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Doolittle, Darwin and the Deeply Dumb 

While American creationists misappropriate the work of a Dalhousie biologist...

[Editor’s note: this story is one of five Coast articles selected as finalists for the 2010 Atlantic Journalism Awards. All five stories are collected here.]

Because it is both the 150th anniversary of the publication of The Origin of Species and the 200th anniversary of author Charles Darwin's birth, 2009 has been dubbed the Year of Darwin. Scientists around the world are using the twin anniversaries as excuse to hold academic conferences discussing evolution, to publish papers exploring the current state of research and to simply celebrate the life and work of what some say is the greatest figure in modern biology.

In Texas, however, the Year of Darwin began with an attack on the teaching of evolution in public schools. On January 21, the Texas Board of Education was considering a resolution that would require textbooks to discuss the "strengths and weaknesses" in the theory of evolution---a phrase science education advocates say is a backdoor approach to introducing creationist literature into the curriculum.

Modern science has established that life on Earth arose about four billion years ago, and that all creatures alive today have evolved from common ancestors. Creationists reject that view, and say life is the handiwork of god, the creator.

Texas has special importance in the evolutionists-creationists fight, because it is a large state with a large student population, publishers tend to produce textbooks that meet the state's standards and sell them across the US.

But more, Texas has an influential religious conservative movement. Republican governor Rick Perry, for example, believes the Bible is the literal word of god, and that non-Christians are condemned to hell. Don McLeroy, the chair of the board of education, rejects the scientific view that the Earth is four-and-a-half billion years old, saying instead that the Earth is merely several thousand years old, as related in the Bible.

Crammed into the board hearing room that January day were 14 board members (including 10 Republicans), dozens of spectators (most of them creationists), representatives of both the National Center for Science Education (a defender of the teaching of evolution) and the Discovery Institute (the leading creationist advocacy group) and reporters.

At one point in the proceedings, reports the Dallas Morning News, board member Barbara Cargill, a Republican "who supported the weaknesses requirement, said there have been 'significant challenges' to evolution theory. She cited a recent news article in which a European scientist disputed Darwin's 'tree of life' showing common ancestors for all living things."

The article Cargill cited was from that day's edition of New Scientist, a respected weekly publication that covers the scientific community. It's unknown if Cargill had actually read the article she cited, but the contents of the article were immaterial; what mattered was the packaging.

As she made her argument, say NCSE reps who were present at the hearing, Cargill waved a copy of the magazine cover before her. It read: "Darwin was wrong: cutting down the tree of life."

The article discusses several scientists working on the frontiers of evolutionary research, starting with microbiologist Ford Doolittle, an American by birth who has spent the bulk of his career working at Dalhousie University.

Enlightenment philosophers were cataloguers. They looked at the animal and plant world and heroically compiled taxonomies, classification systems for all living things. Such taxonomies, including Linnaeus', which we still use today, grouped creatures based on physical characteristics that appeared to be similar.

It was Charles Darwin, however, who first suggested that all living things are actually related. That is, like distant human cousins who share a common great-great-grandparent, different animal species, including humans, have a common ancestor. And just as a genealogist can map out the living descendants of, say, Thomas Jefferson and draw a "family tree" originating with Jefferson, the history of all life can be represented by a "tree of life," with one long-past species, the trunk, branching out into all of today's living species, the twigs at the end of the branches (see below).

Darwin held that there were small variations between individual members of a species, and through a struggle for survival, only the most fit individuals survived. These individuals passed on the traits that made them survivors to the next generation, and so on from generation to generation. As species gradually transformed, new branches arose on the tree of life.

Remarkably, though, Darwin came up with this theory without knowing what physical mechanism could explain how traits are passed from one generation to the next. Through the early 20th century, scientists rediscovered Gregor Mendel's work with the inheritance of traits, and worked out the basics of chromosomes, genes and DNA. In 1953, James Watson and Francis Crick famously discovered the "double helix" structure of DNA.

Born in Urbana, Illinois in 1942, Ford Doolittle came of age during the Cold War, as the United States asserted its primacy in science.

Doolittle says the Soviet Union's 1957 launch of Sputnik determined his future life path: "It made American boys want to be scientists and engineers---if they wanted to get any girls for one thing---and they wanted to feel like they were doing their duty for their country. I think I would've gone into the arts if it wasn't for the emphasis on science education after Sputnik."

