DIGITIZING THE TREE OF LIFE COULD FINALLY IDENTIFY THOUSANDS OF NEW SPECIES
Over the past 20 years, Richard Pyle figures he’s discovered 100 new species of fish. But he’s identified only one fifth of them. Pyle, an ichthyologist at Bishop Museum in Hawaii, isn’t a slacker—he spent hundreds of hours tracking down those fish. It’s just that proving that a new species is unique can be as tough as finding it in the first place.
“There are literally thousands of new species sitting in storage at museums,” says Quentin Wheeler, a renowned taxonomist and founder of the International Institute for Species Exploration at Arizona State University. Identifying these species isn’t just to satisfy curiosity; we need a clear understanding of species in order to best organize conservation efforts. Here’s the snag: To verify a new species, a taxonomist must examine the type specimens—the preserved representative samples of every known plant and animal—of each similar existing species to document the differences. Some animals must be compared with hundreds of specimens, and those might be anywhere in the world. Many are too fragile to ship. But Wheeler thinks he has a solution that could dramatically speed up the classification and identification of species.
This month, Wheeler and his collaborators at Microsoft and the Woods Hole Oceanographic Institution in Massachusetts applied for National Science Foundation funding to create digital type specimens—“e-types”—for the more than one million known insects. To generate an e-type, a curator will simply slide the bug into a custombuilt scanner that will take 100 or so 20-megapixel images and stitch them into a three-dimensional model using Microsoft’s Photosynth software. With a dozen of these machines working through the archives of the world’s natural-history museums, Wheeler expects that the effort could digitize all the insects in five years and, with additional funding and projects, the rest of the world’s 1.8 million known species within a decade. Every year, taxonomists introduce about 20,000 species. In the same period, an estimated 30,000 vanish. At that rate, the majority of Earth’s inhabitants could disappear before they’re known to science. Simply by making it easier to examine existing organisms, Wheeler says his project will help bump the species description rate to 200,000 a year—a clip that could make it possible to name the world’s commonly estimated 20 million unknown species within 50 years.
Some scientists, however, think even e-types won’t get the job done fast enough. Genetic testing, they argue, is the key. Leading this movement is Canadian evolutionary biologist Paul Hebert, who wants to assign every species a DNA “bar code” based on variations in a gene that nearly all organisms possess. A new species would be identified not by its physical divergence from existing type specimens but by the difference between its bar code and all the others. Because the system is fast and cheap—the technique requires basic laboratory skills and can process 95 samples in two hours for $10 apiece—Hebert says it could uncover every unknown plant and animal by 2025. But bar-coding is fast and cheap because it uses just one piece of one gene—and that makes it prone to errors. In 2008, Pyle made a definitive distinction between two new fish species, even though their bar codes were essentially identical. “It’s a blunt instrument,” Wheeler says of the DNA system. “One gene just isn’t sufficient.” Looking at actual specimens is an art, he says. Plus, it’s fun. Although he admits that someday it might be possible to define new species using only DNA, he doesn’t like that idea much: “That would make taxonomy too boring to be worth doing.”—PAT WALTERS
Source of Information : Popular Science February 2010
Showing posts with label Research. Show all posts
Showing posts with label Research. Show all posts
Friday, March 5, 2010
Thursday, October 8, 2009
Surviving in the Suburbs
A fossil search for why some critters made it past the dinosaur-killing event BY CHARLES Q. CHOI
Outside Freehold, N.J.—The water is icy cold and the stone is slippery as I wade in up to my calves. Along the banks of this slow-flowing stream, guarded by prickly brambles, lies one of the richest caches of fossils dating back to the extinction that claimed the dinosaurs. The remains of marine creatures buried here, kept secret to prevent looting, tell an unusual tale: rather than dying off 65 million years ago, these creatures lived on afterward, albeit briefly. The discovery is causing scientists to rethink why some creatures survived the socalled KT extinction while others did not. Unlike this one, significant fossil sites tend to be found in exotic locales such as the searing hot Gobi Desert or the windswept pampas of Patagonia, areas remote from the kind of urban development that can ruin them. “You don’t expect to fi nd them here in suburban New Jersey some 90 minutes away from New York City,” explains Neil Landman, curator of fossil invertebrates at the American Museum of Natural History.
The fossils here are not of dinosaurs, but ammonites. These cousins of squid and octopus were the iconic marine animals of the age of dinosaurs, flourishing worldwide for 300 million years or more before the KT extinction wiped them out. They bore shells that often resembled those of nautiluses, which rapidly evolved into hundreds of different shapes, ornamented with undulations and bumps.
