Origins

by Julia Galef

CHICAGO, ILLINOIS—The birthplace of modern evolutionary biology can arguably be located at a landmark 1959 conference at the University of Chicago, which synthesized the then-new discoveries of DNA and genetics with Charles Darwin's observations on evolution. Last weekend, the university reprised that famous meeting with a "Darwin 2009" conference (right) that highlighted just how much has changed in the past 50 years: Dizzying genetic and genomic advances are allowing us to answer questions our 1959 counterparts couldn't even have dreamed of asking.

For instance, only recently have scientists begun to suspect that much of evolutionary change might be due not to mutations in the familiar protein-coding DNA but to other, noncoding DNA that regulates how and where the coding DNA expresses itself. The role of noncoding DNA in evolution has been hotly debated by scientists, but even as recently as last year the evidence was still spotty.

That's why one talk at the 29 to 31 October conference set off a particularly excited wave of coffee-break chatter: Stanford University evolutionary biologist David Kingsley revealed new results demonstrating how a change in the regulatory DNA of a single gene can produce a dramatic, adaptive change in an animal's anatomy.

Stickleback fish originated in marine environments, where they evolved a pelvis that protected them against predators by pushing out its spines, turning them into prickly, swimming pincushions (left). Over time, however, many stickleback populations spread to neighboring freshwater regions, where their pelvises were suddenly a disadvantage. In place of their traditional predators, they now faced large carnivorous insects like dragonflies who used the sticklebacks' prominent spines to nab them as they swam in shallow waters. So stickleback populations in freshwater began to lose their pelvises, a classic adaptive trick that Darwin himself could have appreciated; Kingsley's team wanted to know how, exactly, the sticklebacks' genes pulled it off.

Several years ago, Kingsley traced the loss of the pelvis back to a single gene called Pitx1.  Because the coding DNA in that gene was present in both the marine and freshwater sticklebacks, he reasoned that some part of Pitx1's noncoding DNA must be regulating the gene's expression, producing pelvises in the marine fish and none in the freshwater fish. Although his hypothesis made a big splash upon its publication (and has been widely cited since) it was still just a hypothesis, until this year.

After testing piece after piece of noncoding DNA from the spiny marine sticklebacks, Kingsley's team zeroed in on a sequence that seemed to correspond to pelvic development. So they cloned that sequence from the marine fish and injected it into the embryos of freshwater fish in order to produce the phenotype of a marine fish, a feat rarely attempted, let alone accomplished, in live animals. Sure enough, the resulting sticklebacks developed pelvises.

It's a particularly striking piece of evidence for the regulatory gene hypothesis, in part because the anatomical change is so large. "Losing an entire limb is the kind of dramatic change you usually see between only distantly related species," Kingsley said, so to produce such an effect from a single regulatory sequence of one gene is a bombshell. His results are also remarkable for including multiple, independent lineages of stickleback, addressing another hot topic in evolutionary biology: Do organisms exposed to the same selective pressures use the same genetic mechanism to adapt? Kingsley's results suggest that, at least in some cases, they do.

"The Holy Grail of research on adaptation is to identify adaptive mechanisms, the traits that contributed to adaptation and the genetic basis of adaptive traits," evolutionary biologist Doug Schemske of Michigan State University in East Lansing said after the conference. "Most of us can at best answer one of these questions—Kingsley has done it all."

Photo credits: Lucas Canino (conference); Frank Chan (marine stickleback)

by Elizabeth Pennisi

Charles Darwin worked hard to figure out how cooperation within a species—self-sacrifice among worker bees, for example—could have evolved. But he was stumped when it came to understanding cooperation between species. In his book, On the Origin of Species, he wrote, “Natural selection cannot possibly produce any modification in a species for the good of another species.” If that could be proved to have happened, “it would annihilate my theory, for such could not have been produced through natural selection.” And he scoffed at supposed examples perpetuated by some natural historians, such as a rattler using its rattle to warn prey. “I would almost as soon believe that the cat curls the end of its tail when preparing to spring, in order to warn the doomed mouse.” Instead, he argued that the rattle was meant to scare off birds and other potential predators.

Nonetheless, countless examples of cooperation between species exist—albeit many perhaps outside Darwin’s knowledge. Many long-standing partnerships are strengthened by specialized structures or traits in one species that benefit the other. Many of these relationships are dynamic, shifting back and forth over evolutionary time between exploitative and mutualistic.

Take the ant plants and their ants (see left). In tropical forests, certain types of trees make a home for ants that inhabit them, providing hollow stems or leaf pouches where the insects can roost and raise young. In return, the ants keep hungry herbivores at bay and sometimes kill off surrounding vegetation, creating a clearing around the trees.

