Thursday, 8 April 2010

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Possible New Human Ancestor Discovered

Posted: 08 Apr 2010 07:53 AM PDT

berger1hr

Two 1.9 million-year-old skeletons found in a South African cave have added a new and intriguing member to the primate family.

Dubbed Australopithecus sediba, it has many features —including long legs and a protruding nose —common to Homo, the genus that eventually spawned humans. Other features, such as extra-long forearms and flexible feet, date from deep in our primate past.

Paleontologists disagree over whether A. sediba is a direct human ancestor, or just looks like one. But whatever their lineage, the fossils provide rare insight into a period shrouded in paleontological mystery.

"We feel that A. sediba might be a Rosetta Stone for defining for the first time what the genus Homo is," said paleontologist Lee Berger of the University of Witwatersrand. "They're going to be a remarkable window, a time machine."

The skeletons, described April 8 in Science, were found two years ago in a South African cave where they fell two million years ago.

On one side of that date in the fossil timeline are the various species of Australopithecus, the first great apes to walk on two feet. On the timeline's other side is the Homo genus, the first creatures whom one would recognize —with all due respect to Lucy's famous A. Afarensis — as close to human.

In between is uncertainty. The fossil record is mostly bare. Some Australopithecus lineage split, with one branch becoming Homo. But the identity of that lineage, and the characteristics of early Homo, are unknown.

According to Berger's team, A. sediba's combination of old and new features make it a likely descendant of A. africanus —one of Lucy's direct descendants — and either a direct ancestor of early Homo and ultimately us, or what Berger calls "a very close side branch."

"It sits at a very critical moment in time," said Berger. It "fills a critical gap in the line."

a_sedibaOther paleontologists say Berger's fossils are a marvelous find. But as expected in a field where entire fossil records spanning millions of years could fit on a coffee table, and where the mostly-missing A. sediba skeletons are considered remarkably complete, the new hominin's taxonomical position is being interpreted in many different ways.

While the Australopithecus designation is correct, "the proposed link between A. sediba and early Homo is forced and tenuous at best," said William Jungers, a Stony Brook University paleoanthropologist. He doesn't consider a juvenile specimen — the most complete of the two skeletons comes from the human equivalent of a teenager — a reliable indicator of adult features.

To this criticism, Berger said the teen's brain had "clearly reached about 95 to 98 percent of adult capacity." Few changes would be expected in its cranial size and shape, which are critical in characterizing a primate species.

Jungers also noted that the first Homo fossils predate A. sediba by 500,000 years, while Homo ergaster had reached western Asia just 200,000 years after A. Sediba's known date. Both these figures suggest that Homo was established well before A. sediba came along, said Rick Potts, curator of anthropology at the Smithsonian National Museum of Natural History.

"The connection with the origin of Homo doesn't seem to hold much water," said Potts, and the confluence of some A. sediba traits with Homo is just coincidence. "Evolution produces a universe of features that are combined and recombined," he said.

According to Berger, however, A. sediba may have older roots than they think. "The site we found is simply a point in time. It doesn't represent the first appearance of this species," he said.

Meanwhile, Arizona State University paleoanthropologist William Kimbel argued that A. sediba should have been classified as Homo, though it may not have been a direct human ancestor.

"In my way of thinking, it belongs in Homo because of the brow ridge, the face, the pelvis," he said. "It's true that it has the small brain and long upper limbs indicative of Australopithecus, but those are signs of its ancestry, not its future."

These arguments may be settled as more A. sediba skeletons emerge. Berger is currently assembling at least two. However, taxonomical debates may ultimately prove less important than the questions A. sediba provokes.

Already the fossils suggest that Australopithecus didn't morph suddenly into Homo, but adapted in gradual, piecemeal fashion. What pressures led to these adaptations, and their relationship to tool use, cognitive developments, dietary shifts and climate changes, have yet to be determined.

"The significance is in the patterns and insights it provides," said Kimbel. "These specimens fall at the young end of a very puzzling million-year period in hominin evolution."

Whether or not A. sediba is our ancestor, "it could help us understand the dynamics that led to the split producing the lineage culminating ultimately in us," said Kimbel.

Images: Lee Berger/Science.

See Also:

Citations: "Australopithecus sediba: A New Species of Homo-Like Australopith from South Africa." By Lee R. Berger, Darryl J. deRuiter, Steven E. Churchill, Peter Schmid, Kristian J. Carlson, Paul H. G. M. Dirks, Job M. Kibii. Science, Vol. 328 No. 5975, April 9, 2010.

"Geological Setting and Age of Australopithecus sediba from Southern Africa." By Paul H. G. M. Dirks, Job M. Kibii, Brian F. Kuhn, Christine Steininger, Steven E. Churchill, Jan D. Kramers, Robyn Pickering, Daniel L. Farber, Anne-Sophie Mériaux, Andy I. R. Herries, Geoffrey C. P. King, Lee R. Berger. Science, Vol. 328 No. 5975, April 9, 2010.

Brandon Keim's Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecological tipping points.

Mystery Object Defies Astronomical Classification

Posted: 07 Apr 2010 02:42 PM PDT

brown_dwarf_mystery

A mysterious object discovered near a brown dwarf doesn't fit into any known astronomical category.

The newly discovered mystery companion forms a binary system with the brown dwarf, located 460 light-years away in the Taurus star-forming system. The object is too light to be another brown dwarf, but it's too young to have formed by accretion, the way a typical planet does.

"Although this small companion appears to have a mass that is comparable to the mass of planets around stars, we don't think it formed like a planet," said astronomer Kevin Luhman of Penn State University, co-author of the study April 5 in The Astrophysical Journal. "This seems to indicate that there are two different ways for nature to make small companions."

Luhman's team made the discovery with the Hubble Space Telescope and the Gemini Observatory. The discovery was made using the Wide Field Planetary Camera 2 on the Hubble Space Telescope and the Gemini Observatory.

brown-dwarf-companion-1

The new object and its companion brown dwarf are orbiting as a binary pair, 15 astronomical units from each other. If they were superimposed on our solar system, the companion would be orbiting midway between Saturn and Uranus. The oddball object's mass is somewhere between five and 10 Jupiter masses, making it too small to fuse deuterium. The International Astronomical Union currently uses this fusion line, which occurs at about 13 Jupiter masses, as the defining characteristic of a brown dwarf.

But the object appears to be around the same age as its binary partner, which doesn't fit conventional ideas about planet formation. Traditional theories describe planets forming from the gaseous disk that swirls around the equator of a newly formed star. Particles in the gas and dust cloud collide, and gradually accrete into larger objects, eventually becoming planets. These rocky planets can grow into sizes up to 10 Earth masses before they become gas giants.

And 1 million years is much shorter than the expected time for a planet to be born this way. Planets can form this quickly when there is a gravitational instability in the gaseous disk, but the brown dwarf's disk probably didn't have enough material to form a planet larger than a single Jupiter mass.