Amateur paleontologist Ralph Johnson, a New Jersey park ranger, discovered ammonites in this stream in 2003 when construction workers exposed them while setting up bridge foundations. The site is now kept quiet from all but scientists—poachers have already trawled nearby areas, on the prowl for fossil shark teeth. Although this shallow, inconspicuous creek has no formal name on maps, after enduring many thorns on the way there, Landman and his team dubbed it Agony Creek.
At the time of the KT extinction, the water level at this site was some 30 meters higher than it is now. Landman investigates the iron-rich glauconite rocks here with his colleagues and students from the museum’s graduate school, using iron spikes and sledgehammers to knock off slabs that are picked apart with screwdrivers and fingers. They find the fossil bed rich with dozens of species of marine invertebrates, such as crabs, snails, clams, sea urchins, large flat oysters and ammonites, as well as fish teeth and scales.
Past digs unearthed ammonite shells up to some 35 centimeters wide. These lay amid pinna, triangular bivalves that all died here relatively undisturbed: they jut upward as they would have been posed in life. Their position suggests they were all snuffed out rapidly, “perhaps by a Pompeii-like disaster, like a pulse of mud,” Landman says. To see if these deaths were linked with the KT extinction, the researchers tested for iridium, the rare metal found throughout the world near the KT boundary, thought by most to be evidence of a cosmic impact.
Unexpectedly, the researchers discovered that the iridium was laid down before the pinna layer, which means that the ammonites and other creatures there died after the event “by 10 to maybe 100 years,” Landman concludes. Their survival runs “counter to everything we’ve been taught,” he adds. He plans to go to a site in Denmark to retrieve more potential evidence of ammonite survival past KT.
Their existence in the post-KT world raises a host of questions. “If they made it through this event like they did through other mass extinctions, why didn’t they take off again?” asks invertebrate paleontologist Peter Harries of the University of South Florida. “Why did the ancestors of the modern nautiluses make it through and not the ammonites? That’s extremely intriguing to me, and the broader message to me is that mass-extinction events are much more complex than we think.”
The trove’s proximity to cities is a bit of a double-edged sword. “In Mongolia, you don’t really have the danger that a good site today might be paved over by asphalt tomorrow, and you can’t walk into people’s backyards,” Landman remarks. “But who knows if we could have found this site otherwise without urban development.”
Source of Information : Scientific American September 2009
Outside Freehold, N.J.—The water is icy cold and the stone is slippery as I wade in up to my calves. Along the banks of this slow-flowing stream, guarded by prickly brambles, lies one of the richest caches of fossils dating back to the extinction that claimed the dinosaurs. The remains of marine creatures buried here, kept secret to prevent looting, tell an unusual tale: rather than dying off 65 million years ago, these creatures lived on afterward, albeit briefly. The discovery is causing scientists to rethink why some creatures survived the socalled KT extinction while others did not. Unlike this one, significant fossil sites tend to be found in exotic locales such as the searing hot Gobi Desert or the windswept pampas of Patagonia, areas remote from the kind of urban development that can ruin them. “You don’t expect to fi nd them here in suburban New Jersey some 90 minutes away from New York City,” explains Neil Landman, curator of fossil invertebrates at the American Museum of Natural History.
The fossils here are not of dinosaurs, but ammonites. These cousins of squid and octopus were the iconic marine animals of the age of dinosaurs, flourishing worldwide for 300 million years or more before the KT extinction wiped them out. They bore shells that often resembled those of nautiluses, which rapidly evolved into hundreds of different shapes, ornamented with undulations and bumps.
Amateur paleontologist Ralph Johnson, a New Jersey park ranger, discovered ammonites in this stream in 2003 when construction workers exposed them while setting up bridge foundations. The site is now kept quiet from all but scientists—poachers have already trawled nearby areas, on the prowl for fossil shark teeth. Although this shallow, inconspicuous creek has no formal name on maps, after enduring many thorns on the way there, Landman and his team dubbed it Agony Creek.
At the time of the KT extinction, the water level at this site was some 30 meters higher than it is now. Landman investigates the iron-rich glauconite rocks here with his colleagues and students from the museum’s graduate school, using iron spikes and sledgehammers to knock off slabs that are picked apart with screwdrivers and fingers. They find the fossil bed rich with dozens of species of marine invertebrates, such as crabs, snails, clams, sea urchins, large flat oysters and ammonites, as well as fish teeth and scales.
