other features to classify them.

Linnaeus spent the rest of his life expanding that little pamphlet into bigger and bigger tomes. Two hundred and fifty years ago this year, he came out with the tenth edition. That’s generally considered that definitive one, the book that launched modern taxonomy. It’s there that Linnaeus presented all the rules for naming species. That’s where we got our name, Homo sapiens. The names were short, sweet, and easy to remember.

By the time that book came out, Linnaeus was Europe’s greatest naturalist. Catherine the Great sent him Russian plants for his collection. Rousseau said he learned more from one of Linnaeus’s books than all books on morality.

Students flocked to learn from him, and then took expeditions of their own to other continents to find new species, which they named according to his system and which he added to new editions of Systema Naturae.

It must be pointed out, though, that Linnaeus was a nasty, stingy man. He loved to haggle over the creatures he bought for his botanical garden. He once wrote “All the beasts are splendid, but money more splendid.” Linnaeus hated his rivals, and he liked to name noxious weeds after them. We still utter Linnaeus’s insults today, because a species can never be renamed.

Linnaeus’s arrogance came from his sense that he was doing something incredibly important. He was organizing creation itself. “God created, Linnaeus classified,” was his motto.

Linnaeus believed that his system would reveal the true order of nature. Linnaeus was something of an early ecologist. He beleived that each species was exquisitely suited to the particularly place it lived, whether it was in the tropics or in the coldest reaches of Lapland. Each species also played a crucial role in nature. After all, God would never create a species with no purpose.

Linnaeus’s impact on modern biology was huge, although invisible. In Linnaeus’s time, there were 20,000 named species. Today there are something like 1.8 million. Instead of Systema Naturae, you can go online to a site like the Encyclopedia of Life, which is amassing information on every species on Earth. But you’ll still find Linnaeus’s original system of species, genus, class, and so on. He gave taxonomists a common language, and we still speak it today. He set up the rules by which taxonomists could describe species and share their discoveries. In a sense, he had invented a biological Wikipedia in the eighteenth century. Once everyone accepted the same set of rules for sharing information, the body of knowledge exploded.

But Linnaeus has another legacy. His system helped to create a sense that there are unbreachable barriers between species. Each species has its own essence, and breaching them goes against nature or against God’s will. I see this attitude very much at work today. It’s at work when people condemn experiments that combine cells from humans with other animals as an affront to human nature. It’s at work when people complain that genetic engineering destroys the integrity of animal or plant species. I’m going to get back to this subject at the end of my talk, to explain why it doesn’t hold water.

What’s ironic about Linnaeus is that he was actually more open-minded about nature than his rigid system would suggest. John Wilkins, a philosopher of science at the University of Queensland, has observed that Linnaeus was willing to entertain conclusions that were shocking in his day.

For example, Linnaeus changed his mind about whales. He first thought they were fish, but then decided they were mammals.  This was a scandalous idea, and even in the early 1800s, the United States fought in court to keep whales classified as fish, because they could charge a tax on fish but not mammals. But Linnaeus recognized that whales nursed their young, and for him, that was the key trait for mammals.

Linnaeus really riled people up with his treatment of Homo sapiens. He placed humans in the primate order along with monkeys and apes. He even wanted to put humans in the same genus as chimpanzees. He knew that wouldn’t make theologians happy. In fact, he wrote this to a friend:

“It is not pleasing that I placed humans among the primates, but man knows himself. Let us get the words out of the way. It will be equal to me by whatever name they are treated. But I ask you and the whole world a generic difference between men and simians in accordance with the principles of Natural History. I certainly know none.”

Linnaeus was also willing to push the boundaries of what the Bible taught. He believed that God had created species at the beginning of the world with the facts of nature today. He wrote, “There are as many species as the Infinite Being produced diverse forms in the beginning.”

