Thursday, 1 October 2009

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Throwaway GPS Info Reveals Snow Depth Data

Posted: 01 Oct 2009 10:11 AM PDT


GPS receivers installed to measure the movements of tectonic plates and help you find tacos could find yet another purpose: measuring snow depth.

By analyzing the way the GPS signals are transformed as they travel through snowpack, a team of scientists from the University of Colorado, Boulder, may have found a cheap, easy way to optimize an important variable in climate models.

"It'll be hard, but it looks pretty good so far," said Kristine Larson, a GPS specialist at CU, and lead author of a paper on the technique published earlier this month in Geophysical Research Letters.

Her team, basically, is using waste data from the global positioning process. When a wave leaves a GPS satellite heading for a receiver, not all of it reaches the antenna directly. Some of it bounces off the ground around the actual antenna. For standard GPS purposes, people try to suppress this "multipath" signal, but Larson realized it could yield valuable information about the surfaces it's hitting. A few years ago, they trialed measuring soil moisture data based on the reflectivity of the ground. Snow, theoretically, should reduce the frequency of the multipath wave.

"It's one thing to say that you used a signal from a GPS satellite to estimate the depth of the snow, but unless I go out there with a yardstick and say this is 18 inches of snow, you don't know," Larson said.

So, after securing a seed grant and setting up the experiment, she went out there with a yardstick, husband and 10-year old son in tow. They drove out on Highway 36, past the Costco, and took measurements of snow depth and density. Though it might not have been the most glamorous fieldwork, it revealed two very important problems with existing measurement systems like the National Weather and Climate Center's SNOTEL sensor network.

First, point measurements — no matter how accurate — do not account well for snow-depth variability due to wind or other hyperlocal conditions.

"The snowpack can be 12 inches here and you walk one foot and it can be 18 inches there," Larson said. "That's your signal plus or minus 50 percent."

GPS can measure a wider area than any current ground-based method, allowing it to account for that variability. Theoretically, one could measure snow depth from space and get very broad area coverage. Unfortunately, no current satellite can do it. And any space-based system would be vastly more expensive and have a relatively limited life-span, maybe five years.

Second, climate modelers aren't interested in snow depth in the way that a skier might be. Really, what they're after is how much water is locked up in the snow. To calculate that, you need both the depth and the density of the pack. Right now, the best way to get snow density remains low-tech.

"We literally took plastic piping that you'd use in your house and you put that into the snow, then cover up the bottom, then you pull it up," Larsen said. "Then you wait for it to melt."

A little bit of high school math later, and you've got a density measurement for the snow in the PVC pipe. By matching up GPS signals with those density measurements, you can calibrate a model that yields snow density from GPS information alone. With the depth and density in hand, you can calculate the snow-water equivalent data that climate modelers covet.

Someday soon, the hundreds of GPS receivers scattered around the world's wintery wonderlands could be sending out snow data. It's about as close to getting something for nothing as a scientist could hope for.

"You've got to convince people that are measuring what you say you're measuring. You have to have people with sticks. You have to have ultrasonic snow-depth sensors," she said. "I'm not there yet, but it's a good first step."


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WiSci 2.0: Alexis Madrigal's Twitter, Google Reader feed, and green tech history research site; Wired Science on Twitter and Facebook.

Humanity Has a New 4.4 Million-Year-Old Baby Mama

Posted: 01 Oct 2009 07:54 AM PDT


As of today, humankind may have a new mother, and she looks nothing like we expected her to.

Described in a series of papers published Thursday in Science, Ardi —short for Ardipithecus ramidus — likely walked upright one million years before Lucy, the famous fossil skeleton whose species was regarded as the first member of the human lineage.

That position now belongs to Ardi, and the reconfiguration of our family tree is not merely cosmetic. Lucy's story placed humanity's origin on the savannah; Ardi took her first steps in the forest. From the shape of Lucy's bones, scientists reasoned that the last common ancestor of humans and other great apes had resembled a chimpanzee; Ardi does not.

"This is a landmark," said Dean Falk, a University of Florida evolutionary anthropologist who reviewed the findings. "The field will go into a frenzy."

Falk's assessment was echoed by paleontologists around the world, who have waited for15 years since a handful of 4.4 million-year-old fossils, belonging to an unknown hominid species, were found in sediments along the Awash River in Ethiopia.