Past digs unearthed ammonite shells up to some 35 centimeters wide. These lay amid pinna, triangular bivalves that all died here relatively undisturbed: they jut upward as they would have been posed in life. Their position suggests they were all snuffed out rapidly, “perhaps by a Pompeii-like disaster, like a pulse of mud,” Landman says. To see if these deaths were linked with the KT extinction, the researchers tested for iridium, the rare metal found throughout the world near the KT boundary, thought by most to be evidence of a cosmic impact.
Unexpectedly, the researchers discovered that the iridium was laid down before the pinna layer, which means that the ammonites and other creatures there died after the event “by 10 to maybe 100 years,” Landman concludes. Their survival runs “counter to everything we’ve been taught,” he adds. He plans to go to a site in Denmark to retrieve more potential evidence of ammonite survival past KT.
Their existence in the post-KT world raises a host of questions. “If they made it through this event like they did through other mass extinctions, why didn’t they take off again?” asks invertebrate paleontologist Peter Harries of the University of South Florida. “Why did the ancestors of the modern nautiluses make it through and not the ammonites? That’s extremely intriguing to me, and the broader message to me is that mass-extinction events are much more complex than we think.”
The trove’s proximity to cities is a bit of a double-edged sword. “In Mongolia, you don’t really have the danger that a good site today might be paved over by asphalt tomorrow, and you can’t walk into people’s backyards,” Landman remarks. “But who knows if we could have found this site otherwise without urban development.”
Source of Information : Scientific American September 2009
Wednesday, October 7, 2009
Animals by the Numbers
Counting may be an innate ability among many species BY MICHAEL TENNESEN
Scientists have been skeptical of claims of mathematical abilities in animals ever since the case of Clever Hans about 100 years ago. The horse, which performed arithmetic and other intellectual tasks to delighted European audiences, was in reality simply taking subconscious cues from his trainer. Modern examples, such as Alex the African grey parrot, which could count up to six and knew sums and differences, are seen by some as special cases or the product of conditioning.
Recent studies, however, have uncovered new instances of a counting skill in different species, suggesting that mathematical abilities could be more fundamental in biology than previously thought. Under certain conditions, monkeys could sometimes outperform college students.
In a study published last summer in the Proceedings of the Royal Society B, Kevin C. Burns of Victoria University of Wellington in New Zealand and his colleagues burrowed holes in fallen logs and stored varying numbers of mealworms (beetle larvae) in these holes in full view of wild New Zealand robins at the Karori Wildlife Sanctuary. Not only did the robins flock first to the holes with the most mealworms, but if Burns tricked them, removing some of the insects when they weren’t looking, the robins spent twice as long scouring the hole for the missing mealworms. “They probably have some innate ability to discern between small numbers” as three and four, Burns thinks, but they also “use their number sense on a daily basis, and so through trial and error, they can train themselves to identify numbers up to 12.”
More recently, in the April issue of the same Royal Society journal, Rosa Rugani of the University of Trento in Italy and her team demonstrated arithmetic in newly hatched chickens. The scientists reared the chicks with five identical objects, and the newborns imprinted on these objects, considering them their parents. But when the scientists subtracted two or three of the original objects and left the remainders behind screens, the chicks went looking for the larger number of objects, sensing that Mom was more like a three and not a two. Rugani also varied the size of the objects to rule out the possibility the chicks were identifying groups based simply on the fact that larger numbers of items take up more space than smaller numbers.
For the past five years Jessica Cantlon of the University of Rochester has been conducting a series of experiments with rhesus monkeys that shows how their numerical skills can rival those of humans. The monkeys, she found, could choose the lesser of two sets of objects when they were the same in size, shape and color. And when size, shape and color were varied, the monkeys showed no change in accuracy or reaction time. One animal, rewarded with Kool-Aid, was 10 to 20 percent less accurate than college students but beat them in reaction time. “The monkey didn’t mind missing every once in a while,” Cantlon recounts. “It wants to get past the mistake and on to the next problem where it can get more Kool-Aid, whereas college students can’t shake their worry over guessing wrong.”
Elizabeth Brannon of Duke University has conducted similar experiments with rhesus monkeys, getting them to match the number of sounds they hear to the number of shapes they see, proving they can do math across different senses. She also tested the monkeys’ ability to do subtraction by covering a number of objects and then removing some of them. In all cases, the monkeys picked the correct remainder at a rate greater than chance. And although they might not grasp the deeper concept of zero as a number, the monkeys knew it was less than two or one, conclude Brannon and her colleagues in the May Journal of Experimental Psychology: General.
Although Brannon feels that animals do not have a linguistic sense of numbers— they aren’t counting “one, two, three” in their heads—they can do a rough sort of math by summing sets of objects without actually using numbers, and she believes that ability is innate. Brannon thinks that it might have evolved from the need for territorial animals “to access the different sizes of competing groups and for foraging animals to determine whether it is good to stay in one area given the amount of food retrieved versus the amount of time invested.”