"It looks like this new system formed by the collapse and fragmentation process that forms binary star systems," Alan Boss, president of the IAU Commission on Extrasolar Planets said in an e-mail to Wired.com. Boss theorized that these sorts of planet-sized objects exist in a paper published in 2001.

"While people like to use the 'p-word' to describe objects with masses below 13 Jupiter masses, given the attention given to exoplanets these days, they should more properly be called 'sub-brown dwarfs,'" Boss said.

Because this strange object seems more likely to have formed the same way as its binary partner, the brown dwarf, Luhman believes it is probably best classified as a very small brown dwarf.

"This object, because it formed like a star, its composition is probably the same throughout," Luhman said. This homogenous composition is in stark contrast to the innards of gas giants, like Jupiter, which probably have a heavy-element rocky core surrounded by a gaseous shell composed mainly of hydrogen and helium.

The presence of another nearby binary system, of a red star and a brown dwarf, supports Luhman's theory. It seems to have been formed around the same time as the mystery pair, indicating that all four may have formed the same way, as stars.

"This configuration — two tight pairs that are widely separatedfrom each other — is called a hierarchical configuration and is commonlyseen in quadruple star systems," Luhman said.

Images: 1) NASA, ESA, K. Todorov, K. Luhman, Penn State University. 2) Artist's rendering fromGemini Observatory/L. Cook.

Pigeon Flocks Let the Best Bird Lead

Posted: 07 Apr 2010 01:46 PM PDT

pigeon-backpack-zsuzsa-akos

Even the bird-brained can follow a leader. When pigeons fly in flocks, each bird falls behind another with better navigational skill, and the savviest among them leads the flock, scientists report in the April 8 Nature.

sciencenewsThe research suggests hierarchies can serve peaceful purposes in the animal kingdom, where dominance by brute force is often the rule. "A pecking order tends to be just that — a pecking order," says Iain Couzin of Princeton University, an expert in collective behavior who was not involved in the research.

The research also suggests that for pigeons, dominance isn't set in stone. While one bird often emerged as the leader, other birds also stepped up. This flexibility in leadership had previously been seen only in some small groups of fish.

From schools to packs to swarms to flocks, collective behavior is widespread among animals. But in many cases, the important interactions are with nearest neighbors, and control of the group's movement is distributed among members rather than hierarchical.

pigeon-flight-zsuzsa-akosBiological physicist Tamás Vicsek of Eötvös Loránd University in Budapest and his colleagues studied flight dynamics in homing pigeons, which fly in flocks but conveniently return to their roosts. The researchers outfitted 13 pigeons with tiny backpacks carrying GPS devices that measured shifts in birds' flight direction five times per second. Flocks of eight to 10 birds flew with the devices during homing flights (a roughly 14-kilometer trip back to the roost) and spontaneous "free" flights near home. Each bird also flew solo flights of about 15 kilometers each.

Analysis of GPS logs showed that for each excursion, the flock had one leader followed by at least three or four other birds. Each of these followers was in turn followed by other birds in the flock. Comparing the solo flight paths to the group flights showed that the birds with the best navigational skills led the flock.

While flocks have hierarchies, they're not dictatorships, notes Vicsek. One bird led eight of the 13 flights, while other birds took the lead on the rest of the trips. Vicsek likens the dynamics to a group of peers deciding where to eat dinner. "Maybe someone knows the area restaurants best, or there is a person who's a gourmand — or maybe they are the most outspoken," he says. This one person might pick the place to eat for several nights, although another person might chime in now and then. And then there is the person with no say, whom everyone knows has terrible taste in food.

"These pigeons know each other. They know which is the smartest. The fastest bird will even follow the slower one who knows the way home the best," say Vicsek. Videos of the birds' positions during flight showed that if the best navigator moves a little to the left, it takes about a third of a second for other birds to do the same. But if the least savvy bird makes a move "the others don't care," Vicsek says.

Pigeons' brains may be wired for follow-the-leader, comments behavioral neuroscientist Lucia Jacobs of the University of California, Berkeley. When the left eye sees something, for example, it sends all the visual information to the right brain hemisphere, and vice versa. This "extreme lateralization" may play a role in organizing flocks, the new work suggests. A pigeon following another was most likely to be flying on its partner's right, seeing this leader with its left eye. "It's very cool," Jacobs says.

pigeon-flight-2-zsuzsa-akos

Images: Zsuzsa Ákos

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First Animals Found That Live Without Oxygen

Posted: 07 Apr 2010 01:05 PM PDT

loricifera

In the muck of the deep Mediterranean seafloor, scientists have found the first multicellular animals capable of surviving in an entirely oxygen-free environment.

Some types of bacteria and other single-celled organisms can live without oxygen, but nothing as complex had been found as these three species of Loricifera, a group of marine-sediment dwellers who inhabit one of Earth's most extreme and little-known environments.

"The discovery of these life forms opens new perspectives for the study of metazoan life in habitats lacking molecular oxygen," wrote researchers led by Roberto Danovaro, a marine biologist at Italy's Polytechnic University of Marche, in a study published April 6 in BMC Biology.

Like other Loricifera, the new species are sub-millimeter–long, Lovecraftian tangles of tentacle and shell, with their closest taxonomical relatives found among mud dragons and penis worms.

The new species, however, don't have the mitochondria found in almost every other animal cell, converting oxygen and nutrients into chemical energy.

Even the few parasite species once thought to be mitochondria-free seem to have had them at some point in history, and possess mitochondrial remnants that perform the same essential functions.

Instead the new Loricifera species have structures called hydrogenosomes, which are found in some single-celled organisms and require no oxygen to produce chemical energy.

The evolutionary history of these creatures is not known, but they live in an environment reminiscent of Earth's oceans some 600 million years ago, before the deep seas were oxygenated and large animals evolved, wrote Comenius University (Slovakia) biochemist Marek Mentel and Düsseldorf University (Germany) biologist William Martin in an accompanying commentary.

These "fascinating animals" provide a "glimpse of what a good part of Earth's past ecology might have been like," they wrote.

Image: Roberto Danovaro/BMC Biology.

See Also:

Citations: "The first metazoa living in permanently anoxic conditions." By Roberto Danovaro, Antonio Dell'Anno, Antonio Pusceddu, Cristina Gambi, Iben Heiner and Reinhardt Mobjerg Kristensen. BMC Biology, Vol. 8 No. 32, April 6, 2010.

"Anaerobic animals from an ancient, anoxic ecological niche." By Marek Mentel and William Martin. BMC Biology, Vol. 8 No. 32, April 6, 2010.

Brandon Keim's Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecological tipping points.

New Giant Lizard Discovered in the Philippines

Posted: 07 Apr 2010 10:29 AM PDT

lizard_varanus

Scientists couldn't see the lizard for the trees.

sciencenewsBut now they've tracked down and named Varanus bitatawa, a skittish reptile that's hard to spot even though it grows up to 2 meters long and sports bright yellow speckles.