As a teenager, Doolittle had a summer job in the lab of molecular biologist Sol Spiegelman at the University of Illinois.

"It was probably one of the more exciting labs to be in in the late '50s and '60s," he says. "It had the atmosphere of a hospital emergency ward---everything was important, people worked all night, shifts of people, it was very exciting."

Doolittle went on to Harvard, where he studied under Alwin Pappenheimer, a biologist who looked at infectious diseases, then to Stanford, in California, where Doolittle received a PhD in biochemical genetics, and then back to Urbana for a post-doctorate appointment, to work alongside Spiegelman. But Doolittle found himself gravitating to the work of another University of Illinois researcher, Carl Woese.

"Sol Spiegelman," says Doolittle, "was very intimidating---brilliant, but you didn't want to say something stupid around Sol. Carl Woese was much more approachable. You could drink beer with Carl and talk about sex and things. Many of Sol's people were closer to Carl Woese personally."

Woese literally reordered the world of biology. Up until that time, biologists considered all life to consist of two different fundamental types: prokaryotes and eukaryotes. Prokaryotes are relatively simple cells with no nucleus; eukaryotes are cells with a nucleus that contain the cell's chromosomes. But by looking at a piece of genetic material called ribosomal RNA, which makes proteins in the cell, Woese showed that there are two different kinds of prokaryotes---bacteria and archaea, which are as fundamentally different from each other as they are from eukaryotes. Woese found that life had three fundamental types, not two.

Doolittle was one of a small group of scientists referred to as Woese's Army. Through the '70s and '80s they mapped out the relationships between bacteria, archaea and eukaryotes. By about 1990 that work had coalesced into a new view of how primitive life had developed, an understanding that most biologists share to this day.

The new picture (see illustrations at the end of this article) filled in some of the details of Darwin's tree of life: The trunk of the tree of life splits into two main limbs, bacteria and archaea. Archaea in turn sprouts a new limb, eukaryotes. And that eukaryotic limb leads to multi-celled organisms and branches into all the stuff we commonly think of life: plants and animals and people.

Doolittle was hired by Dalhousie University in 1975.

"For an American to come here at that time---if you weren't a Buddhist---was a pretty rare thing," he says. "Or if you weren't a draft dodger, but I was neither of those."

Dalhousie at the time was just beginning to find its research legs. "I asked if there were any post-docs, and they said, 'We had one once, but it didn't work out.' And of course post-docs are the lifeblood of modern research."

As he was piecing together a research team of his own, Doolitle began working with blue-green algae. "I realized that nobody had ever done any work on them in terms of molecular biochemistry," he explains. "As a scientist, that's what you want, something no one else is working on."

Soon, another member of Woese's Army, Linda Bonen, came to Dalhousie as a grad student. Bonen brought with her a technology Woese had developed for sequencing RNA molecules, and Doolittle applied it to the blue-green algae. He and Bonen were the first to prove the theory that an ancestor of blue-green algae had been incorporated, whole, inside the cell of a eukaryote, evolving into the chloroplast, the part of plants that is responsible for photosynthesis.

That discovery showed that the tree of life was a bit more complex than once imagined: a bacterial ancestor of blue-green algae had fused with an eukaryote, like two trunks coming together to form a new limb. (A similar event explains another part of the cell, the mitochondrion.)

"That put Dalhousie on the map in terms of molecular evolution," says Doolittle.

Doolittle then began looking at the strange, and seemingly needless, duplication of the DNA molecule in some genes. The zoologist Richard Dawkins had in 1976 coined the term "selfish gene"; Doolittle borrowed the language to refer to what he called "selfish DNA," and wrote a paper on it with student Carmen Sapienza. He and Sapienza fired the paper off to both the journal Nature and to Francis Crick, co-discoverer of DNA, who was simultaneously working on much the same theory. Crick called the editors at Nature and insisted that both his and Doolittle's papers be published in the same 1980 issue, with Doolittle's leading.

"Genes doing weird stuff has always been something that's interested me," says Doolittle. "And genes not behaving the way that they should and things not being the way people think they are, that's always interested me."