Nineteenth century naturalists fiercely debated whether these ants forced their way into trees as parasites, wounding trees to make their nests, or whether they had a more benign relationship with the plants they lived in. In 1873, botanist Richard Spruce likened the ants to fleas on a dog—a nuisance. But others contended that some plants, acacias in particular, provided hollow thorns and food rewards to keep ants around for protection from herbivores. Many studies have supported this hypothesis over the past 4 decades. It seems the ants bite and poison surrounding vegetation, reducing the competition for space, water, and sunlight.

In the November issue of American Naturalist, David Edwards of the University of Leeds, U.K., and his colleagues describe how sometimes these ants get carried away. “I think most [researchers] believed that ants’ relationship with their host plants had been pretty well defined,” says John Tooker, a chemical ecologist at Pennsylvania State University, University Park. But in 1996, scientists observed a new, peculiar ant behavior. While exploring the jungles of southeastern Peru, a team of ethnobotanists came across a number of "devil's gardens," what many locals call the ant-made clearings around trees. Although they had seen such clearings before, the researchers were surprised by what the natives showed them next: Trees of other species on the outside of the clearing were scarred and swollen (see right) with networks of cavities filled with worker ants, queens, brood, and mealy bugs. "These galls made up a large percentage of the swollen trunk volume," says Edwards. Sometimes the internal excavations were so extensive that the tree had collapsed. The locals blame the scars on forest spirits.

The researchers think the ants are attacking these other trees because there aren’t enough ant plants to house ever-expanding colonies. “It suggests a level of ecosystem engineering [by the ants] not previously recognized,” says Tooker. And at this point, the relationship seems anything but mutual. “I expect this to be an antagonistic relationship because of the range of tree species that are galled by the ants,” Tooker notes. These are trees not typically associated with ants, and so there’s been little opportunity for a partnership to evolve. But if the ants patrol the area and ward off herbivores, then perhaps there is some payback by the ant to the tree, he adds.

The ants involved belong to the genus Myrmelachista, which typically nest in stems. Some species in the genus do not form associations to particular species, says John Longino, an entomologist at Evergreen State College in Olympia, Washington. He suggests that devil’s garden ants coevolved with new queens, gradually evolving a preference for certain plant species as the best nesting spots. Their targets eventually provided housing rather than chance having irregular holes chewed into their stems. Then, “perhaps it doesn’t take much to turn a mild-mannered and inconspicuous stem-nesting ant into a ferocious devil’s gardener. Maybe just the right kind of plant can encourage and manipulate those latent talents,” he says.

These enticements can lead to trouble, however, as Edwards's collaborator, Megan Frederickson of the University of Toronto in Canada, has discovered. Ever in need of more room, the ant Allomerus octoarticulatus takes a devious step to promote its host tree’s growth. It destroys any flower buds that the host produces. When Frederickson measured the growth rates of sterilized and reproductive plants, she found that the ant’s drastic maneuver did encourage more vegetative growth—and more living space for the ants. She reported those findings in the May issue of American Naturalist.

Darwin did not have the benefit of these experiments that show reciprocated benefits and the dynamic balance between giving and taking. But if he had, “he would have found ant-plant symbioses a real hoot,” says Mike Kaspari, an ecologist at the University of Oklahoma, Norman.

Photo credits: (ants) Megan Frederickson; (tree) Douglas Yu

“Ardi,” the oldest known skeleton of a hominin, or member of the human family, has grabbed headlines around the world since her unveiling in Science Thursday. Not surprisingly, the press coverage of the 4.4-million-year-old Ardipithecus ramidus has sometimes been sensational—and, in some cases, completely wrong.  Some newspapers and broadcasters have misinterpreted the authors’ finding that Ardi did not look like a chimpanzee or gorilla. Based on this anatomy, the authors proposed that Ardi shows that humans did not evolve from a “chimpanzee-like ape.” By that, they meant that Ardi evolved from an ancient ape that didn’t look like a chimpanzee or gorilla does today and that humans have retained some of those primitive traits.

But the word “chimpanzee-like” sometimes got lost in translation. Even the first version of a press release from Kent State University, where co-author C. Owen Lovejoy is on the faculty, said “Man Did Not Evolve From Apes.” And some media were clearly confused. The Torstar News Service in Canada wrote: “Man didn’t descend from apes. What is closer to the truth is that our knuckle-dragging cousins descended from us.”

A radio announcer in Baltimore, Maryland, asked me in an interview Monday if it was true that we were not apes—or even primates—and that we had our own, separate lineage that was more ancient. The same question came up in a Facebook chat with me and my editor at Science, Elizabeth Culotta, and has popped up in other media. 