But how did those species survive Noah’s Flood? Linnaeus gave up on the Flood and claimed that at the beginning of the world, there was only a single island on Earth where all life was created. It was a vast mountain sticking out of the ocean. At each elevation there were different animals suited to the climate. All the species Linnaeus encountered above the Arctic circle had originally lived at the peak of the mountain; all the tropical species lived at its base. The ocean then subsided and the animals and plants somehow got from the original mountain to everywhere in the world.

There were, of course, some problems with this Eden Island. How did you get polar bears from the equator to the Arctic without killing them in the heat? But it was still an ingenious idea, and it showed how willing Linnaeus was to challenge conventional wisdom.

Linnaeus even changed his mind about whether species could change. In his first version of the Systema, he wrote that there were no new species. He dropped that line in the last editions he published. He could see that plants could hybridize into perfectly healthy new forms. Linnaeus did not embrace evolution, but he did recognize change.

When you consider Linnaeus as a real person rather than a caricature from a world before Darwin, you can really appreciate Darwin’s accomplishments. Darwin practiced a kind of scientific jiujitsu. He took the scientific research of others, like Linnaeus, and flipped it upside down. Suddenly, arbitrary patterns and biological puzzles became compelling evidence for evolution.

Darwin’s life is far more familiar to people than Linneaus’s, so I’m not going to go into as much detail about it today. He was born in 1809, 31 years after Linnaeus died. At 22, Darwin was on the road to a life as a parson. Out of the blue, an opportunity came up to go on a voyage, serving as a companion to the captain of a ship called the Beagle.

Darwin was much more interested in geology and natural history than in theology, so he jumped at the chance. Like young Linnaeus, he took a long, transforming journey. Instead of traveling from southern Sweden to northern Sweden, he went around the world. Five years later he came back home, with the seeds of his theory of evolution in his head.

Darwin put his theory together in a set of notebooks. On one page in 1837 he drew a simple picture of a tree. Each branch tip was a species. Above it, he wrote, I think.

Darwin abandoned the idea that species were fixed. He decided they evolved from common ancestors. The hierachy of Linnaeus’s system–the species, the genera, the orders, and so on–made sense as evidence of evolution. Species were more closely related to other members of their genus than they were to other members of their order. The traits that Linnaeus used to put species in a genus or an order were inherited from a common ancestor. So, for example, the fact that whales nurse makes sense if you consider them to be the descendants of mammals on land–our cousins, in other words.

So how did the branches grow apart on Darwin’s tree of life? Darwin introduced his readers to natural selection.

Some individuals have more offspring than others thanks to traits they inherit. The traits may make them better able to survive in a particular climate, or they may make an animal better at attracting mates. Those traits become more common over time.

To anyone who doubted that animals or plants couldn’t change, he pointed out how breeders had transformed pigeons and other animals and plants in just a few centuries. And to anyone who would claim that species are fixed, Darwin zeroed in on a weak spot in Linnaeus’s old system of classification: deciding exactly what is an is not a species.

Consider a bird called the willow ptarmigans. In Ireland, willow ptarmigans have a slightly different plumage than the willow ptarmigans in Finland. They are different in turn from the ones in Norway. Even with Linnaeus’s magnificent system, naturalists could not agree about whether Irish and Finnish and Norwegian ptarmigans belonged to different species or were just varieties.

Darwin was amused by these struggles. He once wrote, “It is really laughable to see what different ideas are prominent in various naturalists’ minds, when they speak of ‘species. It all comes, I believe, from trying to define the indefinable.”

Darwin argued that each group of organisms that we call a species started out once as a variety of an older species. Over time natural selection altered that variety, adapting it to its environment. As some varieties evolved, others became extinct. And after thousands or millions of years, the varieties that survive became so different that we call them species.

Darwin wrote, “I look at the term ‘species’ as one arbitrarily given, for the sake of convenience, to a set of individuals closely resembling each other.”