In the following years, Doolittle kept at the top of the field, authoring or co-authoring an astounding 246 papers. Along the way, he and Dawkins independently found time to take a swipe at James Lovelock's Gaia Hypothesis, a theory much beloved in counter-culture circles that holds that the entire global ecosystem is in fact a single organism.

"It was just an instinctive reaction of a biologist who believes in natural selection, who doesn't see how it's possible for a global entity to arise," he says of his Gaia critique, published in CoEvolutionary Quarterly. That side project was probably his mostly wide read work, until recently.

The tree of life map holds that species evolve with the passage of time, through what scientists call "vertical descent." There were a couple of exceptions---the "fusing" of the two branches brought together when the ancestors of chloroplasts and mitochondria were absorbed into eukaryotes---but otherwise the tree explained pretty much everything, at least so long as scientists were looking at ribosomal RNA.

But around 1995, new techniques for sequencing genes became available, and biologists began looking at other genetic material, including the DNA found on chromosomes in the cell nucleus. And some of those genes tell a different evolutionary history, yielding a different tree.

It's now known that sometimes---rarely---a gene will shift from one species right over to another species, a process scientists call "lateral gene transfer." A gene that's in a certain kind of bacteria, for example, might through lateral gene transfer get absorbed into a eukaryotic cell, and become part of the eukaryote's genetic profile, where through vertical descent it's handed down from one generation to the next.

Lateral gene transfer confuses the tree of life. As with Darwin's tree, a gene will go through vertical descendent, from one generation to the next, for billions of generations, but over those billions of generations, it only takes one instance of lateral transfer to muck up the simple tree picture.

When Doolittle's lab began making trees of life with the new techniques, "instead of showing archaea and eukaryotes together and bacteria separately, it might show bacteria and eukaryotes together and archaea separately," he says, "or it would show one particular archaea had a bacteria version of a gene though another archaea had a different kind of version."

While lateral gene transfer creates some problems with mapping, it's been fully integrated into the science. Biologists know of three mechanisms for lateral gene transfer and, for the most part, say it happens so infrequently it doesn't matter for the purposes of truly understanding the tree of life.

But a growing number of microbiologists, say that lateral gene transfer happens much more often than was previously thought.

"It became a question of, 'How big of an iceberg was this the tip of?'" says Doolittle. "It began to look like there was going to be more discordant signal than there was going to be concordant signal, and so in 1999, I boldly published a paper in Science"---"Phylogenetic classification and the universal tree"---"that turned out to be a quite influential paper. I'm quite proud of it in retrospect, because I think I was reasonably careful in there to say, we don't actually know yet that most of the signal is discordant, but if some significant fraction of it is discordant, we have to rethink what we're doing.

"It made a lot of people angry. It still makes a lot of people angry."

Nowadays, Doolittle suggests all genes have been laterally transferred.

"That's my claim," he says. "I could be wrong about that, but I wouldn't be more than 10 percent wrong. It couldn't be more than 10 percent of the genes that have not been exchanged.

"The overwhelming pattern of bacterial evolution is vertical descent," he continues. "But if you ask, In this particular bacterial genome that I have just sequenced, how many of those genes got there by lateral transfer? I'll say, for gene X, right here, there only has to have been one lateral transfer in its entire four billion year history. So the frequency can be once every four billion years, on average."

If Doolittle is right, than the prevailing Darwinian view---in which all existing species can be traced back to one common ancestor---is wrong: there is no tree of life. Instead, the picture is more complicated, with a tree-like branching for multi-cellular organisms (plants, animals and people) arising out of a confused mess, with no discernable trunk (see illustration, page 15).

None of Doolittle's research has anything at all to do with creationism, but that doesn't stop creationists from cherry picking his data and taking his findings out of context.

(Creationists themselves have given up the "creationist" label, preferring the term "intelligent design" to explain their views, but while they usually drop off the reference to the Bible, by definition "intelligent design" requires a designer---a god---and some act of creation.)

For example, one of the most prominent creationists---Jonathan Wells, a follower of Sun Myung Moon, founder of the Unification Church---cites Doolittle in Icons of Evolution: Science or Myth, Wells' attack on evolution. The Discovery Institute likewise uses Doolittle in its "Primer on the Tree of Life," published on its website (

"Doctor Doolittle---he's an evolutionist," says Casey Luskin, who wrote the several articles published by the Discovery Institute in preparation for the battle before the Texas board of education. "He's no proponent of intelligent design, and we're not trying to claim that he is.

