A conversation with Lynn Margulis is an effective way to change the way you think about life. Not just your life. All life. Scientists today recognize five groups of life: bacteria, protoctists (amoebas, seaweed), fungi (yeast, mold, mushrooms), plants, and animals. Margulis, a self-described “evolutionist,” makes a convincing case that there are really just two groups, bacteria and everything else.

That distinction led to her career-making insight. In a 1967 paper published in the Journal of Theoretical Biology, Margulis suggested that mitochondria and plastids—vital structures within animal and plant cells—evolved from bacteria hundreds of million of years ago, after bacterial cells started to collect in interactive communities and live symbiotically with one another. The resulting mergers yielded the compound cells known as eukaryotes, which in turn gave rise to all the rest—the protoctists, fungi, plants, and animals, including humans. The notion that we are all the children of bacteria seemed outlandish at the time, but it is now widely supported and accepted. “The evolution of the eukaryotic cells was the single most important event in the history of the organic world,” said Ernst Mayr, the leading evolutionary biologist of the last century. “Margulis’s contribution to our understanding the symbiotic factors was of enormous importance.”

Her subsequent ideas remain decidedly more controversial. Margulis came to view symbiosis as the central force behind the evolution of new species, an idea that has been dismissed by modern biologists. The dominant theory of evolution (often called neo-Darwinism) holds that new species arise through the gradual accumulation of random mutations, which are either favored or weeded out by natural selection. To Margulis, random mutation and natural selection are just cogs in the gears of evolution; the big leaps forward result from mergers between different kinds of organisms, what she calls symbiogenesis. Viewing life as one giant network of social connections has set Margulis against the mainstream in other high-profile ways as well. She disputes the current medical understanding of AIDS and considers every kind of life to be “conscious” in a sense.

Margulis herself is a highly social organism. Now 71, she is a well-known sight at the University of Massachusetts at Amherst, where she is on the geosciences faculty, riding her bike in all weather and at all times of day. Interviewer Dick Teresi, a neighbor, almost ran her over when, dressed in a dark coat, she cycled in front of his car late at night. On the three occasions that they met for this interview, Teresi couldn’t help noticing that Margulis shared her home with numerous others: family, students, visiting scholars, friends, friends of friends, and anybody interesting who needed a place to stay.

Most scientists would say there is no controversy over evolution. Why do you disagree? All scientists agree that evolution has occurred—that all life comes from a common ancestry, that there has been extinction, and that new taxa, new biological groups, have arisen. The question is, is natural selection enough to explain evolution? Is it the driver of evolution?

And you don’t believe that natural selection is the answer? This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create.

That seems like a fairly basic objection. How, then, do you think the neo-Darwinist perspective became so entrenched? In the first half of the 20th century, neo-Darwinism became the name for the people who reconciled the type of gradual evolutionary change described by Charles Darwin with Gregor Mendel’s rules of heredity [which first gained widespread recognition around 1900], in which fixed traits are passed from one generation to the next. The problem was that the laws of genetics showed stasis, not change. If you have pure breeding red flowers and pure breeding white flowers, like carnations, you cross them and you get pink flowers. You back-cross them to the red parent and you could get three-quarters red, one-quarter white. Mendel showed that the grandparent flowers and the offspring flowers could be identical to each other. There was no change through time.

There’s no doubt that Mendel was correct. But Darwinism says that there has been change through time, since all life comes from a common ancestor—something that appeared to be supported when, early in the 20th century, scientists discovered that X-rays and specific chemicals caused mutations. But did the neo- Darwinists﻿ ever go out of their offices? Did they or their modern followers, the population geneticists, ever go look at what’s happening in nature the way Darwin did? Darwin was a fine naturalist. If you really want to study evolution, you’ve got go outside sometime, because you’ll see symbiosis everywhere!

So did Mendel miss something? Was Darwin wrong? I’d say both are incomplete. The traits that follow Mendel’s laws are trivial. Do you have a widow’s peak or a straight hairline? Do you have hanging earlobes or attached earlobes? Are you female or male? Mendel found seven traits that followed his laws exactly. But neo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change—led to new species. I believed it until I looked for evidence.

What kind of evidence turned you against neo-Darwinism? What you’d like to see is a good case for gradual change from one species to another in the field, in the laboratory, or in the fossil record—and preferably in all three. Darwin’s big mystery was why there was no record at all before a specific point [dated to 542 million years ago by modern researchers], and then all of a sudden in the fossil record you get nearly all the major types of animals. The paleontologists Niles Eldredge and Stephen Jay Gould studied lakes in East Africa and on Caribbean islands looking for Darwin’s gradual change from one species of trilobite or snail to another. What they found was lots of back-and-forth variation in the population and then—whoop—a whole new species. There is no gradualism in the fossil record.

