Wednesday, May 19, 2010

We've MOVED!

We're changing channels here at Duke Research blog -- moving from the friendly confines of Blogger to a Duke server inside the Duke Research site.

We'll have the same great action-news team, (well, minus Monte the Weatherman, who has retired) and the same great coverage. Please tune the RSS feeds on your mobile devices and neural implants accordingly.

Vansh and Becca are off campus this summer, doing wonderful things in London, New Delhi and St. Louis, but they'll be back in the fall.

Please join us at

Tuesday, May 18, 2010

College Substance Abuse Is a Lot More Than Alcohol

Guest post from Jamese Slade, NCCU Summer intern

Underage drinking and drug use may not be a big deal to most college students, but these behaviors can have effects that will last a lifetime.

At a two-day forum on college student drinking and drug use sponsored by the Center for Child and Family Policy, drug abuse researchers touched on the issues of not only alcohol use, but also marijuana, and prescription drug abuse.

University of Cincinnati psychologist Krista Lisdahl Medina presented studies on the emerging adult’s brain and how it is affected by drug and alcohol use. She said 40 percent of adults aged 18-25 binge drink, which has been shown to cause verbal memory loss affecting their ability to learn new words.

Marsha Bates from Rutgers University's Center for Alcohol Studies said that alcohol and marijuana effect emotional regulation, causing inappropriate reactions to emotional stimuli. And during a one-month study, students who smoked marijuana were found to have brains that appeared more immature, while thinking slower and having lower grades.

University of South Florida psychologist Mark Goldman connected substance abuse to college students being in a new environment and trying to relate to their peers.

“We are teaching kids from a very early age that alcohol will take us from being picked on to being a cool kid,” said Goldman. He used an example from the movie Dumbo, when the elephant got drunk and all the trainers were laughing.

Of students who have prescriptions, 65 percent misuse their prescription drugs, and 62 percent give their drugs away to others, according to Sean Esteban McCabe, a substance abuse researcher from the University of Michigan. He said 72% of undergraduates are able to get stimulants for free, and that 90 percent of prescription drugs obtained from peers are stimulants.

“College students have said, ‘it’s easier to get 500 pills than it is to get alcohol. I don’t even have to leave my dorm room,’” McCabe said.

Students use prescription drugs with a purpose. According to David Rabiner, from Duke's Center for Child and Family Policy, nine percent of students at Duke have used drugs that had been prescribed to someone else to concentrate better while studying, to study longer, to feel better or to get high. He said that 70 percent of Duke students believe the prescription drugs have positive or very positive effects on them.

“They really believe it works,” said Rabiner, however there has been no evidence to prove that prescription drugs have helped students academically.

All presenters agreed there is a tie between drug and alcohol abuse. “It’s not likely to find students misusing medications who are not engaged in alcohol and other drugs,” said Bates.

Rabiner said prevention efforts should educate students to deal with attention difficulties appropriately, including getting a professional evaluation.

Wednesday, May 12, 2010

Build-A-Brain Workshop

That snap-crackle-pop sound you hear around a newborn human's head is the baby's brain being assembled at an alarming rate. The manufacturing of brain cells and getting them wired into meaningful circuits in the first months of life lays a foundation for abilities – and deficits – that seem to last a lifetime. And though the program is remarkably robust, parts of it can be derailed.

A spectacularly diverse panel of Duke experts on various aspects of this process came together Wednesday in another Duke Institute of Brain Sciences workshop called "Building a Brain: Order and Disorder." I missed the order part – Fan Wang and David Fitzpatrick – but got plenty of the disorder!

Tina Williams of Psychology and Neuroscience reviewed the "sensitive period phenomenon" from her own and others' studies of rats. There is a connection between early life events and later behaviors, but the mechanics of it are a vast landscape of unknowns so far. "There may be a cascade of complex events that occur between point A and point B," she said.

Indeed, said Mohamad Mikati, chief of pediatric neurology, there is a known sequence of events when the infant brain is deprived of oxygen in whole or in part, for whatever reason, and the recovery and outcomes seem to rely on when in the developmental program the insult occurs. Sometimes a brain injury in infancy doesn't do damage directly, but leaves the brain more vulnerable to subsequent insults.

Liz Brannon of the Center for Cognitive Neuroscience updated us on her work with babies' innate sense of number, and showed an adorable movie of a 6-month-old gnawing on the edge of the high chair table with his gaze snapping right and left while going through one of her protocols. Length-of-gaze is just about the only way to figure out what the little goobers are thinking about. (There was a great story in the May 3 New York Times about this.)

Before I had to go, I also caught Simon Gregory from the Center for Human Genetics talking about how improvements in genome technology are allowing him to zero in on a particular hormone system as a possible contributor to autism. It's more than genes, though: methyl groups clamped on to the backbone of DNA can control whether a gene is active or not. Your mom can do this for you and then you inherit the gene turned off. But that's epigenetics, and that's enough for a whole other symposium.

Marie Lynn Miranda from the Nicholas School reviewed the connections between lead – which is still a huge problem – and cognitive abilities. And Ted Slotkin from pharmacology and cancer biology talked about environmental contaminants, like pesticides, that are like pervasive, harmful drugs.

Friday, April 16, 2010

Bonobo Business

Do you know what a bonobo is?

Only about 10% of people do, according to Duke evolutionary anthropology professor Brian Hare. By comparison, roughly 90% of people know what a gorilla is.

Bonobos have many remarkable qualities, including the fact they “are the only really peaceful ape,” according to Hare. “They don’t kill each other.” Bonobos are more closely related to humans than any other kind of ape or monkey. However, bonobos are frequently hunted for pets and for bushmeat.

Hare gave the bonobo primer to introduce renowned conservationist Claudine Andre, widely known as the Jane Goodall for bonobos. Andre spoke as part of the Department of Evolutionary Anthropology's Lemur Center's Primate Palooza event.

“Let me bring you in my country,” Andre began. She then described the Democratic Republic of the Congo, the only country bonobos call home.