Even then, the fossils were clearly special. The name of the species, chosen by paleontologist discoverers Tim White, Gen Suwa and Berhane Asfaw of the Middle Awash Project, means "root ground ape" in local dialect. The fossils likely "represent a long-sought potential root species for the Hominidae," they wrote in a 1994 Nature paper.

From that original site, the Middle Awash team has since collected hundreds more A. ramidus fragments from 35 individuals, including a partially complete skeleton of the 4-foot-tall, 110-pound female now known as Ardi.

familytreeThe researchers' original assessment is not strictly correct: Ardi's A. ramidus preceded Lucy's Australopithecus afarensis, but some of her ancestors had already branched several million years earlier into a lineage that ends, for the moment, in chimpanzees and bonobos. But even if A. ramidus isn't at the root of all hominids, it's likely at the root of those hominids who became human.

Ardi "occupied the basal adaptive plateau of hominid natural history," wrote the researchers in one of the Science papers, and "is so rife with anatomical surprises that no one could have imagined it without direct fossil evidence."

ardi11hrLacking arches, and with thumb-like big toes, A. ramidus had grasping feet still fitted for tree-climbing, but its pelvis appears suited to walking upright. And though A. ramidus' teeth were appropriate for eating fruits and leaves, they also display evidence of root and insect consumption. Ardiappears adapted to life both in the branches and on the ground.

That interpretation fits the environment implied by thousands of plant and animal fossils, as well as ancient soil deposits, also collected at the site. Most belonged to residents of woodlands, not grasslands: whereas Lucy ventured onto the savannah, Ardi lived in a world of patchy, sun-dappled forests.

The savannah-as-cradle narrative is not the only conventional wisdom upset by Ardi. From Darwin on, most scientists thought that the last common ancestor of humans, chimpanzees and gorillas would be chimp-like. The discovery that chimps share 99 percent of our DNA, and possess many of the skeletal features found in Lucy, supported this.

But A. ramidus lacks many typical features of chimpanzees, including large male canine teeth — a sign, say the researchers, that the ultra-aggressive social behaviors seen in chimpanzees were lost early in the human lineage. If so, male A. ramidus may have competed for female attention by bringing them food, rather than fighting each other. That could have contributed to the evolution of pair-bonding behavior, which later took the form of monogamous reproductive relationships. Ardi's hands and pelvis were relatively human-like; so, perhaps, was her heart.

All this suggests that chimpanzees and other great apes have changed far more than thought since we split from them, and are perhaps not the near-human analogues that scientists presumed.

"One effect of chimpanzee-centric models of human evolution has been a tendency to view Australopithecus as transitional between an ape-like ancestor and early Homo. Ardipithecus ramidus nullifies these presumptions," wrote C. Owen Lovejoy, a Kent State University anthropologist, in Science. "No ape exhibits an even remotely similar evolutionary trajectory to that revealed by Ardipithecus."

William Jungers, a Stony Brook University paleoanthropologist, called the fossils "incredibly important."

He disagreed with the researchers' interpretation of A. ramidus' ability to walk upright —a skepticism seconded by Falk —but stressed the difference between this research and the hoopla that followed Ida, a 47 million-year-old lemur whose evolutionary importance was overhyped in May.

The fossils "will be intensely scrutinized and debated foryears to come," said Jungers. "The Ardipithecus saga impacts many aspects of human evolutionin genuinely profound ways."

Images: Science

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Citations: "Ardipithecus ramidus and the Paleobiology of Early Hominids." By Tim D. White, Berhane Asfaw, Yonas Beyene, Yohannes Haile-Selassie, C. Owen Lovejoy, Gen Suwa, Giday WoldeGabriel. Science, Vol. 326, No. 5949.

"Reexamining Human Origins in Light of Ardipithecus ramidus." By C. Owen Lovejoy. Science, Vol. 326, No. 5949.

"The Great Divides: Ardipithecus ramidus Reveals the Postcrania of Our Last Common Ancestors with African Apes." By C. Owen Lovejoy, Gen Suwa, Scott W. Simpson, Jay H. Matternes, Tim D. White. Science, Vol. 326, No. 5949.

"Combining Prehension and Propulsion: The Foot of Ardipithecus ramidus." By C. Owen Lovejoy, Bruce Latimer, Gen Suwa, Berhane Asfaw, Tim D. White. Science, Vol. 326, No. 5949.

"The Pelvis and Femur of Ardipithecus ramidus: The Emergence of Upright Walking." By C. Owen Lovejoy, Gen Suwa, Linda Spurlock, Berhane Asfaw, Tim D. White. Science, Vol. 326, No. 5949.