Most disconcerting to the authors was the reporting on Ardi by the Arabic news network Al Jazeera, based in Doha, Qatar. A translation of the article written in Arabic starts with a headline that reads “Ardi Refutes Darwin’s Theory,” and the first sentence reads “American scientists have presented evidence that Darwin’s theory of evolution was wrong.” The article states that Ardi’s discovery “refutes the long-standing assumption that humans evolved from monkeys.”

Dr. Zaghloul El-Naggar, a professor of geology in several Arab universities (the article does not specify which ones), exclaims in the story that Westerners were beginning to “come to their senses after they used to deal with the origins of man from a materialistic perspective and by denying religions.” He goes on to claim that the age of Earth does not exceed 400,000 years, and that Ardi’s age of 4.4 million years is an exaggeration. 

For the record, all of this is plain wrong. Ardi is a primate descended from more ancient apes, as are all humans and human ancestors. Apes in turn are descended from monkeys. Chimpanzees are our closest living relatives— we share 96% of our DNA with them, and our lineages shared an ancestor sometime between 6 million and 8 million years ago, possibly earlier. The authors’ point is that the last common ancestor we shared with chimpanzees didn’t look like a chimp—which means that chimpanzees also have been evolving since the two lineages diverged. Finally, Ardi confirms rather than refutes Darwin’s prediction in 1871 that our progenitors lived on the African continent, as well as providing another link in the evolutionary chain from primitive apes to humans.

by Elizabeth Pennisi

As a year of meetings and celebrations of Darwin anniversaries winds down, mathematicians are planning their own Darwin fest: "The Mathematics of Darwin's Legacy" (23 to 24 November 2009 in Lisbon, Portugal).The legacy begins with Darwin, even though he was no mathematician and took only a qualitative approach to natural history. As Warren Ewens of the University of Pennsylvania will point out at the meeting, Darwin was quite hampered by the lack of knowledge at the time about Mendelian genetics. Offspring were instead thought to be “blends” of the parents’ traits—a process that was problematic because it should lead to the homogenization of traits and the loss of that same variation needed for evolution to occur.

But Darwin’s view that systems could evolve without the guidance or interference of a planner “has the generality and power of a mathematical idea,” says theoretical biologist Peter Jagers of the University of of Gothenburg, Sweden. And within a few decades, mathematics became a boon to the ideas promoted by the father of evolution.

“Once the Mendelian hereditary system [came into] use, mathematics becomes inevitable,” says Ewens. Quantitative methods quickly showed that variation is preserved in offspring.

Throughout the past century, mathematicians have helped promote a better understanding of evolution. In the early 20th century, mathematically minded biologists founded population genetics and put modeling on a firm footing in evolutionary biology. In the 1960s, another set of equations helped explain how cooperation could evolve, the subject of a recent Origins essay.

“There is an increasing community of applied mathematicians working on problems inspired by biology and, in particular, problems related to the theory of evolution,” says meeting organizer Fabio Augusto da Costa Carvalho Chalub of the Universidade Nova de Lisboa, Portugal. And more biologists want to take a mathematical approach to their work. “Our intention is to put these two communities in closer contact.”

by Michael Balter

GIBRALTAR—The first known Neandertal skull, left, was discovered here in 1848, and some of the last Neandertals may also have taken refuge in Gibraltar’s caves before they finally went extinct about 30,000 years ago. So Clive Finlayson of the Gibraltar Museum organizes a meeting here every few years on the evolution of Neandertals and other ancient humans.

This year, one presentation detailed the links between Charles Darwin himself and that first skull, which was found by workmen at Forbes’ Quarry on the north face of the Rock of Gibraltar. But its significance was not understood until sometime after 1856, when miners working in Germany’s Neander Valley discovered a partial skull and other bones.

Darwin was long interested in the Gibraltar skull, which he recognized as an ancient human, although many years passed before he got to see it. The circumstances of this historic encounter between Darwin and a Neandertal were described at the meeting by Alex Menez, a biologist and science historian at the Gibraltar Museum. Menez mined the 14,500 letters written by and to Darwin available online as part of the Darwin Correspondence Project maintained by Cambridge University and the American Council of Learned Societies. He found that although Darwin never visited Gibraltar, he had a keen interest in discoveries there on Mediterranean plant life and geology, as well as a fascination with the skull.

