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March 2009 Archives

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Did early humans take care of the sick, the wounded, and the aged? Modern humans, of course, count on our families, friends, and society to look after us, for better or worse. Many researchers consider such strong social bonds a hallmark of humanity. But evidence of earlier species of humans taking the less fortunate under their wings has been sparse, although in recent years researchers have made a number of claims for such helping behavior. The latest one comes from the site of Atapuerca, near Burgos, Spain, where researchers have been digging up fossils of early humans since the early 1990s. A team led by anthropologists Ana Gracia and Juan Luis Arsuaga of the Complutense University of Madrid reports finding the deformed skull of a child (shown above) estimated to have been between 8 and 12 years old when he or she died about 530,000 years ago. The sex of the child could not be determined, but it suffered from a rare syndrome called craniosynostosis, in which the sutures of the skull close early, the team concludes online this week in a paper in the Proceedings of the National Academy of Sciences (PNAS). In modern humans, craniosynostosis can cause brain damage and developmental defects such as mental retardation, and children suffering from it need special treatment and care.

The skull was recovered in many pieces during the 2000 and 2001 excavation seasons at Atapuerca and came from a part of the site called the Sima de los Huesos (Pit of the Bones), where the remains of nearly 30 Homo heidelbergensis individuals have been found; the species is thought by many researchers to be the direct ancestor of Neandertals.

Although the team admits that it cannot know how debilitated the child was, the skull deformation was serious enough that it could have caused both mental retardation and a markedly deformed face and head. Nevertheless, the child managed to live a number of years, which the team concludes was very unlikely if adults had not been taking care of it. To support their claim, Gracia, Arsuaga, and their co-workers point to a number of other recent papers that may also indicate caring behavior by early humans.

If recent debates are any guide, however, this contention is bound to be controversial, as have been nearly all the previous claims the team cites. In 2001, for example, anthropologist Erik Trinkaus of Washington University in St. Louis, Missouri, and his colleagues reported in PNAS finding a toothless Neandertal jawbone at the site of Bau de l’Aubesier in southeastern France. They concluded that its possessor, who lived nearly 200,000 years ago, had needed help from its fellow Neandertals in finding suitable things to eat. That claim led to 2 years of jawboning between Trinkaus and anthropologist David DeGusta, now at Stanford University in Palo Alto, California, in the scientific literature and the news media, as noted in a brief item in Science. DeGusta cited numerous cases in the literature in which toothless, nonhuman primates had survived to relatively ripe ages by finding ways to feed themselves.

A much older sighting of toothlessness—a 1.7-million-year-old skull found at Dmanisi in Georgia and missing all but one tooth—also sparked the suggestion that the hominin might have needed special care from family and friends. But it too was met with skepticism. Still, the Atapuerca team might have one of the strongest cases so far for caring behavior, as a handicapped child would definitely require special attention.

—Michael Balter

PHOTO CREDIT: PNAS

As described in this month's Origins essay, power-hungry bacteria devised a way to capture solar energy more than 3 billion years ago, and the world hasn’t been the same since. To find out more about the nitty-gritty of how photosynthesis works, you might scour the Internet—and be disappointed to learn that the major texts on the subject aren’t available free online.

But there are plenty of other places to feed your curiosity. To learn the basics, start with this article from Arizona State University, Tempe, or this backgrounder from Estrella Mountain Community College in Avondale, Arizona. A more technical tutorial from the University of Illinois, Urbana-Champaign, delves into the mechanics of photon absorption by the photosystems, where chlorophyll and other pigments that capture light reside.

The Web abounds with animations of the photosynthetic reactions—some enlightening and some reminiscent of filmstrips you might remember from junior high science class. Two sites stand out. Part of a set on cell biology, these animations from San Francisco-based biologist and artist John Kyrk render the molecular events of the so-called light reactions, which stash solar energy as chemical energy, and the dark reactions that manufacture carbohydrates. In this narrated animation from North Dakota State University in Fargo, you can follow along as proteins ferry electrons and pump hydrogen ions. A second animation from the same group explores photosystem II, one of the light-harvesting protein complexes in plants, algae, and cyanobacteria that probably evolved from simpler structures in bacteria.