"Careful Climbing in the Miocene: The Forelimbs of Ardipithecus ramidus and Humans Are Primitive." By C. Owen Lovejoy, Scott W. Simpson, Tim D. White, Berhane Asfaw, Gen Suwa. Science, Vol. 326, No. 5949.

"The Ardipithecus ramidus Skull and Its Implications for Hominid Origins." By Gen Suwa, Berhane Asfaw, Reiko T. Kono, Daisuke Kubo, C. Owen Lovejoy, Tim D. White. Science, Vol. 326, No. 5949.

"Paleobiological Implications of the Ardipithecus ramidus Dentition." By Gen Suwa, Reiko T. Kono, Scott W. Simpson, Berhane Asfaw, C. Owen Lovejoy, Tim D. White. Science, Vol. 326, No. 5949.

"Macrovertebrate Paleontology and the Pliocene Habitat of Ardipithecus ramidus." By Tim D. White, Stanley H. Ambrose, Gen Suwa, Denise F. Su, David DeGusta, Raymond L. Bernor, Jean-Renaud Boisserie, Michel Brunet, Eric Delson, Stephen Frost, Nuria Garcia, Ioannis X. Giaourtsakis, Yohannes Haile-Selassie, F. Clark Howell, Thomas Lehmann, Andossa Likius, Cesur Pehlevan, Haruo Saegusa, Gina Semprebon, Mark Teaford, Elisabeth Vrba. Science, Vol. 326, No. 5949.

"Taphonomic, Avian, and Small-Vertebrate Indicators of Ardipithecus ramidus Habitat." By Antoine Louchart, Henry Wesselman, Robert J. Blumenschine, Leslea J. Hlusko, Jackson K. Njau, Michael T. Black, Mesfin Asnake, Tim D. White. Science, Vol. 326, No. 5949.

"The Geological, Isotopic, Botanical, Invertebrate, and Lower Vertebrate Surroundings of Ardipithecus ramidus." Giday WoldeGabriel, Stanley H. Ambrose, Doris Barboni, Raymonde Bonnefille, Laurent Bremond, Brian Currie, David DeGusta, William K. Hart, Alison M. Murray, Paul R. Renne, M. C. Jolly-Saad, Kathlyn M. Stewart, Tim D. White. Science, Vol. 326, No. 5949.

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

Tamiflu in Rivers Could Breed Drug-Resistant Flu Strains

Posted: 30 Sep 2009 05:10 PM PDT


The premier flu-fighting drug is contaminating rivers downstream of sewage-treatment facilities, researchers in Japan confirm. The source: urinary excretion by people taking oseltamivir phosphate, best known as Tamiflu.

sciencenewsConcerns are now building that birds, which are natural influenza carriers, are being exposed to waterborne residues of Tamiflu's active form and might develop and spread drug-resistant strains of seasonal and avian flu.

For their new study, Gopal Ghosh and his colleagues at Kyoto University sampled water discharged from three local sewage treatment plants and water at several points along two rivers into which the treated water flowed. Sampling started early in December 2008, as flu season got underway. The researchers sampled again at the height of the seasonal flu's onslaught in early February and again as infection rates waned.

Tamiflu's active form, oseltamivir carboxylate or OC, turned up in the treated sewage on every occasion, the researchers report online September 28 in Environmental Health Perspectives. Values were in the low nanograms per liter range during the first and last samplings, and reached a high of almost 300 ng/L at one outflow during the flu's peak, a week when there were 1,738 recorded flu cases in Kyoto.

River residues showed up during only that second sampling — from low nanogram levels at most sampling points to a high of 190 ng/L in a portion of the Nishitakase River where treated sewage accounts for 90 percent of the flow.

Computer modeling has shown that OC should survive sewage treatment, notes Wolf von Tümpling Jr. of the Helmholtz Center for Environmental Research, a federal institute in Magdeburg, Germany. Ghosh's team is now the first to confirm this, he says. Von Tümpling's own data show that once exposed to sunlight, OC will break down, albeit slowly. Concentrations would fall at best by half every three weeks, he says.

If correlations predicted by earlier studies are correct, concentrations measured at some river sites in the new Kyoto study seem "high enough to lead to antiviral resistance in waterfowl," Ghosh says

And the Kyoto team didn't test during a pandemic, when Tamiflu prescription rates might be 10 times higher, von Tümpling notes.

