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February 2009 Archives

The publication of Charles Darwin’s On the Origin of Species in 1859, the 150th anniversary of which we celebrate this year, was a landmark event in the history of biology and widely noted at the time. But when, 7 years later, Gregor Mendel published his findings on the laws of inheritance, they were widely ignored. Not until the 20th century did scientists realize that the two theories were entirely compatible and put them together in what we now call the modern evolutionary synthesis.

In a fascinating paper published online this week in the Journal of Biology, geneticist Jonathan Howard of the University of Cologne ponders why Darwin, who took it as a given that natural selection acted on traits that were passed from generation to generation, didn’t scoop Mendel when he had the chance. The answer, Howard suggests, is that Darwin was focused on very small, often infinitesimal variations in plants and animals, which he saw as the raw material on which natural selection could work. Yet, as Mendel brilliantly demonstrated, inheritance is actually based on the passing on of discrete units—what today we call genes—from one generation to another.

Howard points out that Darwin had many chances to understand inheritance, but his mind was focused elsewhere. For example, Howard writes, in The Different Forms of Flowers on Plants of the Same Species, published in 1877, “Darwin wrote an entire book on a perfect Mendelian character” with “numerically precise and well-established behavior, yet he failed to extract Mendelian insights from his work.”

The article is available free online at the Journal of Biology (registration required.)

—Michael Balter

February 26, 2009

Is a Hand Ax Really a Hand Ax?


Long before humans painted caves or made colorful necklaces out of snail shells, they manufactured beautifully symmetrical, teardrop-shaped stone tools that archaeologists call hand axes, such as the ones shown at left from Atapuerca, Spain. At least, hand axes seem beautiful to us today, even if their exact function and meaning are a matter of debate. Most archaeologists think that hand axes, which begin showing up at archaeological sites about 1.7 million years ago, were used to cut plants and butcher animals. And many assume that making such a symmetrical object required a mental template and the ability to impose a predetermined form on a piece of stone. As I discuss in this month’s Origins essay in Science, these talents could be considered proxies for symbolic capacities. And some researchers—as I discuss in a Random Sample in this week’s issue of Science—have suggested that hand axes were also the result of Darwinian “sexual selection.” According to this controversial idea, a well-made hand ax was a sign that its maker, presumed to be a guy, had good genes and would be a suitable mate for any gal lucky enough to have him.

So hand axes have been considered to be handy tools, courting devices, and signs of symbolic smarts. But what if they were none of these things? Since the early 1990s, one archaeologist has argued that there is no evidence early humans actually intended to make hand axes. Iain Davidson, now a professor emeritus at the University of New England (UNE) in Armidale, Australia, contends that the hand ax might have been what was left over when toolmakers were done striking sharp flakes from a stone core.

Davidson first argued for what he calls the finished-artifact fallacy in 1993, together with UNE psychologist William Noble, and he has elaborated on the idea in more recent publications. I caught up with him late last year at Harvard University, where he is currently a visiting professor. Over a long and pleasant lunch in Harvard Square, he made it clear that he has not changed his mind on the issue.

For one thing, Davidson says, archaeologists tend to focus their studies on the most symmetrical hand axes, thus introducing a bias into their analyses. They see more patterning than really exists on average and then interpret that patterning as evidence that early humans intended to create tools that look that way. And because hand axes were probably made by striking flakes from a core with a second stone—indeed, the marks where the flakes were taken off are clearly visible on the hand ax—archaeologists are making unproven assumptions when they conclude that the hand ax rather than the flakes were the most important product, Davidson contends. At the 500,000-year-old site of Boxgrove in England, for example, where hundreds of hand axes have been found, there are also signs that the flakes taken from them were used as tools by early humans.

“I can imagine a situation at Boxgrove where [early humans] were walking around with a core, striking off flakes when they needed them, and then abandoning the core when it was no longer useful,” Davidson told me. As for why the core would have that characteristic teardrop shape, Davidson explained that it would be easier to hold in the hand if you only took flakes off of one end.