Gould used the term “punctuated equilibrium” to describe what he interpreted as actual leaps in evolutionary change. Most biologists disagreed, suggesting a wealth of missing fossil evidence yet to be found. Where do you stand in the debate? “Punctuated equilibrium” was invented to describe the discontinuity in the appearance of new species, and symbiogenesis supports the idea that these discontinuities are real﻿. An example: Most clams live in deep, fairly dark waters. Among one group of clams is a species whose ancestors ingested algae—a typical food—but failed to digest them and kept the algae under their shells. The shell, with time, became translucent, allowing sunlight in. The clams fed off their captive algae and their habitat expanded into sunlit waters. So there’s a discontinuity between the dark-dwelling, food-gathering ancestor and the descendants that feed themselves photosynthetically. ﻿

photography by Bob O'Connor

What about the famous “beak of the finch” evolutionary studies of the 1970s? Didn’t they vindicate Darwin? Peter and Rosemary Grant, two married evolutionary biologists, said, ‘To hell with all this theory; we want to get there and look at speciation happening.’ They measured the eggs, beaks, et cetera, of finches on Daphne Island, a small, hilly former volcano top in Ecuador’s Galápagos, year after year. They found that during floods or other times when there are no big seeds, the birds with big beaks can’t eat. The birds die of starvation and go extinct on that island.

Did the Grants document the emergence of new species? They saw this big shift: the large-beaked birds going extinct, the small-beaked ones spreading all over the island and being selected for the kinds of seeds they eat. They saw lots of variation within a species, changes over time. But they never found any new species—ever. They would say that if they waited long enough they’d find a new species.

Some of your criticisms of natural selection sound a lot like those of Michael Behe, one of the most famous proponents of “intelligent design,” and yet you have debated Behe. What is the difference between your views? The critics, including the creationist critics, are right about their criticism. It’s just that they’ve got nothing to offer but intelligent design or “God did it.” They have no alternatives that are scientific.

You claim that the primary mechanism of evolution is not mutation but symbiogenesis, in which new species emerge through the symbiotic relationship between two or more kinds of organisms. How does that work? All visible organisms are products of symbiogenesis, without exception. The bacteria are the unit. The way I think about the whole world is that it’s like a pointillist painting. You get far away and it looks like Seurat’s famous painting of people in the park (jpg). Look closely: The points are living bodies—different distributions of bacteria. The living world thrived long before the origin of nucleated organisms [the eukaryotic cells, which have genetic material enclosed in well-defined membranes]. There were no animals, no plants, no fungi. It was an all-bacterial world—bacteria that have become very good at finding specialized niches. Symbiogenesis recognizes that every visible life-form is a combination or community of bacteria.

How could communities of bacteria have formed completely new, more complex levels of life? Symbiogenesis recognizes that the mitochondria [the energy factories] in animal, plant, and fungal cells came from oxygen-respiring bacteria and that chloroplasts in plants and algae—which perform photosynthesis—came from cyanobacteria. These used to be called blue-green algae, and they produce the oxygen that all animals breathe.

Are you saying that a free-living bacterium became part of the cell of another organism? How could that have happened? At some point an amoeba ate a bacterium but could not digest it. The bacterium produced oxygen or made vitamins, providing a survival advantage to both itself and the amoeba. Eventually the bacteria inside the amoeba became the mitochondria. The green dots you see in the cells of plants originated as cyanobacteria. This has been proved without a doubt.

And that kind of partnership drives major evolutionary change? The point is that evolution goes in big jumps. That idea has been called macromutation, and I was denigrated in 1967 at Harvard for mentioning it. “You believe in macromutation? You believe in acquired characteristics?” the important professor Keith Porter asked me with a sneer. No, I believe in acquired genomes.

Can you give an example of symbiogenesis in action? Look at this cover of Plant Physiology [a major journal in the field]. The animal is a juvenile slug. It has no photosynthesis ancestry. Then it feeds on algae and takes in chloroplasts. This photo is taken two weeks later. Same animal. The slug is completely green. It took in algae chloroplasts, and it became completely photosynthetic and lies out in the sun. At the end of September, these slugs turn red and yellow and look like dead leaves. When they lay eggs, those eggs contain the gene for photosynthesis inside. Or look at a cow. It is a 40-gallon fermentation tank on four legs. It cannot digest grass and needs a whole mess of symbiotic organisms in its overgrown esophagus to digest it. The difference between cows and related species like bison or musk ox should be traced, in part, to the different symbionts they maintain.﻿

But if these symbiotic partnerships are so stable, how can they also drive evolutionary change? Symbiosis is an ecological phenomenon where one kind of organism lives in physical contact with another. Long-term symbiosis leads to new intracellular structures, new organs and organ systems, and new species as one being incorporates another being that is already good at something else. This major mode of evolutionary innovation has been ignored by the so-called evolutionary biologists. They think they own evolution, but they’re basically anthropocentric zoologists. They’re playing the game while missing four out of five of the cards. The five are bacteria, protoctists, fungi, animals, and plants, and they’re playing with just animals—a fifth of the deck. The evolutionary biologists believe the evolutionary pattern is a tree. It’s not. The evolutionary pattern is a web—the branches fuse, like when algae and slugs come together and stay together.