In forests on the Philippine island of Luzon, the newly discovered monitor lizard hauls itself up into trees in search of fruit and melts into the vegetation if humans approach, says herpetologist Rafe Brown of the Biodiversity Institute at the University of Kansas in Lawrence. He and his colleagues describe and name the species in paper published online the week of April 5 in Biology Letters.

The species is "new to us," Brown clarifies, because the Agta and Ilongot peoples living in forests of the Sierra Madre range know the lizard well — as a delicacy. It mostly eats fruit and reportedly tastes better than a much more common scavenging monitor that's "attracted to stinky stuff," Brown says.

A cousin to the giant Komodo dragon, Varanus bitatawa is hard to find but once detected, is pretty hard to ignore. During adulthood, yellow markings differentiate it from a much drabber neighbor — though both species sport colorful patterns as juveniles.

Reptile systematist Michael B. Harvey, who was not part of Brown's group, has helped name another Varanus lizard from New Guinea and examined specimens from Southeast Asia. "I quickly realized that diversity of these lizards had been greatly underestimated," says Harvey, of Broward College in Davie, Florida. "I only hope that we don't lose much of this biodiversity before scientists can study it."

Deforestation poses a major threat to the biodiversity of the Philippines, which Brown and his colleagues describe in their paper as a "global conservation hot spot."

Western scientists first glimpsed the big monitor in 2001, Brown says, when biologists exploring the forest happened on hunters carrying a large lizard home for dinner. The biologists were permitted to photograph it, but theirs was the first of several encounters in which hunters showed no interest in giving up the centerpiece of a big family meal.

Herpetologist Arvin Diesmos of the National Museum of the Philippines in Manila and other researchers persisted in collecting photographs, local intelligence and the occasional juvenile, but they could not secure a full-grown adult specimen.

Then, in the summer of 2009, a team led by Brown and his graduate student Luke Welton got its hands on an adult lizard. They documented identifying anatomical characteristics such as the distinctive little horns on the ends of the lizards' double-barreled male reproductive organs. Which, by the way, are far from unusual in and of themselves: "All snakes and lizards have a paired copulatory organ," Brown says.

DNA tests were even more important, confirming that the species differs from a previously identified fruit-eating monitor living in a different part of the island.

Brown actually learned of the adult specimen's existence via text message. After he and his students spent weeks in the mountains surveying other vertebrates and hoping for an adult Varanus bitatawa, Brown had to return home early to start the fall semester. But he received a message from his students in the expedition's final hours announcing their success — and letting him know that they were having a hard time finding a way to get from their camp to the airport.

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Gut Bacteria Give Super Seaweed-Digestion Power to Japanese

Posted: 07 Apr 2010 10:00 AM PDT

maki

The old adage, "You are what you eat," has a bacterial component.

In a neat confluence of human history, stomach bacteria and food, researchers have found that the intestinal microbes of Japanese people may be souped up for eating seaweed.

"In a marine bacteria, we identified an enzyme that is very specialized for degrading algal cell walls," said Mirjam Czjzek, a biologist at France's Station Biologique de Roscoff. "The only other place we find this enzyme is in the human-gut bacteria of Japanese individuals."

The discovery, described April 7 in Nature, started with Roscoff biologist Jan-Hendrik Hehemann's analysis of Zobellia galactanivorans, a common marine bacteria. In it, he found an enzyme that breaks down porphyran, a carbohydrate found in the cell walls of red algae.

The gene that codes for the enzyme has been found in one other place: the genome of Bacteroides plebeius, a microbe found in human intestines. However, not all B. plebeius strains produce the algae-crunching enzyme. It has only been found in Japanese people.

According to the researchers, the enzyme helps Z. galactanivorans eat red algae, which westerners know best as the nori seaweed wrapping around sushi rolls. At some unknown points and in some unknown stomachs in the Japanese past, the enzyme-coding gene passed from Z. galactanivorans and into B. plebeius. That lucky microbe would have benefited from a new-found ability to process red algae, spreading through its stomach environment and eventually through the human population, which in turn derived more nutrients from an algae-rich diet.

Humans are known to benefit from digestive enzymes produced by the trillions of microbes in each person's intestines, but "I don't think anyone's ever shown an ethnic difference like this," said Andrew Gewirtz, an Emory University immunologist who studies the role of gut bacteria in obesity. "It's perfectly logical, and fits with ideas that scientists have kicked around."

How much the new gene helps people digest seaweed hasn't yet been quantified. The microbes' fate in people with seaweed-free diets is uncertain.

The researchers also don't know when the gene jumped from marine to human microbes, though Czjzek suspects it happened long ago. As for whether other people have seaweed-processing strains, the study isn't absolutely conclusive. It looked only at the gut microbes of 18 westerners — enough to suggest a pattern, but not a final word, though the chances are probably low.

"Often the question comes, 'I've been eating sushi for two years now. Do I have this enzyme?' The answer is, these are very rare events," said Czjzek. "In the early days, seaweed wasn't sterilized. Nowadays, it's cooked, roasted and prepared. The chance to have this type of transfer is much lower."

That's likely the case with most types of food, said Gewirtz. As for whether "that's a good or a bad thing, it's hard to say," he said. But Justin Sonnenburg, a Stanford University microbiologist who wrote a commentary accompanying the findings, is concerned.

"Consumption of hyper-hygienic, mass-produced, highly-processed and calorie-dense foods is testing how rapidly the microbiota of individuals in industrialized countries can adapt while being deprived of the environmental reservoirs of microbial genes," he wrote.

However, globalized diets do give people a chance to eat foods they wouldn't have found before. "The next time you take a bite of an unfamiliar food, think about the microbial inhabitants you may also be ingesting, and the possibility that you will be providing one of your 10 trillion closest friends with a new set of utensils," wrote Sonnenburg.

Image: Javier Lastras/Flickr.

See Also:

Citations: "Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota." By Jan-Hendrik Hehemann, Gaelle Correc, Tristan Barbeyron, William Helbert, Mirjam Czjzek, & Gurvan Michel. Nature, Vol. 464 No. 7290, April 8, 2010.

"Genetic pot luck." By Justin L. Sonnenburg. Nature, Vol. 464 No. 7290, April 8, 2010.

Brandon Keim's Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecological tipping points.

Wednesday, 7 April 2010

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge


Migratory Birds’ New Climate Change Strategy: Stay Home

Posted: 06 Apr 2010 02:42 PM PDT

blackcap

Birds may have an unexpected strategy for adapting to climate change. In addition to migrating at different times to newly hospitable locales, they may also shorten their migrations, expending energy on breeding and eating rather than flying.

"There's lots of data on bird arrival and bird breeding times, and that gives the impression that these are the most important phenomena," said zoologist Francisco Pulido of the Complutense University of Madrid. The basic impulse to migrate is likely just as important, "but it's been much more difficult to show, and so it hasn't been appreciated," he said.