"I find his work interesting," continues Luskin, who received a degree in earth sciences. "The claim of lateral gene transfer is an inference---it is not a hard fact. It's an inference based upon the finding of genetic similarity---just like vertical descent is an inference based on the finding of genetic similarity. Lateral transfer is just invoked when vertical descent fails: it's an ad hoc backup hypothesis to save the view that life is fundamentally related in some sense.

"The notion that all life is related---whether it is through a tree of life or lateral gene transfer---that is an inference, based upon assumptions. That all it is---it's a house of cards based upon assumptions."

But to reject inference, no matter how much data has been collected, as Luskin does, is to reject all of science.

"Casey Luskin is simply reflecting the conventional creationist tradition, when he makes a comment like that," says Susan Spath, of the National Center for Science Education.

"If you read the creationist literature," continues Spath, "from around 1900 to the present, the fundamental issue is that the science of evolution undermines faith in god, which undermines the hold of Christianity on the culture, which therefore leads to moral decay and moral corruption. So if you could stop the teaching of evolution, you could stop the moral corruption of society. That's what they believe.

"Their work doesn't cut it---it doesn't cut it as science, A, and B, it has a particular religious belief embedded within it."

Doolittle's work is a very big deal in scientific and philosophical circles, so much so that philosophers at the University of Exeter in Britain hosted a "Perspectives on the Tree of Life" conference in Halifax over the summer, with Doolittle as the main subject of concern. Spath used the occasion to gently prod Doolittle and other microbiologists questioning the fundamental tree of life to become more media savvy, and to think about how their work can be misconstrued.

"As an evolution education advocate, I see the obvious temptation to use language like 'we're chopping down the tree of life,'" says Spath. "But I also see how profoundly misleading that is for the general public. The tree of life for the general public is plants and animals, and a tree absolutely explains evolution at that level."

Doolittle, for his part, is ambivalent about the creationists, who he calls "deeply dumb."

Other scientists who have read the New Scientist article have told Doolittle they see no problem with it.

"But you see, other people don't read the article," he says. "So in Texas people just ripped off the cover of New Scientist and took them to the Board of Education meeting.

"My position is: What are you going to do with people who don't visit the argument? Are we supposed to deal with that? And the trouble is, we are. I mean, in the States it's a real problem, so it's legitimate to criticize people like me, in the sense I take sort of a 'Fuck you if you can't take a joke' attitude, but I think that's not helping them in their battle against what is really a very strong evil thing which is happening, which is the growing stupidity of the American people.

"It amuses me. But see, it's not fair for me to be amused by it, because it's not a problem here [in Canada]. If I were teaching first-year biology in Arkansas, I'd be deeply pissed off at me saying I'm amused."

The Texas board of education split the difference in January: the board rejected the "strengths and weaknesses" phrase but replaced it with the phrase "sufficiency or insufficiency." The creationist-evolutionist battle continues.

The Origin of Species concerns multicellular organisms---the plants and animals and people that populate the visible world. Darwin didn't know much about microorganisms and, if he thought about them at all, he didn't have the technology to seriously research them. But microorganisms---the single-celled prokaryotes and eukaryotes---are the vast majority of all life forms.

As Spath sees it, Doolittle's work involves organisms that are completely irrelevant to the common understanding of evolution.

"This generation of microbiologists has great science to offer to general biological theory," she says. "What they're trying to do is say, 'the science of evolution is incomplete until you include the microbial world.' [But] when they say 'Darwin was wrong'--- Darwin wasn't wrong, it's just the theory was incomplete, and because of this new research on microbiology there's an opportunity to achieve a new integration of the biological sciences and extend the theory of evolution."

At the "Tree of Life" conference this summer, Spath urged Doolittle to stress that Darwin's theory still explains evolution for plants and animals---multicellular eukaryotes---and that Doolittle's work only applies to microorganisms. Humans and apes still share a common ancestor.