Indeed, the expected coincident hits by seasonal and H1N1 swine flu this winter, could send Tamiflu use skyrocketing. In a July 14 letter, Food and Drug Administration deputy commissioner Joshua Sharfstein noted that "there is no adequate, approved and available alternative to the emergency use of certain oseltamivir phosphate products for the treatment and prophylaxis of influenza."

Once ingested, virtually all Tamiflu will end up in the environment in the active form, notes environmental chemist Jerker Fick of Umeå University in Sweden. The reason: Tamiflu becomes active once the body converts it into a carboxylate form. Roughly 80 percent of an ingested dose becomes this OC, which the body eventually excretes. The body sheds the remaining 20 percent of Tamiflu in its original form, but this phosphate form is immediately turned into the active, carboxylate form when it reaches a water treatment plant, he says.

Two years ago, Fick's team published data showing that most sewage-treatment technologies will remove "zero percent" of any OC present. And ducks love hanging out around warm, nutrient-rich outflows of treated water during winter-flu season. While sampling for waterborne OC last year in Japan, "I saw it myself," he says.

If Tamiflu resistance does develop in exposed birds, the affected flu strains will probably be conventional seasonal and avian flu strains, which claim thousands of lives each year, and not H1N1. That's because H1N1 seems to bypass birds as it spreads among people, notes William Schaffner, chair of preventive medicine at the Vanderbilt University School of Medicine in Nashville, Tenn.

He also notes that U.S. policy is more conservative than Japan's when it comes to Tamiflu use. Federal guidelines, he says, recommend that "Tamiflu be reserved for treatment of the very sick and anyone who is immunocompromised."

Image: Flickr/Karmor

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Do Polynesian Canoes Evolve Like Finch Beaks?

Posted: 30 Sep 2009 01:44 PM PDT


Despite the popularity of cultural evolution as an idea, with cultures as organisms and memes as genes, the actual science has lagged.

But by applying the tools of population genetics to Polynesian boat designs, researchers show that cultural evolution might be studied as rigorously as the beaks of finches.

"Evolution is a logical way of looking at change over time," said Deborah Rogers, a Stanford University evolutionary biologist. "There's nothing inherently biological about it. The logic can be applied to cultural change. Biology was just the first place that people ran with it."

Working with fellow Stanford researchers Marcus Feldman and Paul Ehrlich, Rogers converted archaeological records of Polynesian canoes, the design of which varied between islands and tribes, into standardized descriptions.

The structure of that dataset was described in a paper published last year in the Proceedings of the National Academy of Sciences. In the latest study, published in the November Proceedings of the Royal Society B, the researchers ran their data through a program of the sort typically used to analyze genetic information, inferring trees of relationships from patterns of inherited biological difference.

The resulting cultural tree suggests that New Zealand was at least partially settled from Hawaii, a hypothesis that fell from favor in the early 20th century. It also suggests a course of Polynesian settlement that started in the far western islands, jumped to the far eastern, then worked backwards to the original point of origin.

Those interpretations won't settle anthropological argument over Polynesian migrations, which have lasted for decades. But "what we're excited about isn't specifically what we found for Polynesia, but what we found out about our ability to use cultural data to infer historical patterns," said Rogers.

Earlier generations of anthropologists lacked both the tools of population genetics and the sheer computational power necessary for this study, which involved number-crunching through 10 million possible configurations of canoe taxonomy.

According to Rogers, their methods could be applied to anything from pottery design and fishhook construction to social and legal structures — anything that changed over time, and left a record of itself.

She next hopes to investigate the cultural evolution of class structure and social inequality.

"If culture changes based on some type of model that we can understand, we can understand where we came from," said Rogers.

Image: PNAS

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Citation: "Inferring population histories using cultural data." By Deborah S. Rogers, Marcus W. Feldman, and Paul R. Ehrlich. Proceedings of the Royal Society B, Vol. 276 No. 1674, November 7, 2009.

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

Data-Mining Medical Records Could Predict Domestic Violence

Posted: 30 Sep 2009 12:58 PM PDT


To a busy emergency physician, a split lip or a case of poisoning is just one of those things they deal with. But to a computer mining the patient's medical history, it could be the last diagnosis needed to decipher a pattern of domestic violence.

Now, a group of researchers at Harvard University has created the first computer model to automatically detect the risk that a patient is being abused at home. The results were published Sept. 29 in the British Medical Journal.

