Tuesday, May 10, 2011

Foldit Online Protein Puzzle

Inside your cells, proteins allow your body to break down food to power your muscles, send signals through your brain that control the body, and transport nutrients through your blood. Every protein consists of a long chain of joined-together amino acids, which are small molecules made up of atoms of carbon, oxygen, nitrogen, sulfur and hydrogen. Small proteins can consist of 100 amino acids, whereas some human proteins are much larger, with thousands of amino acids.

Each type of protein folds up into a very specific shape, which specifies the protein's function. The Foldit exploration puzzle game attempts to predict the structure of a protein by taking advantage of our puzzle-solving intuitions and having people play competitively to fold the best proteins. Players can also design brand new proteins that could help prevent or treat important diseases.

Another objective of the project is to find new proteins that can help in turning plants into fuel. For this to happen plant material must be broken down (this is currently done by microbial enzymes—proteins—called "cellulases").

This game is a product of a collaboration between University of Washington Departments of Computer Science & Engineering and Biochemistry.

See more projects in FreeData ProcessingAll Ages.


Why 5, 8 and 24 Are the Strangest Numbers in the Universe

In the May 2011 issue of Scientific American mathematician John Baez co-authors "The Strangest Numbers in String Theory," an article about the octonions, an eight-dimensional number system that was discovered in the mid–19th century but that has been largely ignored until quite recently. As the name of the article implies, interest in the octonions has been rekindled by their surprising relationship to recent developments in theoretical physics, including supersymmetry, string theory and M-theory. Baez and his co-author John Huerta wrote, "If string theory is right, the octonions are not a useless curiosity; on the contrary, they provide the deep reason why the universe must have 10 dimensions: in 10 dimensions, matter and force particles are embodied in the same type of numbers—the octonions."

The eight dimensions of the octonions aren't the only interesting thing about the number eight, however. Baez highlights the number eight as one of his three favorite numbers. (The other two? Five and 24.) In 2008 Baez gave a series of lectures explaining what makes five, eight and 24 such unique and mysterious entities. The lectures, which are intended for a general interest audience, live on the Internet as both pdfs of the slides he used and video recordings. Watching them, you can learn not only a lot more about what makes octonions special, but also sphere stacking, the golden ratio, Islamic tiles, and why the sum of all integers equals –1/12.


Artificial Intelligence: If at First You Don't Succeed...

CAMBRIDGE, Mass.—The last symposium in M.I.T.'s 150-day celebration of its 150th anniversary (who ever said that geeks don't like ritual?) is devoted to the question: "Whatever happened to AI?"

Of course, that is a particularly appropriate self-introspection for M.I.T. because a lot of artificial intelligence action occurred there during the past 50 years. The symposium began Tuesday night with M.I.T. neuroscientist Tomaso A. Poggio setting the tone by declaring that the problem of making an intelligent machine is still "wide open."

Okay, there has been some progress: things like Deep Blue, Watson, MobilEye, among others. But the consensus was that new "curiosity-driven basic research" is needed and that AI-related computer science  should be integrated with neuroscience and the cognitive sciences, with specialized concentrations in areas like vision, planning, language and social intelligence. "I believe that 50 years later it is the time to try again," Poggio said.

M.I.T. has brought together a cast of heavy-weights to take on these big questions. A few gems along the way:

Nobelist Sydney Brenner: "I think consciousness will never be solved but will disappear. Fifty years from now people will look back and say, 'What did they think they were talking about?'"

AI pioneer Marvin Minsky: "Why aren't there any robots that you can send in to fix the Japanese reactors? The answer is that there was a lot of progress in robotics in the 1960s and 70s and then something went wrong."

Noam Chomsky on the purported success of statistical natural language learning methods that function by "approximating unanalyed data," while ignoring the underlying structure of language: "That's a notion of success which is novel; I don't know of anything in the history of science [like this]."  