The Gibraltar skull was first presented in Great Britain in September 1864, to a meeting of the British Association for the Advancement of Science. Darwin had hoped to go, but illness kept him away. So shortly before the meeting his friends Charles Lyell, the famous geologist, and Hugh Falconer, a famed anthropologist, brought the skull to the home of his sister-in-law in London, where Darwin was staying at the time. Darwin’s reaction is recorded simply in a 1 September 1864 letter to his close friend, botanist Joseph Hooker: “F[alconer] brought me the wonderful Gibraltar skull.” As Menez put it: “We can imagine Darwin holding the skull, peering enthusiastically at its well-marked brow ridges, his own eyes beneath brow ridges that were themselves significantly larger than those of most people!”

Exactly what Darwin made of the skull is not known, however. He didn’t mention the Gibraltar or Neander skulls at all in On the Origin of Species and refers to them only fleetingly in the 1871 Descent of Man. Perhaps, as some speakers at the meeting suggested, he deliberately avoided speculating about them out of reluctance to stir up controversy about human evolution.

PHOTO CREDIT: Clive Finlayson, The Gibraltar Museum

by John Travis

Creation, the star-studded biopic of Charles Darwin, opens later this week in the United Kingdom, and scientists and science educators have been bemoaning the fact that the film doesn’t yet have a U.S. distributor. Although the production company behind the movie has hinted that a U.S. deal is imminent, some have suggested that the movie, in which fellow naturalist Thomas Huxley joyfully tells Darwin he has “killed God,” is too controversial to sell in America, where disbelief of the theory of evolution remains strong among religious conservatives. Eugenie Scott, executive director of the National Center for Science Education, even sent out a letter encouraging a lobbying effort on the film’s behalf. Noting that she had seen and liked the movie, she wrote: “But I worry (and can only speculate) that the difficulty the producers have had getting a US distributor might reflect corporate nervousness about getting an audience for a topic that deals with evolution. 'Creation' is definitely honest about Darwin's religious skepticism. The big middle part of America that we are aiming at will see a complex character with a lot of reasons to doubt the Christian pieties spouted by the minister character in the movie.”

From a cinematic standpoint, however, it’s not clear that Creation deserves the fervent support of the scientific community. In a nutshell, the movie, based on the book Annie’s Box, depicts a midlife Darwin at home in an idyllic English village dealing with the grief of his daughter Annie’s recent death and trying to write On the Origin of Species, the book that would make him a household name. The film has many historical inaccuracies, but that’s to be expected when filmmakers condense a life into a few hours. Creation’s larger problem stems from the decision to focus on a narrow slice of Darwin’s life, arguably one of the least interesting.

According to the movie’s press material, the film portrays the “powerful story of Charles Darwin and the single most explosive idea in history. … In Creation, the battleground is a man’s heart. Torn between his love for his deeply religious wife and his own growing belief in a world where God has no place, Darwin finds himself caught in a struggle between faith and reason, love and truth.” What this ultimately means is that the movie centers on why Darwin was so slow to publish On the Origin of Species, attributing the delay to his illness, his grief, and his desire not to offend the world, or at least his wife. In other words, instead of dramatizing how Darwin traveled the world and arrived at the most explosive idea in history, Creation is ultimately about the world’s biggest case of writer’s block.

That’s a flawed choice, especially when one has stars as talented as Paul Bettany and Jennifer Connelly playing the Darwins. Married in real-life, the pair bring a natural, loving chemistry to the well-acted roles (Connelly may need to seek out more ambitious and different roles, however; here she plays the beautiful, supportive wife of a tormented genius who sees things, an almost identical role to the one she had in A Beautiful Mind, the story of Nobel prize-winning mathematician John Nash).  And there’s little question that Creation is beautifully and at times inventively filmed. One scene nicely exploits computer-generated graphics to show how the tragedy of death in nature is necessary for life to continue.

The film periodically tries to suggest the scientific methodology Darwin used, although highlighting his grisly preparation of pigeon skeletons may more likely turn some viewers' stomachs than explain his study of natural variations within species. As Scott notes, the film does reveal a more “complex” picture of Charles Darwin, one that may shock those used to the genius stereotype. The film depicts the celebrated naturalist as a young man so ravaged by depression and illness—whether real or imagined remains a matter of debate; a recent book labels Darwin a hypochondriac—that he avails himself of a quack Victorian water remedy. He’s also seen taking unknown medicinal drugs and hallucinating the ghost of Annie, with whom he discusses his doubts and to whom he relates some of his life’s adventures and scientific undertakings. For example, one interlude shows Darwin studying a captured orangutan, an episode that presumably helped lead to his book The Expression of the Emotions in Man and Animals. But given that he’s telling stories to an apparition, it’s hard for viewers to evaluate how these tales allowed Darwin to form his pioneering ideas. And given that the ghost itself is a creation of the filmmakers’ minds, some viewers may wonder if they can trust the veracity of anything in the movie. As for the topic of science and religion, the movie’s approach would please Richard Dawkins in that it doesn’t offer a middle ground in which one can believe in both evolution and God. Such a compromise would ruin the drama of Darwin’s struggle it seems.