In contrast, the symbiotic view of evolution has a long lineage in Russia, right? From the very beginning the Russians said natural selection was a process of elimination and could not produce all the diversity we see. They understood that symbiogenesis was a major source of innovation, and they rejected Darwin. If the English-speaking world owns natural selection, the Russians own symbiogenesis. In 1924, this man Boris Mikhaylovich Kozo-Polyansky wrote a book called Symbiogenesis: A New Principle of Evolution, in which he reconciled Darwin’s natural selection as the eliminator and symbiogenesis as the innovator. Kozo-Polyansky looked at cilia—the wavy hairs that some microbes use to move—and said it is not beyond the realm of possibility that cilia, the tails of sperm cells, came from “flagellated cytodes,” by which he clearly meant swimming bacteria.

Has that idea ever been verified? The sense organs of vertebrates have modified cilia: The rods and cone cells of the eye have cilia, and the balance organ in the inner ear is lined with sensory cilia. You tilt your head to one side and little calcium carbonate stones in your inner ear hit the cilia. This has been known since shortly after electron microscopy came in 1963. Sensory cilia did not come from random mutations. They came by acquiring a whole genome of a symbiotic bacterium that could already sense light or motion. Specifically, I think it was a spirochete [a corkscrew-shaped bacterium] that became the cilium.

Don’t spirochetes cause syphilis? Yes, and Lyme disease. There are many kinds of spirochetes, and if I’m right, some of them are ancestors to the cilia in our cells. Spirochete bacteria are already optimized for sensitivity to motion, light, and chemicals. All eukaryotic cells have an internal transport system. If I’m right, the whole system—called the cytoskeletal system—came from the incorporation of ancestral spirochetes. Mitosis, or cell division, is a kind of internal motility system that came from these free-living, symbiotic, swimming bacteria. Here [she shows a video] we compare isolated swimming sperm tails to free-swimming spirochetes. Is that clear enough?

And yet these ideas are not generally accepted. Why? Do you want to believe that your sperm tails come from some spirochetes? Most men, most evolutionary biologists, don’t. When they understand what I’m saying, they don’t like it.

We usually think of bacteria as strictly harmful. You disagree? We couldn’t live without them. They maintain our ecological physiology. There are vitamins in bacteria that you could not live without. The movement of your gas and feces would never take place without bacteria. There are hundreds of ways your body wouldn’t work without bacteria. Between your toes is a jungle; under your arms is a jungle. There are bacteria in your mouth, lots of spirochetes, and other bacteria in your intestines. We take for granted their influence. Bacteria are our ancestors. One of my students years ago cut himself deeply with glass and accidentally inoculated himself with at least 10 million spirochetes. We were all scared but nothing happened. He didn’t even have an allergic reaction. This tells you that unless these microbes have a history with people, they’re harmless.

Are you saying that the only harmful bacteria are the ones that share an evolutionary history with us? Right. Dangerous spirochetes, like the Treponema of syphilis or the Borrelia of Lyme disease, have long-standing symbiotic relationships with us. Probably they had relationships with the prehuman apes from which humans evolved. Treponema has lost four-fifths of its genes, because you’re doing four-fifths of the work for it. And yet people don’t want to understand that chronic spirochete infection is an example of symbiosis.

You have upset many medical researchers with the suggestion that corkscrew-shaped spirochetes turn into dormant “round bodies.” What’s that debate all about? Spirochetes turn into round bodies in any unfavorable condition where they survive but cannot grow. The round body is a dormant stage that has all the genes and can start growing again, like a fungal spore. Lyme disease spirochetes become round bodies if you suspend them in distilled water. Then they come out and start to grow as soon as you put them in the proper food medium with serum in it. The common myth is that penicillin kills spirochetes and therefore syphilis is not a problem. But syphilis is a major problem because the spirochetes stay hidden as round bodies and become part of the person’s very chemistry, which they commandeer to reproduce themselves. Indeed, the set of symptoms, or syndrome, presented by syphilitics overlaps completely with another syndrome: AIDS.

Wait—you are suggesting that AIDS is really syphilis? There is a vast body of literature on syphilis spanning from the 1500s until after World War II, when the disease was supposedly cured by penicillin. Yet the same symptoms now describe AIDS perfectly. It’s in our paper “Resurgence of the Great Imitator.” Our claim is that there’s no evidence that HIV is an infectious virus, or even an entity at all. There’s no scientific paper that proves the HIV virus causes AIDS. Kary Mullis [winner of the 1993 Nobel Prize for DNA sequencing, and well known for his unconventional scientific views] said in an interview that he went looking for a reference substantiating that HIV causes AIDS and discovered, “There is no such document.”