Davidson’s view is definitely a minority one. “The form of [hand axes] clearly reflects the intention of the toolmakers,” says archaeologist Dietrich Stout of University College London. But few archaeologists argue that the flakes could not also have been used as tools, and Davidson’s idea does appeal to some. Anthropologist April Nowell of the University of Victoria in Canada, who challenges the sexual-selection hypothesis, told me that she is “sympathetic” to Davidson’s notion. “People get hung up on the symmetrical form that some [hand axes] have,” Nowell said. “We have exaggerated what a typical hand ax looks like, and we don’t think about the less refined ones. There is a variation from tools that just look like cores to those that look like hand axes.”

—Michael Balter

About Iain Davidson

Excavations at Boxgrove

PHOTO CREDIT: José-Manuel Benito Álvarez

Nescent Darwin Meeting Image A chilling tale of science, romance, politics, and death in the Soviet Union set the stage for the National Evolutionary Synthesis Center’s (NESCent's) third annual Darwin Day Symposium, held on 21 February at the Sigma Xi Center in Durham, North Carolina. The birthday boy himself was rarely mentioned; rather, the event emphasized modern applied evolution. Theodosius Dobzhansky famously wrote in 1973, "Nothing in biology makes sense except in light of evolution." But, as speaker Fred Gould pointed out, evolution has become far more than a way to make sense of things. “Today, your quality of life depends on application of a rigorous understanding of evolution,” he argued. And thus began a series of talks that addressed evolutionary approaches to practical challenges in agriculture, disease, and conservation.

But first, Gould provided the opening historical overview—a convoluted story centered on Soviet geneticist Nikolai Vavilov (1887-1943) and his nemesis, state-supported pseudoscientist Trofim Lysenko (1898-1976). Vavilov is best known for his studies of global crop evolution and diversity, as well as his efforts to breed better cereal crops based on Mendelian genetics. Lysenko, on the other hand, is remembered as a proponent of crackpot notions about the inheritance of acquired traits. Despite his more valid scientific approach, Vavilov fell out of favor with socialist leaders and died of starvation in prison, after criticizing Lysenko’s unfounded claims. Gould’s account (like this recent article in The New York Times) was a clear reminder that the practice of science has been, and still is, shaped by its political and ideological milieu.

“You trashed our heroes,” lamented one audience member after hearing how the evolutionary giants Ronald Fisher, Francis Galton, and J.B.S. Haldane supported eugenics or Lysenkoism. But Gould and the other speakers were ready to add their own stories of how politics and ideology affect the way they fund or present their work. Gould, for instance, believes that genetically engineered insects can be used to manage medically and economically important insect pests. But he worries that this approach will meet with resistance because of current attitudes toward genetically modified crops and the big businesses that market them.

Barbara Schaal encountered a different kind of roadblock in her work on the evolutionary genetics of cassava. Although it is a dietary staple in much of the developing world, cassava lacks many important nutrients. Millions would benefit from an improved cassava—but because it is not a cash crop and is not grown in the United States, Schaal found it difficult to fund her initial research. Eventually, her team produced molecular phylogenies of cassava and its wild relatives to pinpoint the crop’s likely origin in the Brazilian Amazon. There, they discovered that villagers were growing varieties with vitamins, pigments, and sugars unknown in the common domestic cassava. Some of those varieties are now involved in a project, funded by the Gates Foundation, to produce a nutritionally complete cassava for widespread cultivation.

Daniel Faith came all the way from Sydney, Australia, to discuss how evolutionary biology can help prioritize conservation areas. His research is part of a growing body of work that highlights the importance of plant phylogenetic diversity, rather than total species diversity, in preserving the characteristics of an ecosystem. Regions with the greatest phylogenetic diversity include more distantly related species and represent evolutionary history more completely—even if they include fewer total species. Faith argues that phylogenetic diversity should, therefore, inform conservation decisions, but he also talked about the challenge of communicating and applying the results without embracing a “naïve efficiency” that sanctions extinction as long as phylogenetic diversity is preserved.

Katia Koelle left the macroscopic world of plants and entered the invisible realm of viruses. She described how an improved understanding of rapid viral evolution can inform efforts in disease control. And in an excursion from the applied theme of the day, Steven Benner talked about how he and his colleagues use evolutionary trees to infer the sequences of ancestral proteins. By recreating those ancestral proteins and studying their function, Benner tries to make evolutionary “just so” stories more concrete.

Although free and open to the public, the symposium drew a largely academic crowd of biology students, faculty members, and postdocs. About 80 people sacrificed at least part of a sunny Saturday to sit in a dim auditorium and take in the talks.