What’s missing in Creation is enough insight into what enabled Darwin to bring together disparate information into a powerful story of how nature works. His daughter is bright and insatiably curious, and presumably a proxy for Darwin the researcher, but the father offers little evidence of being a fountain of brilliant insights. After all, in the movie, his theory is already a fait accompli; he just needs to write it up for publication. While much of the movie is about Darwin trying to get past his grief and illness, in the end it’s only the threat of competition—a letter from Alfred Russell Wallace—that forces him to overcome his writer’s block. And then the filmmakers would have you think that Darwin allowed his wife to decide whether the work should be published. One wishes the script had gone through a few more generations of evolution.

Creation trailer:

by Virginia Morell

Birds are noteworthy not only for their wit, charm, and sartorial splendor but also for their great dancing. So, for its contribution to this year’s Darwin celebrations, London’s Rambert Dance Company is putting on a bird-inspired show.

The company has the ideal scientific adviser: Nicola Clayton, an expert on the cognitive talents of jays and crows at the University of Cambridge and a lifelong dancer. Clayton helped the company’s artistic director, Mark Baldwin, come up with a program that she calls a “distillation of Darwinian ideas about evolution, particularly sexual selection.” One dance, for instance, is inspired by the elaborate displays of the six-plumed bird of paradise. In the wild, males inflate “a tutu” of feathers, then vigorously shake their heads and necks while sliding across a stage—all while being critically observed by a gallery of females. “The males are so constrained in their movements by female choice that it’s comical,” says Clayton. Other dances in the program evoke blue manakins and bee hummingbirds.

The show, titled The Comedy of Change, runs 16–19 September at the Theatre Royal in
Plymouth and 3–7 November at Sadler’s Wells in London.

University of Cambridge has produced a video about Clayton's research and the dance.

On Monday, London’s Natural History Museum (NHM) will formally open its new Darwin Centre with a launch ceremony that will be attended by official and unofficial English royalty—HRH Prince William of Wales and Sir David Attenborough, the celebrated naturalist and TV host whose name is bestowed on a multimedia studio in the center. The glassed addition to the museum has drawn attention mostly for the massive “Cocoon,” an 8-story-tall oblong interior structure that will house the museum’s famous plant and insect collections—more than 20 million specimens. NHM's original Victorian building is now a landmark piece of architecture, notes Michael Dixon, director of the museum, and with the Darwin Centre, “we wanted to make an equally impressive statement about the future of the museum.” From a scientist’s perspective, the Cocoon is more than eye-catching; it’s central to the museum’s efforts to provide a more modern collection facility with improved environmental controls. The new Darwin Centre also significantly upgrades the lab facilities for NHM’s scientists and the thousands of visiting researchers who come to study the collections. And as with many new science museums, the Darwin Centre provides the public with more opportunities to watch scientists in action. “Our scientists have traditionally worked behind closed doors; … now, for the first time, we’re metaphorically throwing those doors open,” says Dixon.

In late January, New York-based internet consultant Phil Terry made a pitch on Facebook for members to post a Happy Birthday Darwin message. By 12 February, more than 200,000 members had signed on, far exceeding his expectations, he said. Since then, he's been shooting to make an even bigger splash. The goal is to have 1 million Facebook members by 24 November celebrating the 150th anniversary of the publication of Darwin's seminal book, On the Origin of Species.

Within a week of setting up the Facebook campaign, Terry started a Web site, Darwin150, complete with Tweets. Self-described as a "grassroots and scrappy" initiative "with a sense of humor,"  the project is run by volunteers with no funding other than in-kind contributions from organizations such as National Geographic. Yet it has set up a lecture series that will be webcast live. The series begins 16 September and runs through 24 November, with speakers that include Harvard University's E.O. Wilson and other biology luminaries.

"This series is unique in both the medium and the audience," says evolutionary biologist and author Sean Carroll of the University of Wisconsin, Madison, who has been active in Darwin celebrations across the globe and is involved in making a TV documentary on evolution. "It will be interesting to see its reach and the make-up of the audience."

Right now, the Facebook campaign is 750,000 members short. But, says So Young Park, head of the volunteer marketing team, "We are confident that we'll make our goal" and are expecting exponential growth in the days leading up to the anniversary. Go here to join.

—Elizabeth Pennisi

Image: The Darwin 150 Project