For more sites, check this roundup from ASU and the University of Illinois. There you’ll find links to pages on everything from the discovery of the vital enzyme RuBisCO (shown below) rubisco.jpgto herbicides, many of which disrupt photosynthesis.

—Mitch Leslie

Image credit: PDB

March 23, 2009

Darwin's College Bills

We know Charles Darwin revolutionized biology with the theory of evolution by natural selection. We know that he was fond of beetles, pigeons, barnacles, and carnivorous plants; that he enjoyed a relatively happy family life at Down House in Kent. But how much did young Charles spend in student accommodation during his 3 years as a university student in Cambridge? And did he eat his vegetables?

DarwinBillsmaller.jpgThanks to the discovery of Darwin's bills, ledgers of his expenses while at Christ's College, University of Cambridge, we can now find the answers to these not-so-pressing questions. The bills were recently discovered by chance in a storage room full of old record books neither cataloged nor listed. Nobody knew they were there, but archivist Geoffrey Thorndike Martin was keeping an eye out for bills from the late 1820s and early 1830s. While studying the old records, he recognized Darwin's name. The six books of bills detail Darwin's expenses, including lodgings, meals, clothing, and the usual services available to young gentleman of that time, from barber and tutors to laundry and shoe-polishing. The bills were published today on the Web site The Complete Work of Charles Darwin Online.

The findings bring a wealth of information that allows us to reconstruct Darwin's life in the college world, says John van Wyhe, director of the Darwin Online Web site. Cambridge students in the 19th century had their expenses recorded daily and paid the bill to the college quarterly. Unlike other students, listed by their surnames, the now-famous biologist is referenced as C. Darwin or Darwin junior, to distinguish him from his elder brother Erasmus, also a student at Christ's.

The records include interesting snippets of information: Charles Darwin arrived at Christ's College on 26 January 1828 and rented one of the most expensive rooms available to undergraduates at £4 per quarter. Some of the records are very detailed: His coal bill for the 1830-1831 winter quarter was £3, 12 shillings, and 6 pence, and he paid about £1 every 3 months to have his bed made and room tidied.

Examining Darwin's accounts doesn't reveal any unordinary expenses, says van Wyhe, who scanned the books and supervised their transcription. "He does spend a lot on food" and paid the extra charge for having vegetables with every daily meal at the college, van Wyhe adds.

The bills add up to a grand total of £636 for the 3 years Darwin spent in Cambridge. In modern standards, this sum translates to about £40,000 ($57,700) according to the Victorian Web's conversion table. A seemingly staggering amount of money, but van Wyhe calls it "nothing unusual for a student from a wealthy background." Still, he admits, "Darwin was a little on the expensive side."

Not everything is listed in Christ's College's books. We still don't know how much Darwin paid for extras such as stabling his horse or entertaining. How much he spent on tobacco and alcohol remains a mystery, too—it was probably a fair amount since he was known among fellow students for his smoking and drinking habits, says van Wyhe. Time to search through the university’s other storage rooms.

—Sara Coelho

March 20, 2009

Tuning Up Photosynthesis

Organisms started capturing the sun’s energy through photosynthesis more than 3 billion years ago, as described in this month's Origins essay (Science, 6 March 2009, p. 1286). So natural selection has had plenty of opportunities to tinker with the photosynthetic machinery. Is it time we took over, overhauling the process to boost plant growth? That might be our best option for continuing to improve crop yields, says plant scientist Stephen Long of the University of Illinois, Urbana-Champaign.

Over the centuries, humans have transformed our crop plants through careful crossing, and lately, through genetic engineering. We’ve increased the percentage of energy that crops channel into edible parts.  As a result, grain now accounts for about 60% of the above-ground mass of a wheat plant, nearly twice the percentage of wheat plants in the 1940s. We’ve also made crops better at capturing light. We’ve bred corn and rice plants on which the upper leaves are more upright, allowing leaves lower on the stem to get their share of solar energy.