NESCent plans to post video of the symposium online—watch the symposium site for updates.

—Elsa Youngsteadt

February 20, 2009

Deconstructing the Ribosome

Our lives depend on a microscopic tangle of molecules called the ribosome. The job of the ribosome is to use the sequence of DNA in a gene to build a corresponding protein. Other enzymes first build a single-stranded copy of the gene from RNA, and then a ribosome grabs onto the RNA and "reads" it, using the information to decide which building block to grab next in order to build a protein. (Here's a video of the process.)

The ribosome has two parts that come together around the RNA like a pair of jaws, and each one is a fiendish nest of complexity. Each of the jaws, known as subunits, is a mix of protein and RNA. This animation, created by David S. Goodsell, shows the structure of the large subunit in bacteria. It contains two RNA molecules in it, a big one here colored orange, and a small one colored yellow. The proteins wrapped around them are in blue. The big RNA molecule alone is a marvelous migraine of complexity. It measures 2900 nucleotides long, and it twists and folds in on itself again and again to form the supreme Gordian knot.

All living things make ribosomes and use them for the same essential purpose. It is a sign of our common heritage with baobabs and starfish, with plague and mold. But the fact that the ribosome is everywhere makes its evolution difficult to study. There is no partial ribosome in nature to offer clues to how it emerged. But in this article in the 19 February issue of Nature, Konstantin Bokov and Sergey Steinberg, two biochemists from the University of Montreal, offer some new hope: It's possible that the evolution of the ribosome is recorded in its very own tangles.

Bokov and Steinberg show that the ribosome is like an onion, with outer layers that can be peeled away from inner ones. The proteins of the ribosome help keep it stable, but they themselves do not actually weld together new proteins. That's the work of the ribosomal RNA. As I wrote in my January Origins essay, many researchers now argue that DNA and proteins were not the first biological molecules to emerge; before they existed, life was based on RNA alone. The origin of the ribosome, Bokov and Steinberg argue, is really the origin of the ribosomal RNA.

Ribosomal RNA is made up of dozens of loops, and loops upon loops, all folded in on each other. But Bokov and Steinberg point out that they have an onionlike order of their own. They inspected all the loops, looking for ones that could be removed without altering the rest of the RNA molecule. They found 19 of these expendable loops. Next, they looked at the loops that had kept those 19 loops stable but which could be eliminated without affecting the rest of the RNA. They found 11 such loops. Below these two layers, Bokov and Steinberg found yet another layer of loops, and another, and another, until they had reduced the ribosomal RNA to a tiny fragment, a core on which all the rest depended.

Bokov and Steinberg propose that the seeming complexity of the ribosome is something of a mirage. Its evolution was actually pretty simple. It evolved from a tiny piece of RNA, perhaps only 110 nucleotides long. At first, this molecule didn't build proteins; it may have carried out some kind of reaction on other RNA molecules in RNA-based cells. Then mutations accidentally duplicated the fragment, building new units that could fold back on the older units. This protoribosome may have been able to add random building blocks together. New layers of loops evolved, making the ribosome more precise, able to build specific proteins when it read specific pieces of RNA. Newer loops made the ribosome even more stable and thus able to crank out proteins even faster. The last major step in the evolution of the ribosome was the addition of its proteins.

The most practical way to test Bokov and Steinberg's hypothesis will be to build the intermediate ribosomes and see if they work as predicted. But perhaps we should not give up on nature just yet. As I have reported, RNA-based life could conceivably still be hiding in refuges somewhere here on Earth, eking out an existence with ribosomes that are a little less hideous than our own.

Carl Zimmer

Lion_man_photo.jpgWhen the Chauvet Cave in southern France was discovered in 1994, it rocked the archaeological world, in part because its paintings of lions, horses, and rhinos were spectacularly sophisticated—and also because radiocarbon dating suggested that these artworks had been executed as early as 32,000 years ago, making them the oldest known cave paintings. (Because there is no agreed radiocarbon calibration curve for dates earlier than 26,000 years ago, all dates are given in uncalibrated "radiocarbon" years; actual calendar dates are probably several thousand years earlier. See Science, 15 September 2006, p. 1560.)

Yet while Chauvet's paintings are unparalleled for their age in skill and technique, they did not stand entirely alone in the prehistoric art world. Indeed, many prehistorians were not completely surprised at their discovery, because there were already numerous indications that modern humans in Europe were making art that early; since Chauvet's discovery, a number of subsequent finds have confirmed that conclusion.