When Andre and her husband lived in the Congo in the early 90s, their town was looted. Many shops and homes were destroyed, but Andre decided to stay. Someone asked her to visit the local zoo and, says Andre, “I opened the door and my life changed.” She found over 200 animals -- lions, bears, chimps. And no food. “I said to my husband, we have to do something. I have to try to save the zoo.”

Andre managed to find food for the animals and she saved the zoo animals, including a baby bonobo named Mikeno. Eventually, more and more bonobos found their way into her care, and Andre expanded her efforts to protect them.

She discovered that education was her most effective tool. At first, poor orphans who lived in the zoo were very rude to the animals. But with Andre’s positive example, the children grew to respect the animals. Andre has built a bonobo sanctuary, Lola ya Bonobo, which is visited by 30,000 children a year.

Bonobos are only found in the Congo, and Andre has successfully established this as a national point of pride. Awareness about the importance of bonobos is spreading; this year, Andre received 50 bonobos from people who bought them as pets and were convinced by area children that they had made a mistake.

“The education is worth it. I’m sure of this.”

Caring for so many animals is not an easy task. Andre has returned some to the wild, and says that it is very difficult to do. Certain guidelines must be followed, and she wants to make sure that the animals are happy in their new surroundings. She maintains that communication with surrounding people is critical.

“It is 25% about the animal and 75% about contact with the local population.” Andre had to meet with traditional chiefs and ask them not to hunt in the areas where bonobos are reintroduced, in return for help for their villages.

Andre described how it felt to return one of her bonobos to the wild: “It was a fantastic moment for me. So many emotions.” She likened it to a father walking his daughter down the aisle.

Andre and her organization decided not to use collars to track the released bonobos because they are heavy and can get caught on branches. Instead, trackers sit below the nests night and day and monitor the bonobos’ movements from tree to tree.

Currently, sanctuary visitors do not have many opportunities to observe the animals. Andre eventually hopes to purchase a small island, “a new sanctuary where people can go around and see the bonobos.” Bonobos are becoming recognized as an important part of Congolese culture and biodiversity, and it is in large part because of Andre’s efforts.

“I’m so proud to be a symbol of peace for the people,” Andre said.

Thursday, April 15, 2010

Bouncing Off The Walls

Guest post from Cara Bonnett, Office of Information Technology

No, it’s not your imagination: Those clouds really are following you, and the sunflowers are waving.

Students walking past the huge media wall at the Link in Perkins Library may not realize that the tiled display is responding to their movements. But thanks to Duke researchers and computer science students, they now can interact with the wall to play with the weather, generate their own poetry and navigate through a collection of ultra-high-resolution “gigapixel” images.

“The challenge is getting people to notice that the display is interactive,” said Robert Duvall, a computer science professor whose students designed the weather simulation. “How do you draw people in, help them understand what’s going on and get them playing with it?”

The media wall – built by Duke’s Visualization Technology Group as part of the Visual Studies Initiative – includes 48 computer screens, six Web cameras and a set of directional speakers, all driven by a 104-core computing cluster. The cameras, positioned on the ceiling, are programmed to detect viewers’ positions or movements and use that data to determine what’s represented on the screen.

Students in Duvall’s advanced graphics class designed the weather simulation to be useful as well as fun. The display, based on real-time data from an online weather site, features cartoonish rainclouds or clear blue skies (depending on the forecast), with sunflowers that “wave” when a viewer steps up to the screen.

“After you’ve been in the Link for a couple hours, you might not know what the weather’s like outside,” Duvall said. “On the wall you can see it at a glance.”

Another display – “Passage Sets,” created by visual studies professor Bill Seaman and programmed by research associate Todd Berreth – includes an interactive poem generator that allows as many as four viewers at a time to choose words or phrases from four lists that then flow in a line of text across the bottom of the screen. An opening for the exhibit will be held Friday, April 16.

Berreth and a committee of faculty, staff and students are seeking new ideas for exhibits on the wall. Students in future classes could help with the programming, and developers can test their programs on a smaller-scale version of the wall at Smith Warehouse.

The only caveat: No marketing allowed.

Faculty and students are invited to submit project ideas to Berreth’s group at Find out more information about developing projects for the Link media wall on the group’s wiki.

Friday, April 9, 2010

A radical transformation

Al Gore -- "I used to be the next President of the United States" -- came to Duke Thursday to deliver the Duke Environment and Society Lecture, and lots of people, both receptive to his message on global climate change, and hostile to it, turned out to watch.

"If you are running a corporation, as long as you can drag your pollution into the air like an open sewer, then you have always have an incentive to work against anything beneficial to the environment," said Gore, who has been awarded both the Nobel Peace Prize and an Academy Award for this work.

Caption: Former Vice President Al Gore met with Nicholas School of the Environment students Eric Ward, Kim Novick, and Angie Lee in the green room of Page Auditorium just prior to Gore's presentation. Photo by Chris Hildreth/Duke Photography

Although many apparently expected a recap of his "Inconvenient Truth" talk, the Duke appearance was more similar to his latest book, "Our Choice: How We Can Solve the Climate Crisis," and included many verbatim quotes from it.

"One hundred and fifty one years ago, two things happened: the first oil well was drilled in Pennsylvania, and at the same time another scientist discovered that carbon dioxide (reflects) infrared radiation. The birth of climate science and the oil age coincided."

Justin Ko, a Trinity sophomore and a Premed student said afterward that Gore's philosophies would make him a great President. "He is extremely passionate about protecting the environment and I like his radical ideas about global warming," Ko said. "Adding a cost to pollution is justified morally, socially and politically. However, his efforts are not very effective right now. That's why he needs to re-enter politics and enforce policies at a broader level."

Gore highlighted four major instruments to combat the environmental disasters, especially global warming. "We need to focus on educating children, empowering women, raising the child survival rate, and improve fertility management."

Further, he added that "we need to make a decision to move wholly into renewable energy, and include forestry and agriculture in our solutions."

Vysak Venkateswaran, a Pratt sophomore and a Biomedical Engineering major, feels that this argument needs to revised a bit. "You simply cannot achieve longstanding change in the market of climate change without significant government intervention. Bringing up the topic of investing in newer and more expensive technology in the current recession is not the best idea. Even if the government does decide to go full out in developing green technology, there is going to be a lag time."