Darwin went public at last with his theory in July 1858–200 years ago last month. A letter from him was read at the Linnean Society–named, of course, after Linneas. It was a joint presentation. A naturalist named Alfred Russel Wallace had sent Darwin a letter in which he sketched some of the same ideas Darwin was working on. So Darwin decided it was time to come forward, lest Wallace scoop him.

The reaction was pretty muted. It was not until 1859, when Darwin’s book, the Origin of Species, was published, that the world began to grapple with the tremendous change Darwin brought to our understanding of the natural world.

There are many ways of gauging Darwin’s impact almost 150 years later. I am a journalist, not a philosopher or a theologian, so I will limit myself to what I’ve learned writing articles about science for places like Scientific American and the New York Times.

Darwin’s fundamental insights are at the core of biology today. They are as important to biology as Newton’s insights are to physics. Biologists look at nature and ask how things are, and they also ask how things came to be the way they are. The two are intertwined.

The human genome project, the biggest accomplishment of modern biology, is proof of that. The genome scientists didn’t simply scan the raw code of our DNA to understand it. They also compared our DNA to our closest living relatives, chimpanzees, as well as to more distant relatives like monkeys, mice, and flies. They identified genes that we inherited from our common ancestor with those animals, and then traced the changes those genes experienced. Some were deleted. Some were duplicated. And their sequences changed, altering the instructions they give to our bodies. By tracing our history on the tree of life, we understand how we work.

Darwin didn’t seek to explain just Homo sapiens, though. Like Linnaeus, he had big ambitions. He wanted to explain it all. And if you look at his books, they’re awesome in their scope. He writes in loving details about orchids, barnacles, finches, orangutans, flounders, and many many other animals and plants. But as hard as you may try to look, you will find precious little about one group of organisms: microbes.

Microbes are invisible to our naked eye, and they are nearly invisible in Darwin’s books.

Darwin certainly knew about them. They had been discovered nearly two centuries before the Origin of Species, in the 1670s. The Dutch lens grinder Antonie von Leeowenhoeck built microscopes and used them to look at ditch water, the scraping of his own teeth, and other ordinary stuff. He discovered they were swarming with tiny creatures.

It was hard to make out much detail on the little creatures, though, so it was hard to classify them. Eight years later, Linnaeus assigned most of the microbes Leeuwenhoek had found into a single species in the animal kingdom. He called it Chaos infusorium. Infusorium was the Latin word for a solution, because microbes were found in liquids of various sorts. Chaos speaks for itself.

Microbes did not get much respect because it wasn’t clear that they were really alive in the way animals and plants are. Some people thought they sprang into existence from rotting material. Few people thought they did anything important. Linnaeus was actually ahead of his time in suggesting that malaria and other diseases were caused by little animals entering the body. The germ theory of disease was still a century away.

For Darwin, microbes mattered mainly because animals and plants had evolved from them. Some people challenged evolution by asking how there could still be microbes if evolution drove simple life to become complex.

He dismissed this argument outright: “On my theory the present existence of lowly organised productions offers no difficulty; for natural selection includes no necessary and universal law of advancement or development–it only takes advantage of such variations as arise and are beneficial to each creature under its complex relations of life.”

He saw that microbes could do just fine as they were. And he also made a very prophetic statement about microbes. He thought it was rash to claim that microbes today had not evolved significantly since the dawn of life. He wrote, “Every naturalist who has dissected some of the beings now ranked as very low in the scale, must have been struck with their really wondrous and beautiful organisation.”

Darwin would have been staggered by what scientists know now about microbes. They are wonderfully intricate. Let me just pick one example I’m very fond of–E. coli. This resident of your gut is a thousandth of an inch long, but it is exquisitely organized. It has four thousand genes in its DNA. If you printed out its genome, you’d end up with a book over a thousand pages long. To replicate, a single E. coli has to make a new genome. It copies its genetic tome at about a thousand letters a second. It usually makes a perfect duplicate.