Pulido and Max Planck Institute ornithologist Peter Berthold describe patterns found in 13 years of data from a southern German population of blackcaps, a common migratory songbird, in a study published April 5 in the Proceedings of the National Academy of Sciences.

As temperatures in central Europe have risen, blackcaps have arrived earlier at summertime breeding areas and departed later for their winter homes. Some researchers have predicted blackcaps would also migrate over ever-shorter distances, and in some cases stop altogether, allowing them to save energy and concentrate on finding food and mates. But this hadn't been tested.

To gauge the birds' migratory energies, Pulido and Berthold removed a few hundred blackcaps from the local population each summer. As captive birds are restless during the time they would typically be migrating, the researchers used them to measure the duration of wild migrations. These dropped slowly but steadily between 1988 and 2001, in keeping with predictions.

(Most of the captured birds were released at the end of each season, eventually catching up to their compatriots.)

In a second part of the study, Pulido and Berthold bred the most sedentary blackcaps. They wanted to accelerate the natural trend, seeing in a few years what would normally take decades. From this, they extrapolated that some blackcap populations could stop migrating altogether within 40 to 50 years. Other birds may do the same.

The next step in the research is connecting changes in migratory impulse to other adapations. Pulido speculates that shorter distances facilitate earlier arrivals, which in turn alter patterns of reproductive development.

However, shorter distances may only be an option for some species. Blackcap migration spans a relatively modest 1,000 miles, and sometimes less. For birds that travel thousands of miles, with no hospitable territory between their destinations, there may be no middle ground.

Blackcaps are also quite common. Species with smaller populations may be more vulnerable to weather extremes that become more common with warming, said Pulido.

"Adaptation requires a large population. Otherwise they'll go extinct," he said.

Image: Ignacio García/Flickr

See Also:

Citation: "Current selection for lower migratory activity will drive the evolution of residency in a migratory bird population." By Francisco Pulido and Peter Berthold. Proceedings of the National Academy of Sciences, Vol. 107 No. 14, April 5, 2010.

Brandon Keim's Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecological tipping points.

Fossil Turtle Had Extra-Thick Shell to Fend Off World’s Largest Snake

Posted: 06 Apr 2010 02:22 PM PDT

turtle_combo

A new fossil turtle species discovered in a Colombian coal mine had a shell as thick as a 400-page book, which may have protected it from crocodiles and the world's biggest known snake.

Scientists from the Smithsonian Tropical Research Institute and the Florida Museum of Natural History uncovered the Cerrejón coal mine. The 60-million-year-old fossilized shell found there was almost 1.5 inches thick and over 3 feet across. The scientists named the species Cerrejonemys wayuunaiki after the language of the local Wayuu people.

The giant snake that lived alongside this is called the Titanoboa cerrejonensis. Fossils of the snake, also discovered in Colombian coal mines in the same area as the turtle, show that it grew to be between 40 and 50 feet long. The longest known living snake species, Python reticulatus, has been measured at 29 feet long.

"The fossils from Cerrejón provide a snapshot of the first modern rainforest in South America — after the big Cretaceous extinctions and before the Andes rose, modern river basins formed and the Panama land bridge connected North and South America," Carlos Jarmillo, staff scientist at the Smithsonian who studies the plants from Cerrejón, said in a press release April 5.

Two more new fossil turtle species have turned up in the mines and will be described by Edwin Cadena of North Carolina State University, first author of the C. wayuunaiki paper publishedin the Journal of Vertebrate Paleontology.

"I hope this will give us an even better understanding of turtle diversity in the region and some important clues about the environment where they lived," Cadena said in the press release.

titanoboa

Images: 1) Edwin Cadena. 2) Artist's rendering of the Titanoboa./Jason Bourque, Florida Museum of Natural History

Citation: Cadena, Edwin A., and Jonathan I. Bloch and Carlos A. Jaramillo. "New Podocnemidid Turtle (Testudines: Pleurodira) from the Middle-Upper Paleocene of South America." Journal of Vertebrate Paleontology 30.2 (2010): 367-382

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Russian Physicists Synthesize New Superheavy Element 117

Posted: 06 Apr 2010 10:36 AM PDT

dubna

Physicists have reported synthesizing element number 117, the latest in the quest to create artificial "superheavy" elements in the laboratory. A paper describing the discovery has been accepted for publication in Physical Review Letters.

sciencenewsA team led by Yuri Oganessian of the Joint Institute for Nuclear Research in Dubna, Russia, reports smashing together calcium-48 — an isotope with 20 protons and 28 neutrons — with berkelium-249, which has 97 protons and 152 neutrons. The collision spit out neutrons to create two isotopes of an element with 117 protons, one with 176 neutrons and the other with 177.

"These are very, very interesting results," says Witold Nazarewicz, a theorist at Oak Ridge National Laboratory in Tennessee. "This was carefully planned, and it would have been very difficult to synthesize this element without the berkelium target."

element-117The new element, which has yet to be named, slips into a place on the periodic table between elements 116 and 118, both of which have already been discovered. Such superheavy elements are usually very radioactive and decay away almost instantly. But many researchers think it is possible that even heavier elements may occupy an "island of stability" in which superheavy atoms stick around for a while.

The new work supports that view. Analyses of the radioactive decay of the new element, Oganessian's team writes in the new paper, "represent an experimental verification for the existence of the predicted 'Island of Stability' for super-heavy elements."

Images: 1) Yuri Oganessian walks from the Joint Institute for Nuclear Research in Dubna, Russia, around 1989 with Ron Lougheed (left) and Ken Moody (right) of Lawrence Livermore National Laboratory, with whom he has collaborated on previous research into superheavy elements./LLNL.
2) Element 117/Wikimedia Commons.

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Tuesday, 6 April 2010

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge


Chain of Offshore Wind Turbines Could Power Atlantic Seaboard

Posted: 05 Apr 2010 12:30 PM PDT

global_ocean_wind_power

A 1,550-mile-long network of offshore wind stations could provide power from Massachusetts to North Carolina with minimal threat of outages, according to a new study.

By connecting stations together, the system could eliminate the biggest downside of wind power: intermittency.

The concept is simple: If you spread out wind stations far enough, each one will experience a different weather pattern. So it's very unlikely that a slackening of the wind would affect all stations at once. The result is steadier power.

"We're designing transmission in a different way, according to meteorological principles," said marine-policy expert Willett Kempton of the University of Delaware in Newark, co-author of the research, published April 5 in the Proceedings of the National Academies of Sciences.

Kempton and a team of scientists analyzed five years of wind data from 11 meteorological stations — buoys and towers — off the Atlantic coast, from Florida to Maine. They found that combining power from all stations with a transmission cable could prevent massive power fluctuations.

buoy-s8The scientists simulated an underwater transmission cable, which they called the Atlantic Transmission Grid, that stretched more than 1,550 miles and connected all 11 stations. Although individual sites showed erratic patterns, the aggregate power output changed only very slowly.