The audience, heavy on Nicholas School faculty and students, gave him a standing ovation both entering and leaving Page Auditorium.

Sunday, April 4, 2010

Hide and Seek in the Open Sea

Duke biologist Sonke Johnson has made many trips underwater to study aquatic organisms. The direct observations enable his research, but he laments that any observation - whether via submersible, diving, or otherwise - causes some disturbance that impedes observation of normal behavior. At worst, with a schoolbus-sized submersible, “you film responses of stark terror,” Johnsen said.

Johnsen’s lecture, April 2, was given in memoriam of Dr. Knut Schmidt-Nielsen, the pioneering physiologist who discovered, among other things, the function of a camel’s hump for storing water and energy. (You may have seen the statue of him with a camel near Bio Sci.)

Johnsen equated trawling, another research method, to “flying over London with a grappling hook and trying to determine the behavior of a London gentleman from what you catch. You can get some information from this, but it’s very limited.”

Blue water diving, sans submersible, is less disruptive, but “you’re left studying the slow and the dumb.”

Johnsen has also spent time researching the ecological pressures (namely predators) that cause ocean organisms to look one way or another. These organisms live in an environment where there is nowhere to hide, and where successful camouflage ensures survival.

“Predation in the open ocean is, even by predation standards, pretty brutal,” Johnsen said.

Johnsen described four modes of camouflage used by ocean organisms:
  1. transparency

  2. cryptic coloration

  3. mirroring

  4. counterillumination (“hiding yourself with lights”)

Transparency is a very common adaptation in the ocean, Johnsen said, but there are strings attached. “The fundamental trick these animals have to solve is how not to scatter light.” Transparent organisms must be extremely flat, because if their bodies give light a chance to scatter (even at a cellular level), they will appear opaque-- and thus vulnerable to predators.

Unfortunately, a flat body is not the only problem transparent animals have to solve. In order for eyes to work, they must have pigment to absorb light. Thus, they must be visible-- unless the organism can find another solution. Some organisms spread out the eye to present less of a target to predators and others compact their retinas (at a great cost to function).

Transparent stomachs also can be troublesome, Johnsen said. Even transparent animals will become opaque when chewed, and perhaps colorful. “You’ll need an opaque gut, otherwise you’ll light up like a Christmas tree when you’re digesting your food.” Some organisms address this problem by making their gut as small as possible, or by resorting to a liquid diet.

Cryptic Coloration
According to Johnsen, “something that is ridiculously colorful on land could actually be ridiculously cryptic underwater.” Organisms’ coloring also depends greatly on where they live in the water column. “As you go deeper, some of the blue light is actually converted into red light,” due to Raman scattering. For that reason, many abyssal creatures are either transparent, red, or both.

“The oceanic light field is fairly symmetrical. Turn around, and you’ll see the same amount of light.” Mirroring takes advantage of this, and works by effectively showing a representation of what should be at a particular spot (if the organism were not). “It’s not lost on nature that this works really well.”

Johnsen tried to evaluate whether mirroring or coloration was a better protection from predators, depending on the effectiveness of each in different environments (coastal vs. oceanic water, noon vs. sunset, different depths). He found that in general, mirroring was more successful because it was more robust, but that coloring was fine if the organism tended to stay in the same spot.

Some deep-sea organisms hide themselves from predators below with bioluminescence (creating their own light). These organisms can replicate light that is the same intensity of daylight, and thus trick predators into thinking they aren’t there.

Friday, April 2, 2010

Mining On a Whole New Level

When one normally pictures wildlife conservation, protection of tigers, pandas and gorillas may come to mind. But what about alviniconcha, or “hairy snails”?

Alvinicocha live near hydrothermal vents on the ocean floor, where temperatures can range from 300-400 C over the course of a few meters. Hot water flowing from the vents contains high levels of dissolved minerals, which precipitate out when exposed to cold sea floor temperatures. Some companies are seeking to mine these deposits, raising brand new environmental concerns: What kind of life exists at hydrothermal vents? And how would these organisms and population structures be affected by mining?

Tom Schultz, Marine Lab professor and director of the Marine Conservation Molecular Facility, has been investigating these questions with his research team, comprised of Cindy Van Dover, Jens Carlsson, Andrew Thaler, Kevin Zelnio, Rebecca Jones and Pen Hsing.

“Hydrothermal vents are teeming oases of life,” Schultz said at a Genomes@4 lecture last Wednesday, sponsored by the Duke Institute for Genome Sciences & Policy.

Far out of reach of sunlight, organisms living in and around hydrothermal vents rely on chemosynthesis (energy from chemicals) rather than photosynthesis (energy from sunlight). Hairy snails, shrimp, crabs, tubeworms and many many kinds of bacteria call this extreme environment home.

Shultz’ team collected water samples to determine the microbial water diversity and found an astonishing 18,000 species of bacteria-- and that’s a conservative estimate. “We probably got about half of what species were present,” Schultz said. “It’s amazing to me.”

There are some difficulties involved in sampling because, as Schultz put it, “you can’t just go in your backyard to collect data.”

Schultz’ team worked with Nautilus Minerals, Inc. to gather the data. Complex robotics are used to collect samples from the sea floor. According to Schultz, the costs of operating underwater are made up for by a higher concentration of minerals: 10x higher than typical land deposits.

From the data, Schultz was able to conclude that populations living on or in hydrothermal vents do not seem small or fragmented (and thus vulnerable to extinction if mining were to occur). Furthermore, hydrothermal vents are prone to sudden eruption events that would disrupt the population as much as mining; organisms living near vents must necessarily be adaptable to perturbation.

But one major concern is the threat to biodiversity and the loss of undiscovered species. Schultz’ team happened upon several new species during the course of their research, and untold more remain undiscovered. Hopefully future research will reveal some of the secrets kept by the deep blue sea.

Wednesday, March 17, 2010

Brain Week Is A Positive Feedback Loop

It's a pretty safe assumption that behavior starts in the brain. But exactly where and how it happens is a little tougher.

As part of "Brain Awareness Week" on Tuesday, neuroscientist Michael Platt gave an audience in Love Auditorium a quick tour of his work on identifying "the basic building blocks of 'other-regarding preferences' that lead to spite, envy, altruism -- you name it."