Its genes encode molecules that work together to sense its environment, break down food, and cooperate with other E. coli. They work together. Some genes switch on other genes, which switch on other genes. There are genes to shut other genes off too. They form feedback loops, in much the same way the parts of an airplane work together to keep it in the air and not spin out of control.

In many ways, E. coli works much like our own cells do. That’s why scientists who studied E. coli have won a dozen or so Nobel Prizes. The French biologist Jacques Monod declared, what is true for E. coli is true for the elephant.

Microbes are also a tremendously important part of the biosphere. For one thing, there are just so many of them.

–If you went outside and picked up a pinch of dirt, you’d be picking up a billion microbes.

–Inside your own body, there are 10 times more microbial cells than your own cells.

–There are so many microbes because they can live so many places. They can live inside a grain of salt, or in acid or in boiling water.

–The sea floor is rife with microbes for half a mile down. According to a recent estimate, the carbon in sea floor microbes alone weigh 90 petagrams. That’s 200 trillion pounds of microbial life.

–There are about a billion times more microbes on Earth than there are stars in the universe.

Because there are so many microbes, and because they have so many different ways of making a living, they’re incredibly important ecologically.
If every human on Earth stepped on a spaceship and abandoned the planet, the ecosystems of the ocean and the land would go on pretty much as before. But if the single-celled life on Earth disappeared, the rest of life would probably die.

Microbes generate about half the oxygen in the atmosphere. They break down dead animals and plants, recycling the nutrients into the soil to feed new growth. They pull out pollutants from soil and water. They suck up inconceivable amounts of carbon from the atmosphere that would otherwise trigger much more global warming than we’re now experiencing.

Plants and animals–ourselves included–carry an internal jungle of microbes that generate nutrients we can’t make ourselves. Microbes are like little biochemical factories far more sophisticated than any chemistry carried out by humans. That’s why scientists are trying to understand the full range of their powers–for clean energy, cheap drugs, and other applications.

Linnaeus hoped to classify the full diversity of life. But he made a big mistake jamming the whole microbial world in a couple species.

Two species of bacteria may look identical, and but if you look at their DNA, they may be more genetically different than we are from a Shitake mushroom.

In that pinch of soil you just picked up, there are a billion microbes–and at least 50,000 species. Bear in mind, on the entire planet, there are 5,000 species of mammals.

And if you went to California, you’d find another 50,000 species, but less than 5 percent would be the same as the ones in the soil here.

And microbes dominate the history of life. The fossil record makes clear what Darwin suspected: early life was microbial. But Darwin didn’t appreciate just how long it stayed microbial. The oldest evidence of microbes is about 3.5 billion years old. It wasn’t until 600 million years ago that our own ancestors evolved from single-celled organisms into animals. So for about seven eighths of our history, our ancestors were microbes.

These facts put Darwin and Linnaeus’s work in a new light. Linnaeus wanted to classify all life, and Darwin wanted to explain the origin of its diversity. And yet they said little about the vast majority of living things.

What makes this really ironic is that today microbes are giving scientists the most detailed look at the processes Darwin wrote about so much: natural selection. We can see natural selection play out over a matter of weeks in microbes. That’s because microbes can reproduce several times a day, and a billion of them can fit comfortably in a flask. With each generation, new mutations arise. If a mutation lets a microbe reproduce faster in that flask, the microbe will leave more offspring than other microbes without the mutation.

One of the most fascinating of these experiments is nearly twenty years old. I went to visit it at Michigan State University. It doesn’t look like much–just twelve little flasks of E. coli being gently rocked in a corner of a lab. They belong to Richard Lenski.

Lenski started off this experiment in 1989 with a single microbe. It divided a few times into identical clones, from which Lenski started 12 colonies. He kept each of these 12 lines in its own flask. Each day he and his colleagues gave the bacteria a little glucose, which was gobbled up by the afternoon. The next morning, the scientists took some bacteria from each flask and put them in a new one with fresh glucose. And on and on and on, for 20 years and running.