Irene Pepperberg of the Massachusetts Institute of Technology, famous for her 30-year work with Alex the parrot, says that even bees can learn to discriminate among small quantities. “So some degree of ‘number sense’ seems to be able to be learned even in invertebrates, and such learning is unlikely without some underlying neural architecture on which it is based,” she remarks.
Understanding the biological basis of number sense in animals could have relevance to people. According to Brannon, it may suggest to childhood educators that math, usually taught after age four or five, could actually be introduced earlier into the curriculum.
Source of Information : Scientific American September 2009
Scientists have been skeptical of claims of mathematical abilities in animals ever since the case of Clever Hans about 100 years ago. The horse, which performed arithmetic and other intellectual tasks to delighted European audiences, was in reality simply taking subconscious cues from his trainer. Modern examples, such as Alex the African grey parrot, which could count up to six and knew sums and differences, are seen by some as special cases or the product of conditioning.
Recent studies, however, have uncovered new instances of a counting skill in different species, suggesting that mathematical abilities could be more fundamental in biology than previously thought. Under certain conditions, monkeys could sometimes outperform college students.
In a study published last summer in the Proceedings of the Royal Society B, Kevin C. Burns of Victoria University of Wellington in New Zealand and his colleagues burrowed holes in fallen logs and stored varying numbers of mealworms (beetle larvae) in these holes in full view of wild New Zealand robins at the Karori Wildlife Sanctuary. Not only did the robins flock first to the holes with the most mealworms, but if Burns tricked them, removing some of the insects when they weren’t looking, the robins spent twice as long scouring the hole for the missing mealworms. “They probably have some innate ability to discern between small numbers” as three and four, Burns thinks, but they also “use their number sense on a daily basis, and so through trial and error, they can train themselves to identify numbers up to 12.”
More recently, in the April issue of the same Royal Society journal, Rosa Rugani of the University of Trento in Italy and her team demonstrated arithmetic in newly hatched chickens. The scientists reared the chicks with five identical objects, and the newborns imprinted on these objects, considering them their parents. But when the scientists subtracted two or three of the original objects and left the remainders behind screens, the chicks went looking for the larger number of objects, sensing that Mom was more like a three and not a two. Rugani also varied the size of the objects to rule out the possibility the chicks were identifying groups based simply on the fact that larger numbers of items take up more space than smaller numbers.
For the past five years Jessica Cantlon of the University of Rochester has been conducting a series of experiments with rhesus monkeys that shows how their numerical skills can rival those of humans. The monkeys, she found, could choose the lesser of two sets of objects when they were the same in size, shape and color. And when size, shape and color were varied, the monkeys showed no change in accuracy or reaction time. One animal, rewarded with Kool-Aid, was 10 to 20 percent less accurate than college students but beat them in reaction time. “The monkey didn’t mind missing every once in a while,” Cantlon recounts. “It wants to get past the mistake and on to the next problem where it can get more Kool-Aid, whereas college students can’t shake their worry over guessing wrong.”
Elizabeth Brannon of Duke University has conducted similar experiments with rhesus monkeys, getting them to match the number of sounds they hear to the number of shapes they see, proving they can do math across different senses. She also tested the monkeys’ ability to do subtraction by covering a number of objects and then removing some of them. In all cases, the monkeys picked the correct remainder at a rate greater than chance. And although they might not grasp the deeper concept of zero as a number, the monkeys knew it was less than two or one, conclude Brannon and her colleagues in the May Journal of Experimental Psychology: General.
Although Brannon feels that animals do not have a linguistic sense of numbers— they aren’t counting “one, two, three” in their heads—they can do a rough sort of math by summing sets of objects without actually using numbers, and she believes that ability is innate. Brannon thinks that it might have evolved from the need for territorial animals “to access the different sizes of competing groups and for foraging animals to determine whether it is good to stay in one area given the amount of food retrieved versus the amount of time invested.”
Irene Pepperberg of the Massachusetts Institute of Technology, famous for her 30-year work with Alex the parrot, says that even bees can learn to discriminate among small quantities. “So some degree of ‘number sense’ seems to be able to be learned even in invertebrates, and such learning is unlikely without some underlying neural architecture on which it is based,” she remarks.
Understanding the biological basis of number sense in animals could have relevance to people. According to Brannon, it may suggest to childhood educators that math, usually taught after age four or five, could actually be introduced earlier into the curriculum.
Source of Information : Scientific American September 2009
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