Changes like these are a big reason that crop yields per hectare have soared, nearly doubling between the 1950s and the 1990s alone. But these avenues for improving plants are nearly exhausted, Long says. Rice plants like these being harvested in Texas (left) rice(2).jpgcan’t support much more grain. “You need some room for stems and leaves.”

So crop scientists are looking toward a variable they haven’t systematically tried to enhance: the efficiency of the photosynthetic reactions themselves. But with 148 proteins taking part, choosing where to start is daunting. To identify some promising targets, Long and colleagues performed what he calls “an unusual marriage of molecular biology, supercomputing, and agriculture.” The researchers used a supercomputer to solve equations that track all of the chemical reactions through which plants transform carbon dioxide into carbohydrates. The computer randomly raised or lowered the levels of certain enzymes and determined the effects on photosynthetic efficiency. The most productive variant from each round moved on to the next round for further tweaking and testing.

The researchers’ surprising conclusion, which they reported in the October 2007 issue of Plant Physiology, is that photosynthetic efficiency is nowhere near its peak. After 1500 rounds of virtual refinements, they had elevated plant output by 76%. Increasing the levels of just four enzymes accounted for much of the gain. This strategy doesn’t require re-engineering the enzymes’ structure, but adjusting only their abundance. Long and colleagues now hope to take what they learned onto the farm, using genetic engineering to revise enzyme levels in tobacco and soybeans.

—Mitch Leslie

For more information, see
S. P. Long et al., “Can Improvement in Photosynthesis Increase Crop Yields?Plant, Cell & Environment 29, 315 (2006).

Photo credit: USDA

Bristletail1.JPGExactly how insects evolved flight is a heated issue, in part because the fossil evidence for winged insects remains full of gaps. But living insects that are similar to ancestral species could also shed light on the origins of insect flight. In a study reported online this week in Biology Letters, researchers report that bristletails, primitive, wingless insects that live in the tropical forests of Peru, can use long antennae-like filaments extending from their rear ends to help them glide to tree trunks as they jump or fall from forest canopies. These observations suggest that winged insects evolved on land, rather than from aquatic habitats, the authors conclude.

According to the fossil record, before about 390 million years ago, the planet was populated by six-legged wingless creatures resembling bristletails and similar living insects called silverfish—those early creatures are considered to be the ancestors to all current-day insects. There’s then about a 65-million-year gap in the insect fossil record. The next known fossils date to about 325 million years ago, and they include insects with and without wings. Given the lack of a fossil showing an intermediate stage of an insect wing, scientists have been left debating two primary theories: that wings developed either from the gills of insects living in water or from extensions on the sides of a terrestrial insect.

To address this debate, tropical insect ecologist Stephen Yanoviak and his team turned to a species of wingless bristletails called Archaeognatha Meinertellidae. Genetic phylogenies suggest they are closely related to the species at the root of the evolutionary tree of insects, and they also lack any aquatic form to help rule out wing development in water. The researchers were interested in whether these bristletails could use their filaments or antennae to help maneuver, or glide, during a fall. Yanoviak says that this ability would have been useful about 400 million years ago when the first trees appeared and wingless insects began to feed on lichens and debris in tree bark. If those insects encountered a spider or other predator while up in a tree, they would need a good escape route. But they couldn't just jump off the tree if they couldn’t guide their fall away from nearby quagmires and to a safe landing point instead.

To explore what aerial control these insects have, Yanoviak and his colleagues collected nearly 200 Peruvian arboreal bristletails and separated them into six different groups. One was left untouched for a comparison, and for each of the other five groups, researchers removed the lateral filament, the medial filament, the medial and one of the lateral filaments, half of all the rear filaments, or the insects’ antennae. When Yanoviak dropped the insects from the top of a forest canopy, he found that 90% of the untouched bristletails successfully glided to a nearby tree before reaching the ground. The insects with either their antennae or their rear lateral filaments removed had about the same overall success rate, but it took them longer to get to their target tree. And those lacking their middle bristle, a filament extending from the insect thoracic segment, often lost the ability to glide under control and wound up on the forest floor. (Here's a video from Yanoviak showing normal bristletails gliding from a tree.)