The areas of the brain that are involved in our social abilities are tightly coupled with the reward systems, and are consistent across primate species, meaning they're valuable to our survival and have been conserved through evolution, he said.

Right from birth, primate infants of all kinds, including ours, appear to be hardwired to recognize and focus in on faces , which signal all kinds of things. "We seem to come equipped to deal with and acquire social information about others."

We're able to read others' faces to infer information about sex, age and mood, for example. (College men, Platt has shown experimentally, are suckers for a pretty face; women, not so much.)

Primates are also able to understand, and apparently care about, what others in their group are experiencing. "Monkeys pay attention to what happens to other monkeys," Platt said, especially when their companions are receiving a squirt of tasty juice and they aren't.

Platt also reprised his famous "pay for view" experiment in which male rhesus macaques gave up some rewards to view sexually explicit photos of females or a picture of the boss monkey's face, but wouldn't pay to view unimportant monkeys' faces.

There was also a bit about lemurs cruising around with wireless video cameras on their heads, but he didn't show the video.

Platt, who is the Director of Duke's Center for Cognitive Neuroscience, has been supported by the National Institutes of Mental Health, the National Eye Institute, the National Institute on Drug Abuse, autism foundations, and the Duke Institute for Brain Sciences.

Brain Awareness Week concludes on Saturday with a Noon to 4 open house, lab tours, and kids activities in the Levine Science Research Building.

Thursday, March 11, 2010

New Look

We've just redesigned Duke Research and relaunched it on March 11, 2010. It's the same broad coverage of Duke's research enterprise you've come to expect with great photos, videos and slideshows. But now it's built on a Drupal platform that allows us to update the content frequently with minimal hassle. We hope you enjoy it, but if you ever have concerns or questions, please drop us a line: dukeresearch-at-

Saturday, March 6, 2010

Narrative Control in the Digital Age

“Can’t the Internet control us just as easily as it can liberate us?” asked Jonathan Zittrain Wednesday night as part of the Provost’s 2010 lecture series. Zittrain is a law professor and co-founder of the Berkman Center for Internet and Society at Harvard University,

Zittrain explained that technology is changing the way we access and add to human knowledge. Our ever-increasing reliance on digital information can create difficult problems with regard to the historical record.

One major issue is that people, governments, organizations or corporations can justify revising the record for various reasons:
  • national security

  • privacy

  • copyright

  • fairness (jury taint, defamation, group insult)

Zittrain offered a few examples where publicly-available information was deemed harmful, and how the problem was dealt with.

Apparently, the EPA used to make “worst-case scenarios” available on the Internet: detailed information about what would have to be done, where, to cause the most damage to life and property. The intent was to let people know that ‘Hey, something really bad could happen. Just FYI.’ However, in the wrong hands, this information could practically be a step-by-step guide.

In response to the uproar that inevitably followed when the scenarios gained publicity, the government decided to establish government reading rooms, where interested parties could go in sans cameras or writing materials of any kind and read as much as their heart desired. According to Zittrain, “It’s quaint. It was totally well-meaning, but there is an element of comicalness to it.”

Another pitfall to recording history in the digital age is that information is increasingly consolidated. Imagine a future where Ebooks are used exclusively over their ink-and-paper counterparts. If for any reason an Ebook vendor changes the book (perhaps due to copyright or governmental regulation), digital rights management would allow the change to be reflected in every copy.

“This is how holes appear in the historical record in way they did not before,” Zittrain said. “It is terrifying!”

Distortions in the record can be just as significant, especially when they can’t be distinguished from truth. For example, sponsored editorials that are favorable of a particular policy or person. As Zittrain put it, “[the record] doesn’t say later ‘By the way, this was fake.’”

“So what do we do? This is not necessarily making for a more complete or accurate historical record.”

His solution: Don’t keep everything in the same place. Lots of copies keep stuff safe! Libraries can play a role by keeping copies to check against other available copies & the Google master copy (when Ebooks eventually predominate, as Zittrain believes).

Furthermore, compromises can be made. For example, if China objects to certain content being shown on YouTube, that content can be restricted to visitors from China without necessitating complete removal (and thus preserving the record).

We must protect the historical record, Zittrain argues, because our view of the past depends on who wrote the story.

Sunday, February 28, 2010

What Are Scientists Made Of?

Last Thursday, the Duke Career Center, the Duke Institute for Genome Sciences & and Policy (IGSP) and Women in Science and Engineering (WISE) sponsored a screening of the documentary “Naturally Obsessed: The Making of a Scientist,” the story of three PHD candidates working to establish their careers in a Columbia University lab. The students are working to isolate proteins and determine their structures using X-ray crystallography, a difficult technique that requires a lot of luck.

The documentary, filmed over the course of three years, captures the heartbreaking failure that can follow months of work, as well as the surprising triumph that can result from a breakthrough. Each of the three students has their own reason for being there, and each approach their research in a different way. (Click here to read a review)

At the beginning of the movie, lab director Larry Shapiro somewhat controversially says that “one of the best things you can do as a scientist is suffer from Obsessive Compulsive Disorder (OCD). You become obsessed with a problem and can’t stop working on it until you find your answer.”

However, Dr. Rochelle Schwartz-Bloom, director of Duke’s Center for Science Education, argues that “you don’t have to be OCD or obsessed to love what you’re doing, you just have to have passion for it.”

Schwartz-Bloom was one of six panelists who shared their thoughts with the audience after the movie.

Grad student Vincent Chen was impressed with the film’s accuracy “in terms of the ups and downs in science. You have a lot of failures, and very few successes.”

Grad student Cynthia Tedore disagreed. “I didn’t see the repeated failure as accurate from my point of view. In any field, it’s bad to pursue one project with a small chance of succeeding. It’s better to pursue several.”

A member of the audience commented that, based on her experience in an X-ray crystallography lab, she thought the filmmakers did a good job. “I was touched by everything that happened. There are upsides and downsides. X-ray crystallography is very different from other fields, so [the movie] might not reflect what happens in other labs.”