Based on what scientists already knew about evolution, Lenski expected that the bacteria would experience natural selection in their new environment. In each generation, some of the microbes would mutate. Most of the mutations would be harmful, killing the bacteria or making them grow more slowly. Others would be beneficial allowing them to breed faster in their new environment. They would gradually dominate the population, only to be replaced when a new mutation arose to produce an even fitter sort of microbe.

Lenski used a simple method to find out if this would happen. He froze some of the original bacteria in each line, and then froze bacteria every 500 generations. Whenever he was so inclined, he could go back into this fossil record and thaw out some bacteria, bringing them back to life. By putting the newest bacteria in his lines in a flask along with their ancestors he could compare how well the bacteria had adapted to the environment he had created.

Over the generations, in fits and starts, the bacteria did indeed evolve into faster breeders. The bacteria in the flasks today breed 75% faster on average than their original ancestor.

Lenski and his colleagues have pinpointed some of the genes that have evolved along the way; in some cases, for example, the same gene has changed in almost every line, but it has mutated in a different spot in each case. Lenski and his colleagues have also shown how natural selection has demanded trade-offs from the bacteria. The bacteria have become adapted to living on a meager diet of glucose. But they’ve also gotten worse at  growing on other kinds of sugars.

When I visited Lenski’s lab, he told me that something weird had happened in one of the lines. But he wouldn’t want to talk about it until he and a grad student named Zachary Blount had run some tests. This summer they were finally ready to report the results. Out of the blue, some of their bacteria had abandoned their glucose diet and had evolved a new way to eat.

After about 33,000 generations Lenski and his students noticed something strange in one of the colonies. The flask started to turn cloudy. This happens sometimes when contaminating bacteria slip into a flask and start feeding on a compound in the broth known as citrate. Citrate is the molecule that makes lemons tart. Many species of bacteria can eat citrate, but in an oxygen-rich environment, E. coli can’t. The problem is that the bacteria can’t pull the molecule in through their membranes. In fact, their failure has long been one of the defining hallmarks of E. coli as a species.

Lenski assumed that the cloudy flask had been contaminated by some other species of bacteria. But it hadn’t. He and Blount tested the E. coli and found that it was eating the citrate. If they took out some of the E. coli and feed it pure citrate, they thrived.

Blount went back through the fossil record of E. coli, and discovered what had happened. There were no citrate eaters for the first 31,000 generations. 500 generations later, they made up half a percent of the population. Their population rose to 19% in the next 1000 generations. And then they nearly vanished at generation 33,000. But in the next 120 generations or so, the citrate-eaters went berserk, coming to dominate the population.

This rise and fall and rise suggests that the evolution of citrate-eating was not a one-mutation affair. Several mutations built up in the bacteria. The first mutations allowed the bacteria to eat citrate, but they were outcompeted by some glucose-eating mutants that still had the upper hand. Only after they mutated further did their citrate-eating become a recipe for success.

Now the scientists must determine the precise genetic steps these bacteria took to evolve from glucose-eaters to citrate-eaters. In order to eat a particular molecule, E. coli needs a special channel in its membranes through which to draw it. It’s possible, for example, that a channel dedicated to some other molecule mutated into a form that could also take in citrate. Later mutations could have fine-tuned it so that it could suck in citrate quickly.

The bacteria are doing what Darwin said life does: they adapt by natural selection. They gain new traits their ancestors didn’t have. You could argue that Lenski has seen the rise of a new species. The big surprise is that natural selection happens fast enough in bacteria for us to witness in a few months or years.

But microbes are also evolving in ways that Darwin never contemplated. Remember, Darwin saw the history of life as a tree. Each branch grows generation by generation. What’s happening, we know now, is that the parents are passing down genes to their children. That’s how genes move from person to person. It’s not as if we pass genes to each other every time we shake hands. It’s not as if you scratch your cat’s ear and pick up genes for growing whiskers. That would be like a tiny shoot coming off the cat branch, and fusing to the human branch.