Meet the Taxicab of the Future

nyc taxi, nissan, transportation, cars, fuel efficiency TAXI ICON: The taxi of the future will be a yellow minivan from Nissan that gets 25 miles-per-gallon in city driving. Image: NYC.gov

NEW YORK -- Japanese automaker Nissan will replace Ford as supplier of New York City's iconic yellow taxicabs as this city abandons its earlier goal of having an all-hybrid cab fleet, after being twice thwarted by federal courts.

But the deal with Nissan will allow the city to launch a pilot test next year to determine whether having all cabs as electric vehicles at some point in the future is an option it could pursue instead.

Yesterday, Mayor Michael Bloomberg and other officials announced that the city has selected the Nissan NV200 as the next generation of yellow cab, to replace the thousands of Ford Crown Victoria cars that now dominate the streets. The deal gives Nissan an exclusive 10-year, $1 billion contract to build New York's next generation of cabs.

Ford and a Turkish company had also competed for the contract but lost to Nissan's bid. Officials say New York's yellow-cab fleet consists of more than 13,000 vehicles, making it the largest in the country.

New York's Metropolitan Taxicab Board of Trade says the first Nissan NV200 yellow cabs will begin appearing on city streets in late 2013. David Reuter, Nissan's vice president for corporate communications, says the NV200 will be manufactured in Cuernavaca, Mexico.

"The new taxis will be custom-designed to meet the specific demands of carrying 600,000 passengers a day in New York City traffic and the vehicle meets the top priorities identified by the public in our on-line survey," Mayor Bloomberg said in a release.

The mayor's office figures that the entire fleet will be switched out over the next three to five years, meaning that this city could be saying goodbye once and for all to the gas-guzzling Ford Crown Victoria cab by 2016 at the latest.

Deal includes pilot all-electric taxi test

As part of the deal with Nissan, the company will give the city six of its new Nissan Leaf vehicles imported from Japan to test as all-electric yellow cabs. The small test pilot will be launched in 2012, the city says, and Nissan has promised that it will be capable of manufacturing all-electric versions of the NV200 by 2017 if the city should decide to purchase more electric cars to use as taxicabs.

"We'll have a demonstration fleet of about six vehicles which will be used by certain medallion owners to test the suitability of a fully electric taxi," said Reuter.

The NV200, designed specifically for use as a cab, was selected primarily for its safety features. The cars will have passenger air bags that work with the special partitions that separate drivers from fares. They will also be built with features to guard against collisions with other vehicles and will be the first cars ever to be crash-tested with taxicab infrastructure built in.

Vehicle fuel efficiency was not a criterion for selecting the winner. The reason, says Bloomberg spokesman Marc LaVorgna, is because of the federal court rulings that struck down New York City's attempt to control the fuel efficiency of its cab fleet.

"Due to what is known as federal pre-emption on this issue, that a city does not have the authority to regulate its own air quality essentially, that that is a federal prerogative, thus we were not able to use fuel efficiency as a specific criteria here," LaVorgna said.

LaVorgna said the pilot electric cab test could eventually prove to be more groundbreaking than Bloomberg's earlier hybrid taxi promotion efforts. But the city would have to go slowly and start with only six vehicles because it has yet to determine how to recharge a fleet that needs to be in operation 24 hours a day, he said.

City thwarted by court ruling barring mpg standard
The so-called "green taxis" initiative was part of efforts by Bloomberg's administration to reduce the levels of greenhouse gas emissions coming from the city over the next few decades, part of the long-term PlaNYC master growth plan. The original aim was to mandate that all new yellow cabs entering the fleet boast a minimum fuel efficiency standard of 25 miles per gallon by fall 2008, rising to 30 mpg by November 2009.


Cancer Testing? There's an App for That

Many people already use their smart­phones as far more than mere telephones—as gadgets for Web surfing, e-mailing or listening to music. Some scientists are now turning them into handheld tools to diagnose cancer or infectious disease, track treatment progress or check water safety. Given that the handsets are so common, they could bring cutting-edge health care technology to the developing world.