Schwartz-Bloom said that the movie made her nervous with its emphasis on hard labor with a small chance of success. “A lot of kids today don’t go into science because they think it’s ‘too hard.’ Even people with some passion for it decide that they don’t want to do it.” She worried that the movie would only encourage this sentiment.

Fortunately, not everyone was so discouraged. My bio major friend told me that, despite the grim portrayal, she had not been dissuaded from her goal to be a scientist.

At the end of the discussion, the panelists offered their advice for aspiring researchers like my friend.

“Sometimes it is important to know when to quit, when a problem is impossible to solve. Otherwise, you can trash your entire career.” -- post-doc Rebekah Fleming

“Be a sponge. Take in everything you can, because you don’t know when you’ll need it in the future.” -- Schwartz-Bloom

“Don’t be afraid to find out what your weaknesses are, and how to fix them.” -- Tedore

“Science should be fun. If you’re doing it for your boyfriend or for your parents, you can do it for a while, but eventually it’ll break your heart.” -- panel moderator, professor Mohamed Noor of the Biology Department

Wednesday, February 24, 2010

Video Game Technology Attacks Cancer

Guest post from Cara Bonnett, Office of Information Technology

Kouros Owzar analyzes huge datasets to identify key genetic markers associated with cancer survival. For him, time is of the essence.

A new Duke computing resource that taps the power of graphics processors commonly used to render pixels in video games is going to enable Owzar and other researchers to complete complex statistical analyses as much as 75 times faster.

“Nobody wants to wait a month for an analysis to finish," said Owzar, assistant professor in biostatistics and bioinformatics. "You may run an analysis once, then want to run different scenarios, and if every one of those runs takes a long time, it’s not practical. This kind of tool allows us to tackle certain computationally intensive problems.”

Duke’s new computing cluster – part of a campus-wide network dubbed the Blue Devil Grid – harnesses the power of graphics processing units (GPUs), typically used in high-end gaming. GPUs deliver an order of magnitude difference in computational power compared with the central processing units (CPUs) found in desktop computers, said John Pormann, director of Duke’s Scalable Computing Support Center (SCSC).

Image: "Exponential Parameter Space Detail PSP Rays" byDr. L. Rempe, Wikimedia Commons

Because GPUs have dozens or hundreds of small “cores” or engines capable of doing lots of little things at once, they’re especially good for crunching away at what researchers call “embarrassingly parallel” problems, which are common in areas such as genetics, biostatistics and molecular dynamics.

"GPUs can split the job into smaller chunks, let the different cores just grind them out, and we collect the results at the end,” said Owzar, who, with his colleagues Ivo Shterev, Sin-Ho Jung and Stephen George, has developed a prototype comparing GPU and CPU processing speeds on different tests and data set sizes.

“Based on our experience, the larger the sample size and the more complicated the test statistic, the larger the benefit is in terms of speed.”

An analysis of data on 600 patients, for example – which would have taken about four days on a traditional CPU – now takes four hours. The prototype will be made available soon through as a stand-alone application and as an extension package for the R statistical environment.

GPUs also are much less expensive than high-performance computer clusters: One card costs $500 to $1,200.

The 16 machines in the Duke’s BDgrid include a mix of consumer-grade GPU cards as well as cards designed specifically for high-performance computing.

To find out more about BDgrid, visit the SCSC wiki or contact Tom Milledge in the SCSC.

Friday, February 19, 2010

Clean Technology- The future of energy

"Environmental innovation is a good business strategy in the current scenario," said Kirk Hourdajian,Project Manager at the Environment Defense Fund, at the Duke Conference on Sustainable Business and Social Impact held at the Fuqua School of Business on the 17th of February.

This conference aimed at promoting social and environmental sustainability in all industry sectors, and explored the most relevant questions on sustainability with the people on the frontlines of social innovation and business. The conference featured executives, scientists and researchers from organizations like IDEO, GreenTeamUSA, Mars Inc., Ogilvy, groSolar and Deloitte, among others.

In the session 'CleanTech: Make It, Fund It', Blake Clifton, Principal of Abundant Power, Scott Starr, Founder of groSolar and Kirk Hourdajian discussed the current state of clean technology, and talked about how the leading industry organizations and non-profits are driving market forces by driving clean technology.

"A 200 square mile area in the deserts of Arizona would be able to supply the entire electricity requirement of the United States for one year," said Starr, referring to the huge potential of solar energy.

Clifton highlighted the importance of government investments in nurturing the pet sustainability projects from conceptualization to completion. "The government involvement has to be huge. If the government doesn't give a 30% grant, then one cannot develop that technology. Infrastructure needs to be there to meet energy."

Other sessions included discussions about designing and engineering social impact, green as the new color of marketing, sustainable investments and strategies for climate change in the new world.

The Duke Conference of Sustainable Business and Social Impact was organized by the Duke MBA Net Impact Gold Chapter.

Friday, February 5, 2010

Carbon Capture Could Be Key

If you've paid any attention to the green movement, you'll know that global carbon emissions have far outpaced natural levels, and that numerous efforts are underway to reduce emissions and the climate change they will cause.

But in spite of these efforts, “we are not on track to reduce global climate emissions,” Thomas Halsey of ExxonMobil Upstream Research said during a public lecture Wednesday. Renewable energy, improved transportation and energy efficiency have the potential to greatly reduce global emissions, but not to the degree that is necessary. If this is true, how do we fill the gap? One major factor will be carbon capture and storage - preventing carbon emissions from entering the atmosphere and causing warming.

“A lot of the carbon dioxide in the atmosphere comes from relatively concentrated sources,” e.g. power plants rather than car tailpipes, Halsey said.

A few technologies exist for capturing carbon at power plants, with varying costs and efficiency. Post-combustion CO2 filtration is commercially available already. Pre-combustion carbon capture separates CO2 and injects only hydrogen as fuel for the turbine. Demonstration plants exist, but are plagued by problems due to the complexity of the technology. Oxy-Fuel combusts pure oxygen, but requires very high temperatures and thus large amounts of energy (somewhat negating the positive benefits).

The one thing all three technologies seem to have in common is their high cost. In countries that have a carbon tax, like Norway, carbon capture is more feasible. But in the United States, adoption of the technology is slow-going.