It can be pretty lonely being an evolutionary researcher if you’re not part of a group of evolutionary thinkers, or at least so says evolutionary biologist David Sloan Wilson of Binghamton University in New York state. He should know: He’s famous for the controversial theory of group selection, which describes how natural selection may act on groups as well as individuals, and he’s thought a lot about how group behavior can benefit individuals. Now he’s urging evolutionary scientists to create their own groups.

There’s been a dramatic increase in the number of researchers applying evolutionary theory to human behavior and other nonbiology topics in the past 15 years, says Wilson. He conducted an informal survey of the authors of evolutionary papers in the journal Behavioral and Brain Sciences, which has the highest impact of behavioral science journals and a rigorous peer-review process. He found that although biologists felt they had evolutionary colleagues, many researchers in other disciplines—including economics, psychology, medicine, history, religion, and the arts—who did evolutionary work felt isolated.

They also reported that they had to teach themselves evolutionary science after they got their Ph.D.s, because, as nonbiology majors, they weren’t encouraged or required to take evolutionary theory in college. “If you’re not a biology student, it’s not easy to get training in evolution in higher education,” Wilson said in a talk at the University of Missouri, Columbia, on Saturday, as part of a symposium to celebrate the bicentennial of Charles Darwin’s birth.

So a few years ago, Wilson formed a campuswide program to introduce evolution into a wide range of fields at Binghamton. His circle of about 20 evolutionary researchers expanded to more than 60 faculty members with evolutionary interests who represented almost every department on the campus. Now, the program, called EvoS for Evolutionary Studies Program, has gone national, thanks to a $500,000 grant from the National Science Foundation last year. A researcher from each school teaches an introductory evolution course called "Evolution is for Everyone"; the program provides the researcher with a curriculum, access to faculty who have taught the class, and examples of how evolution can be applied to a wide range of topics. Faculty and students in participating colleges also get a journal and seminars on topics from outside evolutionary experts. At last count, 34 colleges and universities had signed on for the program, ranging from small colleges, such as Albright College and Broome Community College, to large universities, such as the University of Arizona and the University of California, Los Angeles.

In this case, individuals definitely survive better in academia when they belong to a group, says Wilson. “I have confirmed what I initially expected: An actual community is much more fun than a virtual community,” he says. “You can drink beer, for example.”

—Ann Gibbons

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The famous fossil Lucy has finished her engagement at the Pacific Science Center in Seattle, Washington, and has nowhere to go—yet. After a disappointing run in Seattle, the 3.2-million-year-old partial skeleton is being packed up this week, along with the rest of her traveling show, “Lucy’s Legacy: The Hidden Treasures of Ethiopia.” The fossil hominid and priceless artifacts from Ethiopia will return this month to the Houston Museum of Natural Science, where officials are still trying to line up a new show for her at another museum before she returns to her African homeland.

Ethiopian tourism officials had high hopes for Lucy’s tour in the United States when she arrived in Houston in 2007. After 6 years of negotiations with the Houston Museum, they envisioned a 10-city tour for Lucy, which had never been on public display before, even in her own nation. Officials hoped that Lucy would be the kind of ambassador for Ethiopia’s cultural riches that King Tut was for Egypt’s antiquities. Initially, the exhibit did well—"Lucy’s Legacy" garnered great opening-day reviews in Houston, where the exhibit drew large crowds before it closed last September. But after she opened in Seattle on 4 October, she drew less than half of the 275,000 visitors initially expected. (The final count was 121,336 when the exhibit closed on 8 March.) Pacific Museum officials think that the exhibit ran into trouble because people were worried about the economy and didn’t want to pay $20.75 per adult ticket. “Family outings become a luxury when people are faced with layoffs, wage freezes,” says Wendy Malloy, media and public relations manager at the Pacific Science Center in Seattle.