For example, the power output of individual stations would regularly drop to zero and fluctuate by more than 50 percent in an hour, but the output of the entire grid did not change more than 10 percent in any given hour. And the north-south orientation of the grid meant that a northward cyclone, which can cause wind power to drop quickly after it passes through, would affect only a few stations at a time. Grid power never dropped to zero during the entire five-year period.

"We took an intermittent resource and made it not intermittent anymore," Kempton said.

Scientists had considered offshore wind as a potentially limitless source of power. Compared to land, the ocean has stronger and more constant winds, though still not constant enough to be a primary energy supply. This study indicates that offshore wind deserves more serious consideration as an energy alternative.

"The technology's there, the materials are there, we have the willpower to reduce carbon emissions, we have a reliable power supply that doesn't lead to fuel shortage," said Mark Jacobson, a civil and environmental engineer at Stanford University. "The next step is really to start implementing this on a large scale."

There are currently no commercial offshore wind stations, though companies have started developing six wind farms along the east coast. Together, the developments could produce as much energy as a large coal or nuclear power plant.

Next, Kempton would like to optimize the selection of stations to get the most stable and robust wind power. The current electric grid cannot handle another large source of variability, so it will be important to design the transmission to ensure that wind power is more reliable, he says.

And he recommends the development of a new regulatory body to oversee offshore wind power. But first developers and investors have to be willing to pony up the large capital costs for building wind farms along the coast.

Images: 1) Data from the QuikScat satellite shows wind-power density over global oceans for winter (top panel) and summer (lower panel). Red and white colors indicate high energy is available, while blue color reflects lower energy./NASA/JPL.
2) A buoy used to collect wind data for the study./Willett Kempton.

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95-Million-Year-Old Bugs Found in African Amber Surprise Scientists

Posted: 05 Apr 2010 12:00 PM PDT

formicidae

Newly discovered pieces of amber have given scientists a peek into the Africa of 95 million years ago, when flowering plants blossomed across Earth and the animal world scrambled to adapt.

Suspended in the stream of time were ancestors of modern spiders, wasps and ferns, but the prize is a wingless ant (above) that challenges current notions about the origins of that globe-spanning insect family.

"Most specimens represent a unique fossil record of their group from Africa, and some are among the oldest records in the world," wrote researchers in a paper April 5 in the Proceedings of the National Academy of Sciences.

falsefairywasp2

The amber, which is formed when plant resin fossilizes, preserving flora and fauna trapped within, was found in what is now northwest Ethiopia. Ninety-five million years ago, it was part of a disintegrating Gondwana, one of two vast land masses that spawned the seven modern continents.

pangea_breakup_usgsMost amber deposits have been found in former parts of Laurasia, the other supercontinent of the time. The Gondwana record is relatively sparse.

The amber in the latest study dates to the middle of the Cretaceous era, which followed the dinosaur-dominated Jurassic and witnessed the rise of mammals, birds and flowering plants. Mammals get most of the attention, but changes to flora were just as profound.

Before the Cretaceous, flowering plants —which are now the most diverse type of terrestrial plant — didn't exist. By the mid-Cretaceous, they dominated the land. Existing plants and animals had to adapt, filling the flowery new niches. The new study is a snapshot of that process.

While it will take years to interpret the ecological tales trapped in the new amber, one important story is already suggested. Inside the Ethiopian amber is an ant that looks nothing like ants found in Cretaceous amber from France and Burma. Those deposits had placed the origin of ants in Laurasia. That's no longer certain.

"The Ethiopian amber is of great importance for improving our knowledge of the evolutionary history of terrestrial arthropods, plants and Fungi," wrote the researchers.

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Images: Photos From Alexander Schmidt/PNAS: 1) Wingless ant; 2) False fairy wasp; 3) Tree fern; 4) Springtail. Diagram: Breakup of Pangea./USGS.

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Citation: "Cretaceous African life captured in amber," by Alexander Schmidt, Vincent Perrichot, Matthias Svojtka, Ken Anderson, Kebede Belete, Robert Bussert, Heinrich Dörfelt, Saskia Jancke, BarbaraMohr, Eva Mohrmann, Paul C. Nascimbene, André Nel, Patricia Nel, Eugenio Ragazzi, Guido Roghi, Erin E. Saupe, Kerstin Schmidt, Harald Schneider, Paul A. Selden, and Norbert Vávra. Proceedings of the National Academy of Sciences, Vol. 107 No. 14, April 5, 2010.

Brandon Keim's Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecological tipping points.

Monday, 5 April 2010

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge


Sequencing the Video Genome

Posted: 05 Apr 2010 02:30 AM PDT

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Think organisms are the only ones with genomes? Researchers at the Israel Institute of Technology are sequencing the "video genome" to put an end to video piracy on the internet.

The technique works by detecting features thatremain basicallyunchanged by typical color and resolution manipulations.Current methodsrely on action recognition algorithms, which match video sequences by the movement they contain.

Think of three sample clips: the original lightsaber fight scene from Star Wars, a low quality video of the scene playing on TV and a home video of you and your brother reenacting it with plastic lightsabers. Action recognition algorithms would see all three clips as similar, but video genome analysis would only match the first and the second.

Brothers Alexander and Michael Bronstein and their advisor Ron Kimmel are able to make this distinction using gene sequence matching and alignment algorithms borrowed from the field of bioinformatics. Their research was posted on ArXiv.org on March 27.

"We realized that many problems that exist in the analysis of video match nicely to applications and problems that exist in the analysis of sequences," Michaelsaid.

The technique rests on the idea that changes like clipping and cropping of video are analogous to mutations in DNA. The "DNA" of video clips can be aligned the same way that biological DNA sequences can, using bioinformatics, even with the addition of commercials, deletion of scenes or changes to color or resolution.

"Looking at a very short piece of video, we are able to tell where it comes from, independently of the transformations it may undergo,"Alexandersaid.

For example, when a camcorder is used to capture the video from a movie screen, the camera may be shaking, the colorsmight bedifferent, the resolution may vary, but the video DNA sequence would still be similar.

The video's features are translated into a string of information, like a genome is read as a DNA nucleotide sequence. This video genome is made up of agroup of features including boundaries and shapes, in the same way that search algorithms use a group of words to find similarities in text. These features don't change during normal video manipulations.

"You can think of modifications a video can undergo as analogous to mutations," Michaelsaid. For example, an advertisement would be like an insertion mutation, and removal of content for rating would be a deletion.

The frequency of features in each frame is graphed and translated into a 64-bit binary word. When this information is played over time, the clip's video genome can be compared to a database using bioinformatic analyses. The video genome takes up about one millionth the bandwidth of DVD quality video, and can be translated in real time.

The technology could potentially be used to detect pirated content on YouTube, or to match metadata, like subtitles, user-generated notes or comments, to any version of a video. Theoretically, thousands of hours of video could be processed in a matter of days, with greater than 99 percent matching accuracy.

Though the idea is promising, there are some drawbacks to the technology. While the video genome can be created in real time from video, matching the genome to entries in the database cannot. The team is currently working to simplify and speed up the database search process, so matches can be made in a fraction of a second.