And carbon capture is just one part of the equation. Once extracted, where could the CO2 be put to prevent it from entering the atmosphere? Enhanced Oilfield Recovery (EOR) is one possibility for use; when CO2 is injected into oil or gas reservoirs, it increases rates of recovery. EOR has been practiced for many years and is already in use at more than 100 oil fields, although many more could potentially benefit.

Carbon sequestration, the traditional option, involves injecting captured CO2 into the earth, into either unmine-able coal beds, deep saline aquifers or depleted oil/gas reserves. Geological barriers prevent the gas from returning to the surface.

Oil/Gas ReservoirsIncreased recoveryScale and capacity
Other people have drilled wells; might not know where they all are
Saline AquifersLarge scale, distribution and capacityLack of research
Unmine-able Coal BedsIncrease coal bed methane productionInjectivity problems (coal swells with CO2 injection and blocks pathways);
Pilot programs didn't work

Pros and cons must be carefully considered because “we don’t want to put the CO2 down and have it come back up,” Halsey said.

The Sleipner oil field in the North Sea, in use since 1998, has successfully injected 10 million tons of CO2 into an underground reservoir. Constant monitoring has shown some upward CO2 migration, but there is no evidence for leakage through the overlying shale barrier. The potential for earthquake activity is troublesome, but it is “a standard oil industry technical problem,” according to Halsey.

The monitoring required for such projects bring up an interesting issue-- who will be responsible for long-term storage stewardship? Companies would not be willing to invest if saddled with liability for hundreds of years. At some point, liability would need to be transferred to the public sector. Many issues exist, but if they are overcome, CCS could be a crucial tool for reducing catastrophic climate change.

Tuesday, February 2, 2010

How Do Rodents Make Decisions? A Nobel Laureate Speaks

Ion channels, the small tunnels that allow charged particles to flow through the cell membrane, play a significant role in various physiological functions. For neurobiologists, measuring the electric current associated with these ion channels proved to be a hard task, as a vast amount of information was lost due to noise.

The technique that was developed to overcome the loss of electric signals is called the patch clamp, and is one of the most widely used tools to study physiological processes on a molecular level today. One of the co-developers of this technique and a Nobel laureate, Dr. Bert Sakmann, was here on Friday to talk about his research at a seminar organized by the Duke Institute for Brain Sciences.

'We studied the neural connections in rodents using the Whisker model", Sakmann said to a packed auditorium.

The Whisker model was a whisker-dependent learning task in which the rodents had to make the decision whether to cross a small gap or not. "We wanted to know how many (neuronal) columns (of the brain were) involved in the decision-making process."

Through these experiments, Dr. Sakmann and fellow Nobel Laureate Dr. Erwin Neher identified certain cortical circuits that were activated during this decision-making process. "We measured the latency between stimulus and activation, and found there is a very precise and small latency."

They further discovered that decision-making is possible using a single column in the cortex. To measure the electric current associated within such single cells, they developed the patch clamp technique.

The patch clamp enabled the study of single ion channels and helped gain insight into the role of these channels in hormone regulation, heart diseases, epilepsy, and diabetes among others. A small video demonstrating the technique can be found below.

Sakmann and Neher received the Nobel Prize for Medicine in 1991 for their work.

Tuesday, January 26, 2010

What Comes After Genetics?

Guest post from James Todd, host of Duke's online "Office Hours" program.

Just when you thought you had a grip on genetics and genomics, there's this new thing called "epigenetics” that is becoming increasingly prominent.

One of the pioneers of this new field is Duke's Randy Jirtle. (visit his lab’s website)

Two years ago, the National Institutes of Health announced that it planned to provided $190 million in funding for epigenetics research over five years, as part of its Roadmap Epigenomics Program. Recent stories by NOVA, Time and the Washington Post have highlighted the importance of the field.

So what is epigenetics? Jirtle gives a definition in this video.

Curious to learn more? You can also watch Jirtle’s recent “Office Hours” interview.

Sunday, January 24, 2010

Biomedically Enhancing Humanity

Human enhancement has many forms: medication, caffeine, braces, contact lenses, steroids... but also education and science -- a collective intellectual enhancement. According to philosophy and public policy professor Allen Buchanan, “human beings have been enhancing themselves as long as they have been humans.”

Buchanan kicked off the 2010 A. B. Duke lecture series last week with his thoughts about the ethics of biomedical enhancement. Biomedical enhancements (BEs) are interventions that act directly on the body, improving some particular capacity. But “getting an enhancement doesn’t necessarily make you better off,” Buchanan noted. For instance, a person might wish to enhance their hearing, but enhancing it too much might make life unpleasant.

BEs can be cognitive or affective (improving mood or moral sentiments), can increase one’s resistance to disease or increase life span and quality of life. Different modes of BE include drugs, tissue/organ replacements, computerized neural implants and germline genetic interventions (genetically engineered embryos or sperm).

According to Buchanan, it’s not true that biomedical enhancements differ from traditional enhancements. For instance, if a person is highly reliant on their computer, then how different would it be to make that computer accessible via their mind?

BE certainly raises some interesting ethical questions, and has some incredible applications. One example is the ability to spread adaptive genes laterally, from person to person rather than from parent to offspring. This could have been helpful when infectious diseases like smallpox and bubonic plague wreacked havoc on human populations. Genetic resistance to a disease was uncommon before an outbreak, but quite prevalent afterwards, as only disease-resistant individuals survived to bear children. These deadly diseases produced rapid genetic change across whole populations, but millions died in the process. Alternatively, intentional genetic modification (IGM) “could spread desirable mutations more quickly and without the human cost,” according to Buchanan.

Opponents are concerned that BE could destroy human nature, have unintended bad consequences and/or provide an unfair advantage if only made available to some. Furthermore, there is the possibility for malicious dual use (repressive social control à la Brave New World).

But according to Buchanan, “It’s not a matter of being for or against it... because it’s going to happen. It’s already here.” Biomedical research frequently produces discoveries relevant to human enhancement. The only way to stop this would be to cease all biomedical research... and that’s just not going to happen.

