Thursday, 8 October 2009

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge

Counting Elephants by Voice

Posted: 08 Oct 2009 08:34 AM PDT


By putting microphones in the jungle, researchers are better able to perform the surprisingly tricky task of counting elephants.

Sure, pachyderm polling doesn't seem difficult. They're not exactly hard to see. But covering hundreds of square miles, day after day, requires time, money and personnel — all of which are in short supply in the developing countries where elephants live.

Enter the Elephant Listening Project at Cornell University. Using acoustic monitoring and analysis techniques originally developed for counting birds by song, they track elephants in the jungles of Central Africa.

In a paper published in the September African Journal of Ecology, project researchers describe the calibration of their model at a Central African Republic site. First they personally observed forest clearings where elephants were known to gather, counting the animals they saw and the noises they made. The researchers then turned these observations into a framework for interpreting recordings made by microphones installed throughout the forest.

The same approach "provides an opportunity to improve management and conservation of many acoustically active taxa whose populations are currently under-monitored," wrote the researchers.

In addition to being relatively inexpensive and geographically comprehensive, bioacoustic monitoring offers other advantages over traditional animal counts. It can give detailed ecological snapshots, counting anything that makes a noise.

For the elephant counts, each monitor covered a square mile of ground, "a dramatic increase in coverage over dung survey transects." In other words, it's a lot easier to listen to elephants than gather their poop.

Image: Elephant Listening Project

Via the Conservation Maven.

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Citation: "Acoustic estimation of wildlife abundance: methodology for vocal mammals in forested habitats." By Mya E. Thompson , Steven J. Schwager, Katharine B. Payne and Andrea K. Turkalo. African Journal of Ecology, Vol. 47 No. 3, September, 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.

Nobel Prize for the Chemistry of Protein Production

Posted: 07 Oct 2009 01:48 PM PDT


This year's Nobel Prize in Chemistry went to three molecular biologists who study ribosomes, the protein factories within cells.

Ribosomes were discovered in the 1950's by George Palade, who went on to win the Nobel Prize in Physiology or Medicine for his work on the makeup of cells, but scientists weren't able to take a close look at those organelles till the end of the century. Thomas Steitz, Venkatraman Ramakrishnan, and Ada Yonath developed tricks for examining the tiny structures with x-rays and electron beams. The high-resolution 3D images they acquired will help chemists develop a host of better medications.

"Scientists around the world are using the winners' research to develop new antibiotics that can be used in the ongoing battle against antibiotic-resistant microbes that cause so much illness, suffering and death." said Thomas Lane, president of the American Chemical Society, in a press release.

Dozens of antibiotics — including tetracycline and clindamycin — work by gumming up the ribosomes inside bacteria. Each of those medications is made up of relatively small molecules that can wedge themselves into crevices in the ribosome, destroying the microbes' ability to make protein, and thus rendering them helpless.

Armed with 3D images of antibiotic molecules wedged into ribosomes, medicinal chemists can refine their strategy for fighting bacteria. They can find new weak spots in bacterial ribosomes.

That approach is a lot like the way that the Rebel Alliance destroyed the first Death Star: by looking at its blueprint and finding a weak spot. Except, in this case the researchers are looking for vulnerable nooks and crannies in a blob of RNA and protein, rather than a thermal exhaust port.

Dozens of 3D images that show antibiotics sticking to ribosomes are available in the Protein DataBank, and you can look at them yourself with a tool called First Glance.

Just type the Protein DataBank ID number for the ribosome that you want to look at, and then start exploring.

Here are some of the best structures:

Ribosome with Clindamycin: 1YJN
Ribosome with Azithromycin: 1NWY
Ribosome with Erythromycin: 1JZY

Image: A ribosome reads an mRNA sequence and produces protein according to its genetic code. Credit: Lawrence Berkeley National Laboratory

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Alligator Swamps Are Lousy With Monogamy

Posted: 07 Oct 2009 01:25 PM PDT


Alligators don't seem to be the promiscuous, indiscriminate reptiles scientists once though they were. A new 10-year study of alligator mating habits shows that most female crocodilians prefer to mate over and over with the same male, despite encountering a vast array of eligible alligator bachelors each year.

As the only surviving members of a class of reptiles called archosaurs, which included dinosaurs and the ancient ancestors of birds, alligators are in a unique position to help scientists understand the mating patterns of dinosaurs and birds. For the past 10 years, ecologists have been tracking female alligators at the Rockefeller Wildlife Refuge in Louisiana and recording their mate preferences by looking at the DNA of their young. The data, published today in Molecular Ecology, reveals that up to 70 percent of female alligators choose the same partner year after year.

alligatornest"Given how incredibly open and dense the alligator population is at RWR, we didn't expect to find fidelity," biologist Stacey Lance of the Savannah River Ecology Laboratory in South Carolina said in a press release. "To actually find that 70 percent of our re-trapped females showed mate fidelity was really incredible. I don't think any of us expected that the same pair of alligators that bred together in 1997 would still be breeding together in 2005 and may still be producing nests together to this day."

Finding mate fidelity in alligators is surprising because most reptiles are polygamous, often mating with multiple partners during the same breeding year and producing young from multiple fathers. Alligators do exhibit multiple paternity — in this study, roughly 50 percent of nests contained eggs from more than one father — but surprisingly, females appeared to pick the same male (or males) year after year.

Because of the dense population of alligators at the wildlife refuge, the researchers don't think the repeat pairings were a result of chance. Instead, it appears that female alligators are actively choosing specific males that they've mated with in the past. Only a few other reptilian species exhibit this type of mate preference, and this is the first time anyone has shown fidelity in alligators.