Diagnosing cancer is a challenge because it requires expensive, time-consuming assays. But in a recent study published in Science Translational Medicine, Ralph Weissleder and his colleagues at Harvard Medical School used a cell phone and a lunch box–size machine to diagnose cancer from tiny pieces of tissue, taken via needle from the abdomens of patients with suspected metastatic cancers. Researchers mixed the samples with antibodies that bound to four known cancer-related proteins. The machine analyzed the samples using nuclear magnetic resonance—measuring levels of the antibody-bound proteins based on their magnetic properties. It then sent the results to the smart­­phone, which, using an app that the researchers designed, displayed the data. Because doctors don’t need a laptop or desktop, it would be easier for them to assess patients outside the clinic. In comparison, results from more traditional diagnostic methods are typically not available for three days and require more invasive tissue sampling.

By using different antibodies, doctors could use the device to diagnose any form of cancer, says Har­vard systems biologist and co-author Hakho Lee. They could also track treatment progress. “If there is a decrease in either the number of cancer cells or the expression levels of certain disease markers, then that means the treatment might be working,” he says. He expects a product within five years.

Other researchers are taking advantage of smart­phone cameras to create diagnostic microscopes. Electrical engineer Aydogan Ozcan and his colleagues at the University of California, Los Angeles, have developed a 4.5-centimeter-long phone attachment that shines LED light on biological samples, producing holograms of each cell based on how the light scatters. The phone’s camera then snaps a photograph, compresses the image and sends it to a clinic for evaluation. With the ability to decipher details as small as 1/1,000th of a meter, the microscope could identify sickle-cell disease or malaria from blood samples and perform blood cell counts. The devices could bring an elegant simplicity to nations that struggle with infectious diseases.


Did Rapid DNA Analysis Verify Osama Bin Laden's Death?

A few years ago, I worked as a Writing Department Intern for C.S.I. Crime Scene Investigation and C.S.I. New York. Seeing producers, writers and real C.S.I.s collaboratively bring a story from pitch to beatsheat was intoxicating. Research was meticulous. Science served as mascot, foundation and muse.

Despite the show's dedication to rigorous research, its ultimate success had a lot to do with the fact that the creators didn't try to replicate a day in the life of a C.S.I. Team or a forensic DNA lab. The actual C.S.I. Investigators don't go from the crime scene to the lab. The forensic analysis is done by trained lab techs. What would those award-winning "C.S.I. Shots" be without charismatic stars in starch white lab jackets peering through microscopes, though?

A photo of the real and considerably less glamorous Las Vegas C.S.I. Team taped to the refrigerator was one of many many testaments to the team's awareness of the conscious discrepancy between factual and actual. Another was the timing. Turnaround time for DNA analysis is not instantaneous. Enter the episodic Hollywood procedural fiat clause. Two beats later the DNA is verified.

The evening of May 1, 2011, American audiences were riveted to their computers and television screens watching the most expensive criminal investigations in history unfold. As would be expected, scientists, journalists and laypeople are now scrutinizing the verification details with the fundamental question, "How do we know it was Bin Laden?"

Real forensic science labs may not incorporate the Hollywood fiat into their practices. A European Community–funded portable rapid DNA test, developed at University of Arizona Phoenix, however, might.

Professor Frederic Zenhausern at the Center for Applied Nanobioscience and Medicine said that the technology he is developing through the UK Forensic Science Service "is currently under validation by several crime labs in the UK, Germany, Austria and the Netherlands."

Could those dots connect all the way to Pakistan? Not likely.

Zenhausern reiterated that "there is no rapid DNA system available for a portable deployment in such a mission yet." The system his team is developing is the "only one reported to be close to such requirements," however, it is "not validated yet."

Exciting as it may be to speculate, "it is unlikely USG (U.S. Government) used such a system at the site. More likely they transported the samples (and/or body) to a command center" equipped with the "instrumentation and bench space to accommodate the lab equipment."

Whereas a low profile DNA case would be "processed with the conventional lab-bench techniques" that could "take up to 10-14 days," an extraordinary case, such as the most expensive manhunt in history, "could be performed in less than 24 hours" through an integrated system that has a "turnaround time of less than 2 hours."

