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December 28, 2009

The End of Origins

image This year, the worldwide community of science has marked the bicentennial of Charles Darwin’s birth—and the 150th anniversary of the publication of On the Origin of Species—with dozens of evolutionary-themed meetings, books, review papers, and Science’s own monthly Origins series. In this blog, we’ve both joined in and reported on these celebrations, covering the meetings, expanding on the essays, and highlighting the most current research on evolution in all its many forms. Now the blog, like the year itself, draws to a close; this will be our final entry. We hope you have found it both diverting and useful.

Of course, Science’s interest in origins and all things evolutionary continues. For although 2009’s evolutionary parties are ending, the science behind them continues to serve as the firm foundation of modern biology as well as a rich source of new research. You can see all our Year of Darwin coverage in one place here, and you can continue to find the latest on evolution in online news at ScienceNOW and in the news and research in the magazine itself. Thanks for reading!

The Origins Blog Editors: Elizabeth Culotta, Elizabeth Pennisi, John Travis

If you're tired of watching It's a Wonderful Life or A Christmas Carol yet again, perhaps Darwin can occupy your cold winter nights. As a holiday treat, Origins would like to point out that this summer's Darwin Festival in Cambridge, U.K., has compiled videos of many of its sessions, which typically start with a reading from Darwin's correspondence. You can watch the videos directly here on the embedded media player, even skipping among the talks, or go to where they are posted here on YouTube. Enjoy.


by Lucas Laursen

Charles Darwin may have had his biggest impact on biology, but he began his scientific career as a geologist. So it’s appropriate that earlier this year, retired geologist John Ramsay, who had long studied the famed biologist’s life, accepted a commission to compose a Darwin-themed string quartet.

Darwin “did some pretty fundamental geological mapping," says Ramsay, drawing a parallel to his own geological career, during which he has drawn maps of the Scottish Highlands, South Africa, and the Swiss Alps. Ramsay says he and Darwin also share a penchant for putting "ideas that spring from other parts of one's life" into their current work. He notes that Darwin applied lessons from Earth's landscape to biology, adapting, for example, Charles Lyell's theory of gradual geological change to living things. Similarly, Ramsay's musical tribute draws on his own geology background. "Knowing Darwin's work, I wrote my quartet first of all on the evolution of the Earth," Ramsay says.

At the beginning of the piece, a disorganized Earth takes shape, with the core, mantle, and crust emerging into distinct musical themes. Life then arrives. Next, Ramsay writes in his concert notes, "the 'wriggly' primitive forms evolve into ... stronger and more continuous themes representing reptile and mammal forms."

Performed by the Fitzwilliam String Quartet, Ramsay’s composition premiered in Cambridge, U.K., during the Darwin Festival (Ramsay pictured above and Quartet playing pictured below) on 7 July 2009. The Darwin Quartet gave its second performance late last month during the triennial Cambridge Music Festival. The two festivals jointly commissioned the piece, and Ramsay hopes the Fitzwilliam Quartet will record the composition next year.

How did a structural geologist who spent his career climbing the academic career ladder at British and Swiss universities end up composing evolution-themed music? National service: After completing his Ph.D. in geology at Imperial College London, recalls Ramsay, "I became a cellist in an Army orchestra" in 1955. For 2 years, he toured Britain and British bases in Germany.

When his tour was over, Ramsay had to decide between pursuing music or geology. "I was hard-put," he says, "but I only started playing cello at 18, ... and that's a bit late for someone becoming a top professional." Instead, he continued with geology research and teaching at Imperial College, moved to the University of Leeds, and eventually settled in Zurich, Switzerland, with joint geology appointments at the Swiss Federal Institute of Technology (ETH) and the University of Zurich. But his other passion has come to the forefront again now that Ramsay has retired. Today, he teaches and composes music in the French hamlet of Cratoule, in a wine-growing region near the Rhône River whose landscape he describes as "wild without being fiercely wild."

His music hobby did not directly influence his geological career, Ramsay says, but a night class on life-drawing he took while in the Army probably did shape his interest in geological maps: "They are scientific records of the rocks on the Earth's surface, but they can be exceedingly beautiful things."

Ramsay says he tried to incorporate Darwin's ideas about the fleeting nature of any individual species into the epilogue of his composition; the music is meant to evoke a barren landscape, devoid of today's multitude of species. "Darwin showed that practically all the organisms that have lived on the Earth had a limited species-life, and practically all of them have died out and been replaced by new ones," Ramsay notes.

And what would Darwin have thought of the composition? "I don't know what he would make of my string quartet, [but] he was very worried toward the end of his life about where things were going," Ramsay says. "My idea is that perhaps the world will finish up like Mars, without life but still with a great deal of beauty."

Images courtesy Miranda Gomperts/Darwin Festival

darwin quartet.jpg

December 3, 2009

On the Origin of Tomorrow

by Elizabeth Pennisi

image More than ever before, the future is in our hands. We are shaping not just our own destiny but also the destinies of much of life on this planet. That is the take-home message of the final essay, On the Origin of Tomorrow, in Science's Origins series.

As Carl Zimmer points out in this essay, Charles Darwin gave a nod to the future, finishing On the Origin of Species with a paragraph that talked about continuity: "... endless forms most beautiful and most wonderful have been, and are being, evolved.” He recognized that as long as the ingredients for the evolutionary process still exist, life has the potential to change. He didn’t believe it was possible to forecast evolution’s course, but he did expect humans would have a big effect—they had demonstrated this power already by domesticating plants and animals and driving some species to extinction. Darwin also expected that our own species would change.

As the world celebrates the 150th anniversary of the publication of On the Origin of Species this year, scientists continue to think deeply about what lies ahead. Some feel a new sense of urgency about understanding what might happen. Since Darwin’s day, humans have gained an unprecedented influence over our own evolution. At the same time, our actions, be it causing climate change, modifying the genomes of other organisms, or introducing invasive species, are creating new sources of natural selection on the flora and fauna around us. “The decisions we and our children make are going to have much more influence over the shape of evolution in the foreseeable future than physical events,” says Andrew Knoll, a paleontologist at Harvard University.

In this essay, Zimmer examines Darwin's perspective on the future and discusses how humans have helped to alter the course of their own evolution. He describes the ways humans have shaped the world around them—through global change, for example—and thereby affected the futures of countless other organisms and ecosystems. Finally, he ends with the question of whether humans will ultimately be smart enough to prolong the life of the planet.

Image: Katharine Sutliff

The National Science Foundation has released an online special report  on the influence of Charles Darwin on many walks of science. Evolution of Evolution: 150 Years of Darwin's On the Origin of Species features essays, videos, and podcasts from prominent researchers, as well as a timeline of advances in evolution, all beautifully crafted to enchant anyone curious about the history of life. Special topics cover anthropology, biology, astronomy, polar sciences, and geosciences, as well as Darwin.

Image credit: Illustrations by Nicolle Rager Fuller, National Science Foundation (background and center); © 2009 JupiterImages Corp. (top right); NASA, ESA, M. Robberto (Space Telescope Science Institute/ESA) and the Hubble Space Telescope Orion Treasury Project Team (bottom )

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 thendarwin 16-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.

213027001_16ec6219d5Stickleback 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.

blog_gall.ants 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 acrossblog_gall.tree 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

October 7, 2009

Yes, Ardi Evolved From Apes

by Ann Gibbons

ardicover “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.

The Hollywood Reporter last week noted that Creation had finally been picked for the U.S. market. Now Americans can decide thumbs-up or thumbs-down.

September 24, 2009

Math Tribute to Darwin

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.”