The researchers are still trying to understand what drives alligator mate choice, and how picking the same mate might benefit future generations. Unlike most other reptiles, female alligators spend significant energy nurturing their young, both by sitting on their nests and defending their babies once they're born. It's possible that a successful pairing in the past means a higher chance of successful breeding in the future, but the scientists say further study is necessary to prove what makes an alligator stay faithful.

"In this study, by combining molecular techniques with field studies we were able to figure something out about a species that we never would have known otherwise," Lance said. "Hopefully future studies will also lead to some unexpected and equally fascinating results."

Images: Phillip "Scooter" Trosclair

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More Than Meets the Eye: How the CCD Transformed Science

Posted: 07 Oct 2009 12:45 PM PDT


The 2009 Nobel Prize for Physics went, in part, to the inventors of the charge-coupled device George Smith and Willard Boyle this week. Their innovation, sketched out in 1969, is now the imager in millions of digital cameras and telescopes.

The very first prototype, pieced together months after Smith and Boyle laid out its working principles, is pictured above.

A charge-coupled device, in most applications, translates light into an electronic signal. Photons of light striking an array of capacitors create an electrical charge proportional to their intensity, which the charge-coupler transforms into voltage. That signal can be digitized and transformed by the dull magic of high-performance computing into Hubble's images.

Millions of CCDs are made each year for mass market cameras, but they also proved a transformational technology in science by providing a much more sensitive light sensor than previously existed. After being overlooked for decades, the Nobel win was a mild surprise but well deserved.

"There wasn't anything that could compete in scientific imaging," said Tony Tyson, an astronomer at the University of California, Davis, who built the first CCD camera for scientific applications in the late 1970s. "You're interested in getting very high signal-to-noise ratios. There's nothing that really competes with CCDs."

For the really dim things astronomers look at, the number of photons of light coming from a source is so small that each one counts. Out of every 100 photons, a CCD can record more than 90 of them. Photographic plates can barely reach 10 percent. And your eyes? Their quantum efficiency is in the 1 to 4 percent range.


According to lore, Smith and Boyle sketched out the design for the ubiquitous imaging device in an hour, over lunch at Bell Labs in October 1969. Working under the intense pressure applied by their taskmaster of a boss, Jack Morton, the pair had the device fabricated within a couple of months. George Smith took a photo of it, which you can see at the top of the page.

The road, though, from the creation of the prototype to the development of an actual technology that could be used by scientists and photographers was long and hard. Though CCDs would come to dominate astronomy, the device, as invented, was nowhere near high enough resolution to be worthwhile. With its poor signal-to-noise ratio, it was not immediately clear that the CCD was destined for greatness.

"I joined the company in 1969, the very year that Dick Boyle and George Smith invented this thing," Tyson said. "I actually, frankly viewed it as a toy. It was so small and awfully noisy."

Historians Robert W. Smith and Joseph N. Tararewicz note that "astronomers could not simply procure a CCD 'off the shelf' soon after the device's invention at Bell Labs." In fact, a number of other imaging systems were suggested for what became the Hubble Space Telescope including a panoply of image tubes.

Some astronomers, though, saw the potential for CCDs down the road. They were in Smith and Tararewicz's terms, "counting on invention."

In the face of budget cuts in 1974 that threatened the installation of the still speculative, expensive CCD technology on the Large Space Telescope (Hubble), an astronomer delivered an impassioned plea for the technology.

"To decide now, eight years before the LST can possibly fly, on what is already an out-dated detector, less than state-of-the-art, will be regarded in the future, I think as a poor choice of the options which are conceivable in other directions for cutting the cost of the LST," Margaret Burbidge, a prominent astrophysicist, wrote. "It is like deciding to treat a sick patient by cutting out his heart on the grounds he would be saved the energy used by the heart muscles in pumping the blood around the body."

Hard work by hundreds of scientists and engineers pushed CCDs closer to reality over the next few years. Companies like Fairchild, Kodak and Tektronix, rather than Bell Labs, developed the technology into usable form. Military, scientific and consumer applications were all benefiting from the money being thrown at the CCD problems from different directions, but it was still tough.

"It was a very painful development," Tyson said. "There were all these problems making really large cameras and getting uniform CCDs out of companies that were already pushing the envelope."

Still, scientists like Tyson persevered. After nearly a decade, he put his latest camera on the 40-inch telescope at Mt. Palomar Observatory and was able to measure the distribution of the faint blue galaxies. That work became an important piece of evidence that dark energy — the mysterious force propelling the acceleration of the universe outward — actually exists.

Now, nearly every major astronomical observatory uses CCDs. They also remain the gold-standard for medical imaging, or really any type of science that needs to capture photons. Though CMOS imaging technology is making inroads in consumer technology, there's "still nothing like a huge CCD," Tyson said, for high-end science.

Tyson's latest project is the Large Synoptic Sky Survey, which will incorporate a 3,200-megapixel camera. Plotted against time, CCD performance, measured in pixels, has grown at close to the same dizzying logarithmic rate that computing power has (see below).

Clearly, that hour of lunch at Bell Labs opened up a technological development path that was as broad and deep as nearly any in the 20th century. And after decades of being overlooked for the biggest prize in science, the inventors of the CCD are finally getting their due.

"Back, say, 30 years ago when I was at Bell Labs, we thought that CCDs could very well be a Nobel Prize," said Cherry Murray, dean of engineering and physical science at Harvard University and a one-time colleague of Smith and Boyle at Bell Labs. "It had been overlooked for so long … It's nice to see."


Images: Sent by Tony Tyson to 1. George Smith. 2. Tony Tyson. 3. Tony Tyson.

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