But Lucy had some baggage of her own as well—even before she arrived in the United States, a number of prominent paleoanthropologists protested that transporting and exhibiting the fragile, one-of-a-kind fossil could damage it. If that happened, the loss to scientists who are still discovering new ways to analyze fossils would be profound, because there are only a handful of partial skeletons of early human ancestors. So in 2006, several museums that were approached to sign up "Lucy’s Legacy" refused—including the Field Museum in Chicago, Illinois, and the Smithsonian National Museum of Natural History in Washington, D.C., as noted in a Science news story.

Houston Museum officials haven’t given up hope, though. They are in negotiations and hope to have an announcement of Lucy’s next stop within a few weeks, says Melodie Francis, director of public relations. Otherwise, Lucy will fly home nonstop. But that might not be so bad—she might make it home in time for the opening of a new five-story research lab at her home, the Ethiopian Natural History Museum, later this year.

—Ann Gibbons

Photo credit: Houston Museum of Natural Science

See also: The New York Times story about the Seattle exhibit.

March 13, 2009

Minding the Oxygen Gap

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The origin of oxygen-producing photosynthesis was a major event in Earth's history, not least because it paved the way for air-breathing animals like us. Nailing down the timing of this innovation would help researchers clarify the evolution of bacterial metabolism and better understand how oxygen released by the early bugs transformed almost every habitat on Earth.

So far, though, researchers fall into two camps whose answers differ by hundreds of millions of years, as discussed in Science’s Origins essay this month. The first widely accepted geological evidence for significant amounts of atmospheric oxygen is the great oxidation event (GOE) of 2.4 billion years ago. For some researchers, that means bacteria didn’t begin releasing oxygen until a little before the GOE. But according to other researchers, some clues—such as ancient oil thought to be the remains of oxygen-making photosynthetic bacteria—suggest that microbes turned on the gas several hundred million to more than 1 billion years before the GOE.

It’s no surprise that this is a tough question to answer. The evidence—whether it’s embedded in ancient rocks or inscribed in the DNA of modern bacteria—is hard to find and difficult to read. But scientists who argue for an early start to oxygen-releasing photosynthesis have another hurdle to overcome: explaining why it took so long for oxygen to accumulate in the atmosphere. Researchers are mulling several competing hypotheses.

1859_Origin_F373_001Cambridge University, Darwin Online, and the Huntington Library are trying to track down as many first editions of Darwin's On the Origin of Species as possible before the anniversary of its publication in November. They are looking for books in private collections as well as in institutions. Already, they have come across Francis Darwin's copy, with his annotations, in a private collection.

Here is more information about the census.

If your chrysanthemums look stunted and ugly, take comfort. They're infected with a parasite that may tell us a lot about how life began.

Chrysanthemums and some other plants are victims of invisible enemies with the wonderfully sci-fi name of viroids. Scientists discovered viroids in the 1960s while they were trying to figure out whPSTVD0_02y potatoes sometimes grew in weird long shapes (left). They suspected that this so-called potato spindle tuber disease was caused by an infection, because the condition seemed to be spread slowly through potato fields. As for the infectious agent, it seemed likely to be a virus. After all, viruses have long been known to be able to change the shapes of plants they infect. Looking for a virus in the slow-growing potatoes would have slowed down the search immensely. But researchers figured out how to transfer the disease to fast-growing tomatoes, which became stunted after being infected.

Yet even with this advance, the scientists still struggled to figure out what was making the plants sick. They used centrifuges to get rid of particles larger than certain sizes and found that whatever was infecting the plants was amazingly small—far smaller, in fact, than any known virus. And its chemistry was different from that of any known virus. Viruses carry their genetic information in molecules of either DNA or RNA (a single-stranded counterpart to DNA). They also keep this genetic information in a protein shell. The scientists ground up infected tomato leaves and mixed them with enzymes that chop up RNA. They could no longer use that mixture to infect other plants—suggesting that the pathogens used RNA for their genetic material. And indeed, when the scientists repeated the experiment with enzymes for cutting up DNA, the material was still infectious. But then a third experiment yielded a weird result: When the scientists used enzymes to cut up proteins, the material could still make plants sick. In other words, the pathogen seemed to be nothing but a tiny snippet of naked RNA.