But that’s actually what happens to microbes. The first clues that it did came long ago. In 1945, a young graduate student named Joshua Lederberg wanted to see whether E. coli had sex. He thought there might be male and female bacteria that mated, producing baby bacteria with both their genes. He created mutant strains of E. coli, each unable to make two essential molecule. He could keep each strain alive by feeding it the molecules it couldn’t make itself.

Lederberg then gave his E. coli the chance to have a little orgy. He mixed two mutant strains together. He gave them all the molecules they needed to survive. They grew and divided and grew and divided. And then Lederberg would put some of the bacteria in another dish without any of the molecules the two strains needed. The only way a microbe could survive in that dish was if it carried working copies of genes for all the essential molecules. And on rare occasion, Lederberg discovered, that’s exactly what happened.

Eventually Lederberg realized he was wrong about male and female microbes having baby microbes. That’s not how sex happens among microbes. It’s much weirder. One E. coli built a long tube that reached out and snagged another one. It began to pump some of its DNA into the other microbe, and then the tube broke off. It’s like passing genes with a handshake.

At first this microbial sex seemed like an oddity. It was useful to scientists who could study how genes work by passing them from one E. coli to another. But it could be safely ignored by biologists who studied life out in the real world.

That changed very quickly, because while Lederberg was discovering E. coli sex, doctors were just beginning to hand out antibiotics to kill dangerous strains of E. coli and other bacteria. Resistant mutants started to become more common, thanks to the sort of natural selection Richard Lenski studies. But then other species that showed no sign of resistance suddenly became resistant too. Eventually, scientists realized that the bacteria were trading genes. They might build the tubes Lederberg studied. Or they might slurp up DNA that spilled out of dead bacteria. It turns out that viruses can also move genes from one microbe to another.

But even ten years ago, there was still a sense that microbes were just trading resistance genes. Otherwise, they evolved in a familiar way, branching like a tree. Well, that’s over now. Scientists have sequenced the genomes of E. coli and hundreds of other species. And the evidence from these comparisons for gene trading is overwhelming. Scientists sequenced three strains of E. coli–one that lives harmlessly in the gut, one that causes food poisoning, and one that causes urinary tract infections. They only share 40% of their genes in common. The other genes came from other species.

In a typical microbe genome, 81% of its genes hopped from one species to another at some point in the history of life. These alien genes often join together and move from species to species in packages. They give microbes complicated new gifts, like the ability to inject toxins into our cells. In other words, the vast majority of genes in microbes have been altered by natural genetic engineering.

So let’s say Darwin sat down with his notebook today and wanted to draw the history of life. He’d start off by drawing a tree, but then he’d start joining the branches together into a web. Some parts of this web would still look like a tree. Our own part, the animal kingdom, has evolved like a tree, because our biology makes it hard for genes to move from host to host. But the rest of life would look very different in Darwin’s notebook.

This new view of life is going to take a while to get used to. It doesn’t just make us question some of the things Darwin wrote about. It also demands we rethink the view of life Linnaeus gave us. How can we fit microbes into the Systema Naturae, when their genes are mingled so thoroughly? Some scientists don’t think terms like species, or an order, or a class make any sense at all for microbes. We need a new Linnaeus to make sense of it.

It also means that we must abandon the idea that species barriers are somehow sacrosanct, that it is unnatural to move genes from one species to another. Nature has been moving them for billions of years. It may not be safe for us to move genes, but it’s not unnatural. We must bear that fact in mind as we debate genetically modidied animals, crops, and even people.

One thing that I find people don’t understand about scientists is that they aren’t very interested in what they’ve figured out. They want to head into the darkness, to come up with hypotheses to explain what’s not yet understood. They don’t mind being wrong, if they can at least push other scientists in the right direction.

So let’s celebrate Linnaeus and Darwin for pushing into the darkness, and for being both right and wrong in such a fertile way.