Via the physics arXiv blog, MIT Technology Review

Image: Bronstein

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Saturday, 3 April 2010

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge


Why Volcanic Eruptions Can Spark Lightning

Posted: 02 Apr 2010 02:38 PM PDT

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It's the ultimate love-at-first-sight story: In the middle of the desert, hundreds of miles from anything else, lonely sand grains meet up in a crowd and decide to electrify each other. Sparks fly.

sciencenewsPhysicists have long puzzled over why sand grains and other small particles can build up electrical charges as they collide with one another, sometimes to the point of discharging lightning in dust storms or plumes of volcanic ash. Now, a paper in an upcoming issue of Nature Physics suggests that particles transfer electrical charge vertically during a smashup, such that positive charges move downward and negative charges move up in the cloud.

The findings could help combat a wide variety of practical problems, such as the adhesion of charged dust to solar panels on a Mars rover or the generation of dangerous electrical discharges that sometimes occur when a helicopter takes off in the desert. Dust clouds can create problems in grain silos, where charge sometimes builds up and leads to explosions, and in the pharmaceutical industry, where particles of ground-up drugs can become charged and not mix properly, says Hans Herrmann, a materials researcher at ETH Zurich.

Herrmann says he became interested in the problem after watching lightning in swirling sands over dune fields at night. "Normally when particles collide, they neutralize," he says. "How could it be that charges increase?"

Working with ETH colleague Thomas Pähtz and Troy Shinbrot of Rutgers University's campus in Piscataway, New Jersey, Herrmann developed a model to explain how the charging happened. Before colliding, the grains have an overall neutral charge but are polarized by a background electric field, with a negative charge toward the top of the grain and a positive charge toward the bottom, relative to the ground. Upon colliding, the particles neutralize each other at the point of contact, but when they separate again they became further polarized, with additional charges building up on the grains' edges.

"Every time there's a collision you end up pumping charge from the top to the bottom," says Shinbrot. The researchers ran computer simulations and then a series of experiments with glass beads to confirm the theory.

Daniel Lacks, a materials physicist at Case Western Reserve University in Cleveland, says the new study could be identifying one of several mechanisms at work in particle clouds. In earlier work, Lacks showed that electrical charging depends on the size of particles in question, with smaller particles tending to charge negatively and larger particles tending to charge positively.

"The bottom line is that something is needed to break the symmetry when two particles of identical composition collide, in order for one particle to charge negatively and the other to charge positively," he says. For particles of different sizes, he says his mechanism might be in play; for identically sized particles, the new model might explain it.

Some challenges remain, such as explaining where the background electric field that charges the particles came from. But Herrmann says the work is philosophically satisfying, in answering a long-held question, and may yet have practical applications.

Image: Oliver Spalt/Wikimedia Commons

Inca Skeletons Show Evidence of Spanish Brutality

Posted: 02 Apr 2010 12:19 PM PDT

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If bones could scream, a bloodcurdling din would be reverberating through a 500-year-old cemetery in Peru. Human skeletons unearthed there have yielded the first direct evidence of Inca fatalities caused by Spanish conquerors.

sciencenewsEuropean newcomers killed some Inca individuals with guns, steel lances or hammers, and possibly light cannons, scientists report online in the March 23 American Journal of Physical Anthropology.

Surprisingly, though, no incisions or other marks characteristic of sword injuries appear on these bones, according to a team led by anthropologist Melissa Murphy of the University of Wyoming in Laramie. Spanish documents from the 16th century emphasize steel swords as a favored military weapon.

inca_skeletonMany Spaniards who helped Francisco Pizarro conquer the Incas were fortune-seekers, not soldiers, "so the absence of sword injuries makes some sense," Murphy explains.

Skeletons in the Inca cemetery, as well as at another grave site about a mile away, display a gruesome array of violent injuries, many probably caused by maces, clubs and other Inca weapons, the researchers report. Those weapons may have been wielded by Inca from communities known to have collaborated with the Spanish, or might have been borrowed by the Spanish, they posit. "The nature and pattern of these skeletal injuries were unlike anything colleagues and I had seen before," Murphy says. "Many of these people died brutal, horrible deaths."

Little is known about early European dealings with the Inca, remarks anthropologist Haagen Klaus of Utah Valley University in Orem.

"Murphy's data show the types of violence that emerged from the first moments of contact between Spaniards and the Inca," Klaus says. Pottery and artifacts at the sites date to between 1470 and 1540, placing the deaths close to when Spaniards captured the Inca emperor around 1532. It took the invaders nearly another 40 years to control all Inca lands.

Murphy's team assessed skeletons of 258 Inca individuals, age 15 or older, excavated several years ago at the two cemeteries.

In one cemetery, bodies had been hastily deposited in shallow graves. One-quarter of 120 skeletons displayed head and body injuries inflicted at the time of death, as indicated by a lack of healed bone and other clues. That's a conservative estimate, Murphy notes, since soft-tissue damage doesn't show up on bones.

"I'm struck by the severity of violence in certain individual cases, where the skull was essentially crushed, repeatedly stabbed or struck, or shot through by gunshot," comments archaeologist Steven Wernke of Vanderbilt University in Nashville. Whoever killed these individuals wanted to intimidate survivors as well, he asserts.

One man's skull contained two holes and radiating fractures consistent with damage produced by early guns that shot ammunition at low velocities.

Another male skull sported three small rectangular openings in the back of the head. These injuries resemble those on skulls from a 1461 battlefield cemetery in England, Murphy says. Medieval weapons tipped with steel spikes or sharp beaks probably caused these wounds, she proposes.

Three other skeletons exhibited injuries likely due to Spanish weapons. Other skeletons contained head and body fractures probably inflicted by attackers bearing Inca weapons.

Individuals placed in this cemetery may have been slain in a documented 1536 Inca uprising against Spanish rulers in nearby Lima, Murphy suggests. Family members collected their bodies and buried them quickly near previously deceased relatives, she speculates.

At the second Inca cemetery, 18 of 138 skeletons showed definite signs of violent death, all from Inca weapons. That supports a scenario in which social turmoil around the time Spaniards arrived triggered conflicts between Inca communities, Murphy says.

Images: Melissa Murphy

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Friday, 2 April 2010

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge


Video: Tortoises Learn From Each Other

Posted: 01 Apr 2010 01:45 PM PDT




Animal hermits can learn from their peers, researchers say, even though they rarely encounter one another in the wild.

sciencenewsRed-footed tortoises in the wild live a typically lonely tortoise life, without even being cared for by their parents. But in the lab, they can pick up hints to solving a problem by watching a more accomplished tortoise, says cognitive biologist Anna Wilkinson of the University of Vienna. "It's the first demonstration of social learning in reptiles," she says.