Doolittle agrees that lateral gene transfer is not much of an issue for multicellular creatures, because we are protected by our germ line---in order to have any effect on future generations, a gene would have to transfer directly into our sperm or eggs.

"If you get a piece of bacterial DNA injected into your gut cell, that's fine," he explains. "I mean, it can make you sick or something, but your children aren't going to inherit it."

But in fact, says Doolittle, if there haven't already been genes transferred laterally into our germ line, it's only a matter of time before it happens. "Animals [arrived] fairly recently, so if I'm saying the rate of transfer is once every four billion years, which is enough to make my case for bacteria, we haven't got anything like that kind of time---hundreds of millions of years as opposed to four billion years."

This kind of talk upsets a lot of scientists, including notably Richard Dawkins, who adamantly hold to the tree of life view that all life can be traced back to one ancestor. Doolittle dismisses these critics as "tree huggers," and says that they are making a tactical mistake by reacting to the creationists.

"Genetic and ecological processes that we pretty well understand, operating over four billion years, are more than enough to explain the diversity and adaptations of living things," says Doolittle. "So that's what our theory should be; it shouldn't be that there is a tree of life, or that natural selection is the developmental force, or stuff like that. I think a lot of the internal debates within the evolutionary biology field about natural selection or whether or not there is a tree get solidified on our side in order to defend ourselves against the other side that says, 'See, you guys don't even know what you're talking about.'"

Most biologists, even most microbiologists, still think that there is one tree of life with a trunk of a single ancestor, says Maureen O'Malley, a philosopher at Exeter University who leads a two-year project studying the philosophical implications of Doolittle's work.

"What is interesting," says O'Malley, "is that if you start tracking statements people made in the '80s to what they're saying now in 2009, there have been major conceptual shifts in what they said about the tree. I was reading something in the paper the other day by a 'one true tree' microbiologist who was saying, 'Yes, I do accept that this one true tree is an artificial construct and that we apply it to the world to impose order on it'---that's a radical difference from what he was saying even two or three years ago.

"I don't even know if Dawkins thinks you need to have an opinion on it---he knows there's weird stuff in the microbial world, but it doesn't really interest him---constructing trees of animals, and animals are the real kind of life in the world, so that's good enough, as far as he's concerned."

Dawkins did not respond to a request to be interviewed for this article.

Where does that leave us? As far as O'Malley is concerned, the tree of life is still with us. "It still seems to me that to understand evolution, you have to have this quite motivating idea of vertical inheritance and speciation, and if you lose that than you lose a lot of what we understand as evolution, and I don't think that's going to happen."

"Some biologists find these notions confusing and discouraging," Doolittle wrote in a February, 2000 article for Scientific America provocatively titled "Uprooting the tree of life." "It is as if we have failed at the task that Darwin set for us: delineating the unique structure of the tree of life. But in fact, our science is working just as it should. An attractive hypothesis or model (the single tree) suggested experiments, in this case the collection of gene sequences and their analysis with the methods of molecular phylogeny. The data show the model to be too simple. Now new hypotheses, having final forms we cannot yet guess, are called for."

Today, Doolittle continues to say the tree has to go. "The question is, What were we trying to do in the first place? We should try to change the model of evolution.

"Darwin was wrong, in the sense that Darwin did say that a treelike process explains classification," he continues. "Now, Darwin didn't go on about most of the living world, because he couldn't have, so I'm not going to hold him responsible for it, but he was wrong."

Evolving Trees of Life: a visual primer

Fig. 1 Ernst Haeckel’s 1866 tree of life shows all species originating with one trunk
  • Fig. 1 Ernst Haeckel’s 1866 tree of life shows all species originating with one trunk
Fig. 2 the 1980s-era tree had two main brances, bacteria and eukaryota, with archae branching off the latter
  • Fig. 2 the 1980s-era tree had two main brances, bacteria and eukaryota, with archae branching off the latter
Fig. 3 in the 1990s tree, some branches of bacteria fuse with eukaryotes
  • Fig. 3 in the 1990s tree, some branches of bacteria fuse with eukaryotes
Fig. 4 Doolittle’s latest view shows a hopelessly compex mess, wtih no discernable single trunk.
  • Fig. 4 Doolittle’s latest view shows a hopelessly compex mess, wtih no discernable single trunk.

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