Syphilis has been called “the great imitator” because patients show a whole range of symptoms in a given order. You have a genital chancre, your symptoms go away, then you have the pox, this skin problem, and then it’s chronic, and you get sicker and sicker. The idea that penicillin kills the cause of the disease is nuts. If you treat the painless chancre in the first few days of infection, you may stop the bacterium before the symbiosis develops, but if you really get syphilis, all you can do is live with the spirochete. The spirochete lives permanently as a symbiont in the patient. The infection cannot be killed because it becomes part of the patient’s genome and protein synthesis biochemistry. After syphilis establishes this symbiotic relationship with a person, it becomes dependent on human cells and is undetectable by any testing.

Is there a connection here between syphilis and Lyme disease, which is also caused by a spirochete and which is also said to be difficult to treat when diagnosed late? Both the Treponema that cause syphilis and the Borrelia that cause Lyme disease contain only a fifth of the genes they need to live on their own. Related spirochetes that can live outside by themselves need 5,000 genes, whereas the spirochetes of those two diseases have only 1,000 in their bodies. The 4,000 missing gene products needed for bacterial growth can be supplied by wet, warm human tissue. This is why both the Lyme disease Borrelia and syphilis Treponema are symbionts—they require another body to survive. These Borrelia and Treponema have a long history inside people. Syphilis has been detected in skull abnormalities going back to the ancient Egyptians. But I’m interested in spirochetes only because of our ancestry. I’m not interested in the diseases.

When you talk about the evolutionary intelligence of bacteria, it almost sounds like you think of them as conscious beings. I do think consciousness is a property of all living cells. All cells are bounded by a membrane of their own making. To sense chemicals—food or poisons—it takes a cell. To have a sense of smell takes a cell. To sense light, it takes a cell. You have to have a bounded entity with photoreceptors inside to sense light. Bacteria are conscious. These bacterial beings have been around since the origin of life and still are running the soil and the air and affecting water quality.

Your perspective is rather humbling. The species of some of the protoctists are 542 million years old. Mammal species have a mean lifetime in the fossil record of about 3 million years. And humans? You know what the index fossil of Homo sapiens in the recent fossil record is going to be? The squashed remains of the automobile. There will be a layer in the fossil record where you’re going to know people were here because of the automobiles. It will be a very thin layer.

Do we overrate ourselves as a species? Yes, but we can’t help it. Look, there are nearly 7,000 million people on earth today and there are 10,000 chimps, and the numbers are getting fewer every day because we’re destroying their habitat. Reg Morrison, who wrote a wonderful book called The Spirit in the Gene, says that although we’re 99 percent genetically in common with chimps, that 1 percent makes a huge difference. Why? Because it makes us believe that we’re the best on earth. But there is lots of evidence that we are “mammalian weeds.” Like many mammals, we overgrow our habitats and that leads to poverty, misery, and wars.

Why do you have a reputation as a heretic? Anyone who is overtly critical of the foundations of his science is persona non grata. I am critical of evolutionary biology that is based on population genetics. I call it zoocentrism. Zoologists are taught that life starts with animals, and they block out four-fifths of the information in biology [by ignoring the other four major groups of life] and all of the information in geology.

You have attacked population genetics—the foundation of much current evolutionary research—as “numerology.” What do you mean by that term? When evolutionary biologists use computer modeling to find out how many mutations you need to get from one species to another, it’s not mathematics—it’s numerology. They are limiting the field of study to something that’s manageable and ignoring what’s most important. They tend to know nothing about atmospheric chemistry and the influence it has on the organisms or the influence that the organisms have on the chemistry. They know nothing about biological systems like physiology, ecology, and biochemistry. Darwin was saying that changes accumulate through time, but population geneticists are describing mixtures that are temporary. Whatever is brought together by sex is broken up in the next generation by the same process. Evolutionary biology has been taken over by population geneticists. They are reductionists ad absurdum. Population geneticist Richard Lewontin gave a talk here at UMass Amherst about six years ago, and he mathematized all of it—changes in the population, random mutation, sexual selection, cost and benefit. At the end of his talk he said, “You know, we’ve tried to test these ideas in the field and the lab, and there are really no measurements that match the quantities I’ve told you about.” This just appalled me. So I said, “Richard Lewontin, you are a great lecturer to have the courage to say it’s gotten you nowhere. But then why do you continue to do this work?” And he looked around and said, “It’s the only thing I know how to do, and if I don’t do it I won’t get my grant money.” So he’s an honest man, and that’s an honest answer.

Do you ever get tired of being called controversial? I don’t consider my ideas controversial. I consider them right.