It's also the first demonstration that nonsocial animals can watch a neighbor and then complete a task that they couldn't figure out readily on their own, she says. The tortoises' feats are "challenging the idea that social learning is an adaptation for social living," Wilkinson and her colleagues say in a paper going online the week of March 30 in Biology Letters.

In mammals, birds and insects, the power to learn from watching a neighbor has shown up in animals that live in groups, like chimps and honeybees. So scientists routinely link social learning to social living, Wilkinson says. However, she proposes that watching a neighbor may be just another way that any good learner, social or not, picks up on clues for success.

"It might be the case that social learning in social and non-social species is different in interesting ways, and that would be great to know," says animal behaviorist Bennett G. Galef of McMaster University in Hamilton, Canada, who was not involved in the study.

Video: Anna Wilkinson

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Think You’re Good at Driving While on Your Cellphone? You May Be Right

Posted: 01 Apr 2010 10:31 AM PDT

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Cellphone users frequently drive themselves to distraction while operating cars, and all too often end up in traffic accidents. But a select few multitask behind the wheel with extraordinary skill, a new study finds.

sciencenewsAbout one in 40 drivers qualifies as a "supertasker," able to combine driving and cell phone use without impairing performance of either activity, say psychologists Jason Watson and David Strayer, both of the University of Utah in Salt Lake City. These unusual exceptions to the general rule that performance declines when a person does two things at once (SN: 3/13/10, p. 16) may offer insights into the workings of attention and mental control, Watson and Strayer propose in an upcoming Psychonomic Bulletin & Review.

Laboratory tests of 200 volunteers operating a driving simulator identified five extraordinary individuals. These people were good drivers: They hit the brakes quickly in response to cars that slowed in front of them and maintained a safe distance from other cars. They also excelled at solving simple math problems and remembering words heard over a hands-free cellphone when not driving. Critically, their performance on these tasks stayed just as high while driving and using cellphones at the same time.

"Supertaskers did a phenomenal job of performing several different tasks at once," Watson says. "We'd all like to think we could do the same, but the odds are overwhelmingly against it."

Watson and Strayer studied college students, ages 18 to 43. After learning to operate a driving simulator on a virtual highway, participants followed an intermittently braking pace car driving in the right-hand lane. For each volunteer, the researchers measured time needed to depress the brakes when the pace car slowed and distance from the pace car throughout the trip.

In a separate trial, participants listened through hands-free cellphones as an experimenter read two to five words interspersed with simple math problems that had to be immediately labeled as true or false. Volunteers then tried to recall words in the order that they were presented.

As expected, overall group performance declined markedly when driving and the cellphone task were performed at the same time. Volunteers took an average of 20 percent longer to hit the brakes when needed, and increasingly fell behind the pace car. Word recall fell by 11 percent and math accuracy declined 3 percent.

But the handful of supertaskers maintained their braking times, following distances and math accuracy while multitasking. Their word recall rose 3 percent.

Stanford University sociologist Clifford Nass wonders whether supertaskers in the new study prefer doing many things at once in their daily lives. He and his colleagues have found that young adults who often multitask — say by regularly sending text messages while navigating websites and watching television — perform worse when switching back and forth between two mental tasks than peers who rarely multitask. Frequent multitaskers have difficulty ignoring information irrelevant to a task at hand, Nass argues.

That leads Nass to the somewhat surprising conclusion that supertaskers tend not to juggle multiple duties and don't need to practice multitasking to be good at it.

Researchers need to explore whether supertaskers jointly simply perform well-learned abilities the same way everyone else does but with far more efficiency, or instead deploy mental resources in distinctive ways, says psychologist Randall Engle of Georgia Tech in Atlanta.

Watson and Strayer plan to do that by comparing various measures of brain activity for people who do and don't rank as supertaskers.

Image: CraigOppy/flickr

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End of Gene Patents Will Help Patients, Force Companies to Change

Posted: 01 Apr 2010 09:55 AM PDT

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When you went to sleep last Sunday night, 20 percent of your genome belonged to a researcher or company. One day later, following federal district court judge Robert Sweet's ruling, it belonged to you.

Some activists cheered the landmark decision on general principle, but for others, it was a business and medical matter. They say the end of gene patents could be a boon for patients, who will benefit from gene-testing companies competing for their business.

"They'll have to deliver products to the marketplace faster, better and cheaper. There's all sorts of ways to make money," said Dan Ravicher, executive director of the Public Patent Foundation and a plaintiff in the lawsuit, which pitted civil rights activists and patient groups against Myriad Genetics, a Utah provider of tests on its patented breast-cancer-risk genes. "I'm a strong conservative. I believe companies are good and competitionis good."

Myriad and its supporters, including the Biotechnology Industry Organization, had argued that gene patents were necessary. They made commercial profits possible, and potential financial rewards drove research.

Ravicher's foundation, the American Civil Liberties Union, and their supporters —including the American Medical Association, American Society of Human Genetics and March of Dimes — said this simply wasn't true.

Beyond the absurdity of gene patents —imagine patenting gold, the human arm, or gravity — they said that patents had hurt patients, stifled business and stunted research. Myriad's monopoly prevented women from getting second opinions on their breast-cancer gene tests. More broadly, existing gene patents dissuaded researchers from studying sections of the genome that were already claimed, and high licensing fees discouraged would-be entrepreneurs.

In a public statement, Myriad Genetics said it would appeal the decision.

"My hope is that this ruling stands and companies will need to actually innovate and create new advances based on genetic findings, not dependent on sole access to them," wrote Linda Avey, CEO of personalized genomics company 23andMe, in a comment on the Genetic Future blog. "Rather than relying on obscure patent language and legal strategies, companies will need to develop products that are competitively positioned."

One area of competition will be in the interpretation of gene mutations. Gene testers don't just plug a DNA sequence into a computer and wait for the result. They use an arsenal of interpretive techniques, and must update their approaches with new research.

"There are a lot of algorithms that each of us uses. Some are more right than others. There are differences in how you study mutations, weight them, and interpret the data," said Wendy Chung, a Columbia University breast cancer researcher and plaintiff in the lawsuit.

Chung said that Myriad's tests are well-regarded, but they've lagged in interpreting rare gene variants that each person has, but because they're so unique, have not been ascribed a clinical significance.

"On the academic side, there are a lot of people trying to computationally guess what the functions of these variants will be. Myriad has been conservative in saying, if we don't know what it is, then we won't make guesses," said Chung.

Gene-testing companies will also compete to do the best job explaining often-ambiguous genetic results to their customers. Business relationships with insurance companies and health care providers will become even more important. And companies will still be able to patent tools used to interpret genes.

"Companies can compete on quality, speed and taking the burden off hospitals," said Robert Cook-Deegan, a Duke University gene policy expert. The decision "does threaten some business models but it opens the gate for others."

Image: Dave Fayram/Flickr

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Brandon Keim's Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecological tipping points.

Thursday, 1 April 2010

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge


Hunt for Missing Genetic Killer Comes Up Empty

Posted: 31 Mar 2010 01:07 PM PDT

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A massive search for a prime suspect in the mystery of the missing heritability has come up empty.