"It's a great concept," said Debra Houry, an emergency physician at Emory University, who was not involved in the research. Although around one in four women experience domestic violence at some point in their lives, she says, the problem often goes unnoticed at a doctor's visit. "It's one of those hidden epidemics where they don't come up to you and disclose the issue."

In fact, patients often try to hide the abuse, says Ben Reis, a Harvard pediatrician and computer scientist who designed the new computer model. "Abused people actually go to different emergency rooms each time, so that [the abuse] is harder to track."

To get around this problem, Reis and his colleagues tapped into a public U.S. database containing six years of medical history for around half a million people. They fed a large portion of the database into a simple computer model — known as a naïve Bayesian classifier — which then calculated the abuse risks linked to different diagnoses such as burns, sprains or mental disorders.

riskgelAt present, medical records, even electronic ones, may be hard to interpret in the limited time a physician has to see a patient. "It's usually a big, long wine list," Reis says. "We reduced the entire history to one picture."

That picture is called a risk gel. In essence, it shows the patient's medical history as a bunch of colored bars representing diagnoses made at various visits. A green bar means the diagnosis is not statistically linked to abuse, while a red bar means it is. When the computer determines that the combined abuse risk based on all diagnoses is high, it sounds the alarm, letting the physician know that a face-to-face meeting is called for. "We see this system as a screening support system," Reis said.

But screening isn't the end-all, be-all for victims of domestic violence, says Gene Feder of the University of Bristol. He recently reviewed several trials of screening programs and found that none of them measured whether or not screening led to fewer deaths and injuries among abused women.

"Is [the new computer model] suitable for implementation in in-patient hospital and ER hospital settings without further testing?" he wrote in an e-mail to "Not without suitable training for clinicians in how to ask about abuse of the designated high-risk women and how to manage the women safely."

Still, researchers agree that domestic violence is severely underdetected by health care providers. But it shows up clearly in murder stats. According to the Harvard group, domestic abuse accounts for more than half of the murders of women in the United States. And without detection, there is no chance of helping the victims.

Using the new system, the researchers were able to predict abuse an average of two years before the doctor made the diagnosis. Presumably, the computer is picking up signs of ongoing maltreatment the patient hasn't yet revealed.

The researchers also speculate that, in principle, some subtle signal could precede direct abuse. One surprise finding that could be relevant, says Reis, is that infections turned out to be strongly linked to abuse. That might suggest worsening hygiene in the family or increased psychological stress, possible omens of abuse. But at this point, it is anybody's guess whether true predictions are possible.

Predictions or not, with the current model, fewer than 20 percent of the patients flagged as high-risk cases turned out to have a diagnosis of abuse. Part of the problem may be that the system is only as good as the data it was based on. And as Emory University's Houry points out, that data isn't up to speed when it comes to diagnosing abuse.

The Harvard researchers counter that their approach shows all the more promise because it works even when based on poor, real-world data. Working on a new government grant, they are now trying to improve the model and incorporate more data, a task that will get easier as electronic medical records become widespread among health care providers.

Within four years, the group hopes to have a full-fledged system ready, including a user interface optimized for doctors. "The long-term vision is one of predictive medicine, where vast amounts of information are used to improve health care, diagnosis, screening and outcomes," says Reis.

Yet the question remains how to translate a diagnosis into action that will help the victims of abuse. "Identifying in itself is not enough," says Houry. "But I believe it helps."

Images: 1) "Treemap visualizations of abuse risk associated with different diagnostic categories (for women) / Reis et. al., BMJ. 2) Risk gel visualization /

High-Res Images of New Territory on Mercury

Posted: 30 Sep 2009 11:36 AM PDT


Flying within 228 kilometers of the surface of Mercury on September 29, the MESSENGER spacecraft snapped portraits of a portion of the planet that had never before been imaged close-up.

mercurymapsciencenewsMESSENGER also examined in greater detail Mercury's western hemisphere, which had been imaged during a previous passage in October 2008 (SN Online: 10/29/08).

The September 29 encounter was the third and last flyby and gave the craft the gravitational assistance it needs to settle in March 2011 into a yearlong orbit around Mercury, the solar system's innermost and least explored planet. The first images from the latest encounter, which detail 5 percent of the planet that hadn't been examined by spacecraft before, were released on September 30 and more are expected over the next few days.

Images: NASA/Johns Hopkins University Applied Physics Laboratory/Carnegie Institution of Washington

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