One common argument against BE is that it interferes with nature. But Buchanan thinks we're giving nature, and evolution, too much credit.

“Don’t think of evolution as a master engineer ... Suboptimal design is a pervasive and necessary feature in evolution.” Buchanan went on to list several less-than-intelligent attributes:
  • The dual function of the human pharynx (breathing and swallowing); resultant choking
  • Humans’ inability to biosynthesize Vitamin C (We have the genetic pieces for it to be possible, but one part is missing, probably due to a mutation long ago)
  • The male urinary tract goes through the prostate, instead of around it, making it prone to infection. The primate sinus is also prone to infection.
  • The human birth canal runs through the female pelvis. As humans evolved to walk on two feet, and as human cranium size increased, giving birth became increasingly risky for both mother and child.

“How reliable is evolution as a means for improving human life -- or even for sustaining it?” Buchanan said. “Evolution doesn’t care what happens to you after you reproduce.” This might explain the preponderance of later-life problems, such as cardiovascular degeneration and accumulated mutations that lead to cancer. “There’s no reason to believe that evolution will correct [these problems],” Buchanan said. “In fact, there’s every reason to believe it won’t.”

Buchanan emphasized that humans must look beyond evolution’s haphazard progression. “[Evolutionary success] depends on a fitness between the organism and the environment, and the environment is constantly changing.” Furthermore, “current organisms are not the apex of evolution,” Buchanan said. “We are not completed works. It’s not the end!”

Friday, January 22, 2010

Move Around Inside the Web

Guest Post from Cara Bonnett of Duke's Office of Information Technology:

Instead of clicking through a series of hyperlinked websites, imagine moving through a three-dimensional Web of interconnected virtual worlds.

That’s the idea behind OpenCobalt, a toolkit of open-source software in development at Duke.

The free toolkit allows developers to build and share their own virtual 3-D environments, interacting in real time via video and voice, with collaborative access to Web browsers, 3-D models and documents.

The current 2-D Web interface – a collection of hypertext “pages” on a “desktop” – was designed primarily for sharing text and simple graphics, not for facilitating deeper kinds of social interaction, according to Duke researcher Julian Lombardi, who demonstrated the OpenCobalt technology at Duke’s biweekly Tech and New Media Tuesday forum.

“Wonderful stuff can happen when you move away from the page metaphor,” said Lombardi, one of OpenCobalt’s architects and assistant vice president of Duke’s Office of Information Technology. “We’re living in a 3-D world. We need to interact with each other and with information in 3-D spaces.”

Commercial vendors of today’s virtual worlds – from Second Life to World of Warcraft – offer “walled garden” services, much as AOL, CompuServe and other Internet service providers did in the 1990s, with little incentive to leverage open community standards, Lombardi said.

Built using the earlier open-source Croquet platform, OpenCobalt provides a way to easily create and connect virtual worlds. It works on all platforms and relies on peer-to-peer architecture that doesn’t require dedicated servers.

In his demonstration, Lombardi used the technology to quickly create a virtual workspace, adding 3-D models, audio and video files, then moved into another virtual space created by one of his collaborators in California.

The OpenCobalt project – funded by the Andrew W. Mellon Foundation and two awards from the National Science Foundation – aims to build a viable, scalable infrastructure that supports the needs of education and research.

Developers can learn more about the project and download OpenCobalt at

Tuesday, January 19, 2010

Make Green Video

Guest post from Scottee Cantrell at the Nicholas School of Environment:

If you could make the environment better, what would you do? Can you show us in three words? That’s the challenge posed by a new, nationwide video contest, “Green in 3,” sponsored by Duke’s Nicholas School of the Environment that starts today. The 15 best videos will each be awarded a $500 prize.

The contest, which runs through April, asks members of the public to suggest a simple, three-word approach to greener living – “Join a carpool,” “Use rain barrels,” ”Cuddle for warmth” – and capture it with a digital camera, cell phone or Webcam. Ideas can be large or small, serious or silly.

Dean William L. Chameides says: The contest is part of our continuing efforts to show that although environmental challenges are complex, we can all take steps to help solve them and forge a sustainable future. The contest is open to anyone 18 years or older in the U.S. and D.C. and Canada (excluding Quebec).

Find out more at

Friday, January 15, 2010

Winter Forum Participants: In It to Win It (Day 2)

Day 1 of the inaugural Winter Forum witnessed an impressive range of activities, from lectures to thoughtful deliberation and passionate debate. Day 2 would promise no less.

At a meeting before winter break, law school professor Bill Brown introduced a special component of the Winter Forum: a startup business competition. He charged students with the task of creating a ‘green’ business that would maximize capital while maintaining a negative carbon footprint. Students were given $1 million to get the theoretical business off the ground.

Most work for the competition occurred over break, especially during the last few days.
Teams struggled to develop product / service design, marketing and financing strategies and detailed expense reports. Hundreds of details had to be tinkered with and agreed upon.

The results of this effort were presented Tuesday afternoon, after a morning spent discussing the merits and disadvantages of commercializing wind power in the United States. A panel of four venture capitalists would judge the teams’ proposals.

To get things started, competition organizer Bill Brown described the opportunities offered by green businesses. “We have a problem, and policy is likely to fall short. Innovation is essential, when all else fails and even before you try all else,” Brown said.

He noted how humans have faced seemingly insurmountable problems in the past -- pestilence, oppression and starvation, to name a few -- but applied science and technology made them manageable. He encouraged students to see innovation as the way forward.

“As a university, it’s our obligation to help you think of opportunity as more than just a job,” Brown said.

Photo credit: Hua FanTeam 1 began the presentations with their model for optimizing farmer’s markets. Other ideas ranged from an ecotourism travel site to building retrofitting, home energy metering, and green product certification. Team 4 proposed the winning idea: recycled cellulosic insulation to be installed in homes in Malaysia, an emerging market with fast-increasing emissions. The team received a $2,000 check from President Brodhead at a reception following the competition.

Some students might shrink from returning to school early and working hard when they could be relaxing. But Winter Forum participants saw an opportunity to give a little and gain a lot. For their time and their attention, students learned the ins and outs of an issue, flexed their communication skills and interacted with dedicated faculty.