Known as copy-number variations, or CNVs, these extra or missing sequences of the genome have been linked to some rare diseases. Researchers thought they might play a role in common diseases, too. But a comparison of 19,000 genomes found few links to breast cancer, diabetes and six other major killers.

Copy-number variations "are unlikely to contribute to the genetic basis of common human diseases," wrote researchers from the Wellcome Trust Case Control Consortium in a study published March 31 in Nature.

Formed during glitches in gene duplication, CNVs cover as much space on the genome as standard gene mutations, in which individual letters of the genetic code are mixed up.

Standard gene mutations don't appear to explain much of the heredity that clearly exists in many common diseases, a phenomenon that scientists call "missing heritability." To find whether CNVs might play a part, Wellcome Trust researchers comparedCNVs in the genomes of 3,000 healthy people with CNVs in the genomes of 16,000 patients. The patients were equally divided among people with type 1 and type 2 diabetes, bipolar disorder, rheumatoid arthritis, breast cancer, high blood pressure, heart disease and Crohn's disease.

But when the numbers were crunched, CNVs were cleared. No individual CNVs had a powerful effect on disease, nor did large numbers of them.

Though some rare CNVs are linked to disease, and more remain to be found, the bulk appear to do nothing, wrote the researchers.

The missing heritability is still at large.

Image: Mike Towber/Flickr

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Citation: "Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls." By the Wellcome Trust Case Control Consortium. Nature, Vol. 464 No. 7289, April 1, 2010.

Brandon Keim's Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecological tipping points.

10 Years on, ‘The Genome Revolution Is Only Just Beginning’

Posted: 31 Mar 2010 11:13 AM PDT

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Almost 10 years after the celebrated completion of the human genome's first draft, the expected revolution in medicine and research has only partly come to pass.

The human genome's sequencing has profoundly influenced basic research and the refinement of genome-reading tools. But those advances have had only limited medical impacts.

"The promise of a revolution in human health remains quite real," wrote Francis Collins, director of the National Institutes of Health, in an essay published March 31 in Nature. "Those who somehow expected dramatic results overnight may be disappointed."

Collins' commentary is one of four published this week in Nature in anticipation of the human genome's upcoming 10th anniversary, which officially falls on June 26. On that date in 2000, Collins — then the head of the NIH's National Human Genome Research Institute — met in the White House with Craig Venter, founder of Celera Genomics, and President Bill Clinton.

In the same room that Merriweather Lewis and William Clark presented Thomas Jefferson with a map of the Louisiana Purchase territories, the researchers announced that the human genome's three billion base pairs of DNA had been mapped. "Humankind is on the verge of gaining immense, new power to heal," proclaimed Clinton. "It will revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases."

Mostly lost in the ceremony was the fact that the genome sequence was not truly complete, but only a first draft. About 10 percent of it hadn't yet been read. The parts that had been read, still needed to be verified. Reading the genome had required its breakup into thousands of manageable chunks that needed to be reassembled. Ewan Birney, a Sanger Center geneticist and leader of a group involved in the sequencing, compared the moment to "being given the best book in the world, but it's in Russian, and it's incredibly boring to read."

The human genome's sequencing wasn't formally completed until 2003. Since then, it has guided researchers in investigations of human development and disease. Some of their investigations have yielded new tests and drug targets and insights into the basis of human disease and development. But they've also revealed just how complicated human biology is, and how much remains to be understood.

"Wisely, the president did not attach timetables to his bold predictions," wrote Collins in Nature.

Perhaps the greatest genomic advances of the last decade involve tools. The Human Genome Project — the Collins-led governmental side of the genome-sequencing race, with Venter leading the private side — commenced only when the cost of reading DNA finally approached $1 per unit, or $3 billion for a whole genome. A comparable genome sequence now costs less than $10,000. What took years to complete can be done in a day.

Better tools have driven other genomic advances. The International HapMap project was formed in 2002, and compared the genomes of several hundred people from around the world. This produced a map of genomic hotspots where people — any two of whom are roughly 99 percent identical at the genetic level —are most likely to have DNA differences. This helps researchers narrow their focus on genes involved in disease.

Researchers have also learned that just 1.5 percent of all human genes code for the proteins that make up our cells and tissues. As for what the rest are doing, they are still learning. In 2003, the NIH started the Encyclopedia of DNA Elements, or ENCODE, which supports researchers in identifying functions for the rest of our genes.

Many genes control when protein-coding genes are turned on and off at different places and times in the body, adding a whole new layer of complexity to the genome. This field of study is called epigenomics, and many researchers think it's just as important as genomics. The NIH's Roadmap Epigenomics Program started just two years ago.

Scientists hope these projects will fill the massive gaps that remain in current genetic explanations for most common diseases. Even after the publication of hundreds of genome-wide association studies —the gold standard of disease gene hunting, in which thousands of genomes are scanned and compared —scientists can explain only a fraction of the heritability that clearly exists in common diseases and conditions.

"The ability to make meaningful predictions is still quite limited," wrote Collins. Indeed, personalized genomics companies like 23andMe, Navigenics and deCODE have struggled, as the novelty of genomic information gives way to a realization that it's still of limited medical use.

But all for all that turn-of-the-millennium expectations have been tempered, the genomic age has produced significant medical advances. Analyses of gene disturbances in cancer tissues have produced several promising drugs. Testing for breast cancer mutations is now common. Individual response to about a dozen drugs can be predicted. And even if the big picture isn't yet clear, researchers have thousands of new gene targets, each a providing a foothold on the path to understanding. For some complex diseases, such as schizophrenia, researchers are now looking at genes and physiological systems they never suspected were involved.

Making sense of massive new genomic datasets has fueled the growth of systems biology, now one of the hottest areas of science. And all this research is shaped by another legacy of the genome's sequencing: what Collins calls "the radical ethic of immediate data deposit." Knowledge of the human genome wasn't scattered and hoarded. It was freely shared with any researcher who wanted it.

"My students can gather certain types of experimental data 1,000 and even 10,000 times faster than I could 40 years ago," wrote Robert Weinberg, a Whitehead Institute geneticist, in Nature.

As Venter, now the leader of the eponymous J. Craig Venter Institute, responsible for the designing the first synthetic genome, concluded his essay: "The genome revolution is only just beginning."

Image: A section of the printed human genome/Adam Nieman/Flickr

See Also:

Citations: "Has the revolution arrived?" By Francis Collins. Nature, Vol. 464 No. 7289, April 1, 2010.

"Multiple personal genomes await." By J. Craig Venter. Nature, Vol. 464 No. 7289, April 1, 2010.

"Dive in, the data's lovely." By Todd Golub. Nature, Vol. 464 No. 7289, April 1, 2010.

"Don't forget the hypotheses." By Robert Weinberg. Nature, Vol. 464 No. 7289, April 1, 2010.

Brandon Keim's Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecological tipping points.