It took years of tests to finally confirm that the potatoes were getting sick from bits of raw RNA. Scientists dubbed them viroids (meaning "like a virus") and went on to discover them in a number of plants, including chrysanthemums. In fact, it turned out that a disease that had nearly wiped out the American mum industry in the mid-1950s had been caused by a viroid of their own. (For some reason, no one has found an animal viroid.)

A viroid can contain as few as 250 nucleotides. That's extraordinarily small: The human genome is 3.3 billion nucleotides long, and a single protein-coding gene may be several thousand nucleotides long. Yet that's enough genetic information to let a viroid infect a plant and replicate itself by taking advantage of the enzymes the plant uses to replicate its DNA. Normally, the enzymes pull apart DNA's two strands and add nucleotides to make two new strands, using the old strands as templates. But viroids trick these enzymes into copying their single-stranded RNA. The enzymes use the viroid as a template to make a new viroid progeny. Plants have evolved defenses against these viroids that prevent them from being duplicated. But viroids can often escape the attacks of their hosts, leaving the cell to infect another.

While plant scientists try to figure out how to cure crops of viroids, other biologists are fascinated by them because they strip the processes of life down so far to the bone. Recently, Rafael Sanjuán of the University of Valencia in Spain and his colleagues decided to see how much viroids mutate. Humans, chrysanthemums, and other multicellular organisms have many ways of lowering their mutation rate. They can proofread their DNA as it is copied and correct errors. Bacteria are not quite so careful, but they can still repair a lot of DNA damage. Many viruses are decidedly sloppier. What's intriguing about this pattern is the size of the genomes involved: The higher the mutation rate, the smaller the genome.

Viroids offered a fresh opportunity to test this relationship, because they are hundreds of times smaller than viruses, the smallest genomes for which mutation rates had been estimated. Sanjuán and his colleagues infected chrysanthemums with viroids and then let them breed. The researchers then harvested the new viroids and scanned their genomes for mutations. In particular, they looked for mutations that would keep the viroids from replicating, because these must have been new. (They couldn't be carried down from earlier generations, because they keep the viroids from replicating.) To make sure these really were lethal mutations, the scientists engineered viroids with these mutations and injected the mutant viroids into plants. The plants didn't get sick.

Sanjuán and his colleagues found many mutations. The viroids are the fastest mutators ever found, mutating thousands of times faster than the previous record mutation-v-genomeholders, they report in the 6 March issue of Science. And, as this chart* shows, viroids fall right where you'd expect along the genome size/mutation rate continuum. (The mutation rate is measured in the chances any nucleotide has of mutating per generation.)

As I wrote in my Origins essay in January, many scientists are now persuaded that the earliest form of life on Earth was based not on DNA, RNA, and proteins, but on RNA alone. Some are now building RNA-based protocells to see if they can grow, replicate, and evolve. If life did start out in this RNA world, the early protocells would have had only a few relatively short RNA molecules. As Sanjuán and his colleagues observe, viroids bear a striking resemblance to them. According to the RNA world hypothesis, the original RNA molecules of life would have had to have carried out two different kinds of functions. They'd have to store genetic information and also speed up chemical reactions the way enzymes do today. The viroids that Sanjuán and his colleagues studied contain a stretch of RNA called a hammerhead enzyme that speeds up the viroid's duplication in an enzymelike way.

If early RNA-based life forms had genomes on par with those of viroids, they would have had a gigantic mutation rate. We could not survive with such a high mutation rate because we have such a big genome, with so many vulnerable spots where mutations could deal lethal blows. With a much smaller genome, viruses can survive at a higher mutation rate. And viroids, smaller still, afford mutations an even smaller target.

But the reverse is also true: Without a way to lower their mutation rate, viroids are trapped below a so-called error threshold. The evolution of very accurate gene replication was thus probably a crucial stage in the emergence of more complex life. If life had stayed sloppy, we'd all still be little more than viroids.

Carl Zimmer

*Source: S. Gago et al., "Extremely High Mutation Rate of a Hammerhead Viroid," Science, 6 March 2009 doi: 10.1126/science.1169202