Chauvet may shelter the earliest cave paintings (but see below), yet previous excavations in Europe had found sculptures at least as old. Beginning in the 1930s and continuing until quite recently, archaeologists working in the Swabian Jura region of Germany have uncovered more than 20 figurines skillfully carved from mammoth ivory, including a superb half-lion, half-man sculpture from Hohlenstein-Stadel (see photo at left). Once radiocarbon dating became available after the 1950s, researchers found that these figurines were between 30,000 and 36,000 years old. The most recent objects, including a carved bird and a horse, were found in Hohle Fels Cave and reported by Nicholas Conard of the University of Tübingen in 2003. They too are at least 30,000 years old.

February 17, 2009

Findings From the AAAS Meeting

Don't miss the chance to check on what happened at the annual meeting of AAAS this past weekend at Findings. In just a few busy days, researchers squeezed in discussions on everything from the evolution of kissing to the genetics of dog shape. There were talks on Neandertals and hobbits, even a science dance contest. Also, hear about the origins of emotions or the origins of the human diet in podcasts.

In a letter to the governor of Louisiana, the Society for Integrative and Comparative Biology announced it would not hold its 2011 annual meeting in New Orleans because of the state's antievolution policies. For more on the issue, check out The Chronicle of Higher Education story.

—Elizabeth Pennisi

Baba Brinkman, whose "Rap Guide to Evolution" was recently reviewed by Origins, found time between performances to answer a few questions about his original take on Charles Darwin and his controversial ideas.

What was the toughest evolutionary topic to rap about?

Evolutionary topics are not so much of a challenge as anti-evolutionary topics.  Everything in biology is like an intricate puzzle to which Darwin's theory is the master key.  But for political or religious reasons people have directed a lot of energy into tearing Darwin down over the past 150 years instead of just thinking constructively about what his theory teaches us about ourselves and the natural world.  So my biggest challenge was to engage with Darwin's detractors in a way that was not overly derisive, while at the same time speaking plainly about the misconceptions that are still attached to his work.

February 14, 2009

The Battle of the Sexes

If you entitle your talk Sex and War, it’s bound to draw a good crowd, as was the case last Wednesday when more than 100 people showed up for a talk on the evolution of war at the Woodrow Wilson International Center for Scholars in Washington, DC.  The speaker was human reproductive biologist Malcolm Potts of the University of California, Berkeley, who has just co-authored a new book called…Sex and War. The premise of his talk and book is that men have a genetic predisposition to band together in groups to wage battle-- something known as team aggression. That may seem obvious to any football fan or soldier. But what’s less obvious is that while men have evolved to be more aggressive in this way, women have not: Potts could not find a single case where women banded together in a gang or group to attack other humans. Women murder, commit violent crimes, join armies and even  become terrorists. But they don’t initiate or form groups for the purpose of murdering another member of their own species, as do males in street gangs or terrorist groups, says Potts.

February 12, 2009

Neandertal Artists?

Originsblog_neandertal.jpgDid Neandertals use symbols and create art? This is the subject of one of the biggest, longest, and most contentious debates in the history of archaeology. Today, most researchers would agree that there is not a simple "yes" or "no" answer. But they might not agree on much else—just one more reason why Neandertals, whose genome sequence was announced today, are so intriguing.

Clearly identifiable Neandertal bones (like the front skeleton at left) appear no later than 130,000 years ago, often together with relatively sophisticated stone tools. But for about 90,000 years after that, there is little evidence that Neandertals produced anything that might be called art. There is certainly no indication that they ever painted caves, such as the spectacularly decorated Chauvet and Lascaux caves in France or Altamira in Spain, although one never knows what discoveries the future might hold—and one maverick archaeologist, Robert Bednarik (whom we featured last week) argues that Chauvet might have been painted by Neandertals, a decidedly minority view.

On the other hand, some researchers have complained bitterly that many colleagues are too quick to use the apparent absence of evidence for Neandertal symbolism to deny them their full humanity. John Speth, an anthropologist at the University of Michigan, Ann Arbor, expressed this view in the ironic title he gave to a 2004 paper in the journal World Archaeology: "News flash: negative evidence convicts Neandertals of gross mental incompetence."