Doolittle, Darwin and the Deeply Dumb

[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
(discovery.org).

“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.”

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This article appears in Oct 8-14, 2009.