Zenhausern speculates that "Osama Bin Laden’s DNA analysis may have been performed through cross-validation of processing at different USG labs...possibly located at some strategic and local command centers equipped with conventional and high quality STR (Short Tandem Repeat) profiling platform technologies."

Given the highly orchestrated nature of the operation, surrounding military bases—already prepared with on-site facilities for identifying soldiers—could have been alerted ahead of time, but they still needed to travel there. This explains the gap between the 3:50 pm EST ID confirmation and The White House's 10:30 pm DNA verified announcement.

"In a near future, rapid DNA testing using a single piece of portable equipment will improve the cycle time, mobility and possibly reduce some of the cost of the analysis while providing a much simpler user interface." Zenhausern said, positing that "comparative matches may have been done from previously collected samples from skin, hair, fingerprint or any other object Bin Laden may have been touching (e.g. cup) and/or from samples collected from family members."

It won't be long before the rapid technology being developed will be a legitimate DNA verification process. Right now, however, it's still a Hollywood thing.

Photo credit: picture of Dr. Zenhausern with the machine at his lab in Chandler, Ariz., taken by Keven Siegert, University of Arizona College of Medicine – Phoenix.

Related at Scientific American: How do you ID a dead Osama?

Related, elsewhere on the Web:

Univ. of Arizona scientists have been working with FBI to develop 2-hour DNA fingerprint device. Could it have ID'd bin Laden?

Experts Say DNA Match Is Likely a Parent or Child

It's a Match: How Officials Used DNA to Identify bin Laden

UA Scientists Develop Quick DNA Test Device

Did DNA Finger bin Laden?

Rapid DNA testing being developed at University of Arizona

Center for Applied NanoBioscience and Medicine [video]

Integrated microfluidic system for rapid forensic DNA analysis: sample collection to DNA profile.

About the Author: Although Susanna Speier was never able to formally pursue her passion for science, her "ear" for layman-friendly science explanations—deemed "excellent" by The New York Times—has enabled her to enter through the back door on many occasions. She talks to scientists whenever she can. Conversations often turn into collaborations. Five of her plays have been produced; over 100 of her articles have been published and one of her screenplays remains in liminal purgatory. She dayjobs as a multiplatform social media specialist and digital journalist.

The views expressed are those of the author and are not necessarily those of Scientific American.


Possum-Killing Poison Helps Protect New Zealand Parrot

An endangered New Zealand parrot known as the kaka (Nestor meridionalis) has had a much-needed population boost after poisons were used to kill introduced possums, stoats and rodents in Waitutu Forest

Common brush-tailed possums (Trichosurus vulpecula) were introduced to New Zealand from Australia in 1870 for their fur and meat, but they overran the islands, threatening the country's native fauna, which evolved without any mammalian predators. A survey six years ago indicated that so many female kaka were being killed by possums that the birds were at risk of extinction in Waitutu Forest.

To help the parrots, last October the New Zealand Department of Conservation (DOC) dropped cereal pellets laced with a poison known as 1080 over 25,000 hectares of the forest. The results were dramatic. According to the DOC, possum populations within the area have dropped 99.5 percent. Populations of stoats and other rodents, also introduced species, dropped to a level so low, the animals could not be detected "with standard monitoring methods," the DOC reports.

The birds, meanwhile, are thriving in the absence of these predators. The DOC asserts that female kakas have nests full of healthy chicks, making this a record breeding season.

The DOC monitored the area before and after the 1080 drop and found that no birds were killed by the poison. Water samples also showed no signs of the biodegradable poison.

The use of the 1080 toxin has been highly controversial. Also known as sodium fluoroacetate, 1080 is derived from tea and is deadly to most mammals. It has been effective in New Zealand because there are no native mammals for it to kill, but some fear it is too indiscriminate and may pose an eventual danger to humans.

Kakas face threats from several other introduced species, including deer, pigs and wasps. The wasps eat shimmering honeydew, which is a primary source of the birds' diet, providing necessary energy for their breeding periods.