I did not know what to expect from the Winter Forum. I put in the work over break, did research and emailed teammates I hadn’t even met in person, hoping that it would be good for something. As a result of the process, I built my group dynamics skills and developed relationships with wonderful teammates and faculty sponsors. For its first year, I believe the Forum was very successful at fulfilling its objectives, and no doubt will continue to grow in coming years.

Thursday, January 14, 2010

First-Ever Winter Forum is Cause for Debate (Day 1)

Last October the Pew Research Center surveyed Americans’ opinions about global warming, and found that 57% believed that solid evidence of global warming existed. Only 36% thought that global warming was due to human activity.

These percentages mark a sharp decrease from the Pew Center’s earlier poll in April 2008. At that time, 71% of Americans believed there was solid evidence of global warming, and 47% thought it was human-caused.

"Why has public opinion about the validity of global warming fallen so sharply?" a student asked during a panel discussion in Duke's inaugural Winter Forum, Sunday through Tuesday. The panel included former DuPont CEO Chad Holliday, Winston-Salem mayor Allen Joines and Bill Chameides, dean of the Nicholas School. The discussion was moderated by Tim Profeta, director of the Nicholas Institute for Environmental Policy Solutions.

The panelists said scientists have been unable to effectively communicate the scientific evidence to the public while journalists and policymakers have dominated the conversation. News of one study fudged to support the existence of global warming further increased doubt. Throughout the panel, the speakers addressed possible solutions from their various academic, business and political perspectives.

The event kicked off the first-ever Winter Forum, an annual 2.5-day symposium to examine a global challenge from interdisciplinary perspectives. This year’s Forum focused on the development of a green economy. Students returned early from winter break to participate in the event.

I attended this year’s Winter Forum, and was very impressed with both the quality of instruction and the commitment of participating faculty. Lectures were short but informative, and always followed by discussion of some kind. The activities encouraged students to get engaged and share their ideas, fostering an incredibly creative intellectual environment.

During the morning of the first full day, a series of lecturers briefly discussed “the greatest hits of why we aren’t where we want to be,” as Tim Profeta put it.
  • Duke law professor Jonathan Wiener discussed the risks, tradeoffs and externalities of a green economy.
  • Environmental policy professor Erika Weinthal spoke about policy failure and the problem of collective action: “No one wants to play the cost of the solution and then have everyone else free-ride off the benefits."
  • Fuqua professor Bob Clemen explained how banks aren’t lending to startups, and how inconsistent subsidies and incentives make investors wary to invest in green businesses. Another problem is that “executives want to show profit in three months, but green projects rarely do.”
  • Divinity school professor Norman Wirzba described how “we live lives now that kings and queens of the past could not have imagined. We have it all, but we want more. And we’re doing the planet in.”
  • According to Nicholas School / law professor Jim Salzman, the problem is not simple, and thus neither are the solutions.
The second part of the day followed a more international theme. Brian Murray, director for economic analysis at the Nicholas Institute for Environmental Policy Solutions, gave a brief primer about climate negotiations in Copenhagen in December, which he attended. He did not disclose the outcome of the conference, but rather left it to the members of Duke’s International Relations Association (DIRA) to lead students through an elaborate roleplay. Teams were assigned countries (United States, India, Russia, China) or voting blocs (European Union, OPEC, Forested Bloc, Less-Developed Countries) and formulated their group's priorities during a discussion period.

The teams reconvened for three rounds of debate. Treaties were made, and broken. Low-lying nations pleaded for deep emissions cuts and funds to help them cope with rising sea levels and disappearing farmland. Nations with oil-dependent economies (Russia and the OPEC members) offered to cut emissions some, but not much. Countries squabbled over aid money, technology transfer and intellectual property rights. At the end of the day, haphazard progress had been made, but no comprehensive agreement was reached.

Afterwards, Murray explained how the issues that emerged during the mock conference were the same that plagued real-life policymakers at Copenhagen. However, he expressed hope that a binding international agreement could be reached at the COP16 in Mexico City next year.

Watch for a second post about Winter Forum Day 2 coming soon...

Wednesday, January 13, 2010

Putting His Name on the Map

Duke mathematician and physicist Arlie Petters was recently recognized by his hometown of Dangriga, Belize with a street named in his honor.

When he's not applying new math to astronomical questions about gravity, space and time, Petters devotes significant time and resources to improving educational opportunties for children in Belize. "I am truly thankful to the Duke leadership for setting the tone of 'Duke in service to society' in the US and around the globe," Petters said via email. "When we do selfless acts to empower others, the unexpected can happen."

In 2008, Queen Elizabeth of England named Petters to Membership in the Most Excellent Order of the British Empire (of which Belize is still a part) for his research and teaching.

No word on whether that honor brought a tear to his eyes, but this most excellent one did.

Thursday, January 7, 2010

Blogging from Antarctica (we wish!)

What if you lost the roof over your head? It'd probably be a pretty significant change in your lifestyle.

If you were an organism living on the bottom of the sea under the massive Larsen Ice Shelf of Antarctica, this would be more than a rhetorical question.

Duke Graduate Student David Honig is on a ship just off the ice shelf right now with a team that is exploring those questions.

All sorts of critters have lived in the lightless environment below the shelf for millennia, if not eons, making their living on energy sources other than sunlight, namely methane that seeps from the ocean floor. But the Larsen shelf is breaking apart and calving like crazy, exposing huge new areas of this delicate ecosystem to sunlight for the first time in a very long time.

What happens next?

Tune in to the Deep Sea News blog and follow along with David for the next two months as the team tries to find out.

Monday, January 4, 2010

Brian Hare on PBS This Month

Duke anthropologist Brian Hare is one of the stars of an upcoming three-part PBS documentary on the links between humans and other primates: The Human Spark.

In a nutshell, the show asks, what makes us so different from our nearest relatives? What makes us special? Hare studies chimps, bonobos and domestic dogs in an effort to figure out some of these questions.

Yes, Brian got to meet host Alan Alda, comic actor turned science journalist. In fact, he took Alda to the North Carolina Zoo to meet some chimps.

Social psychologist Tanya Chartrand of the Fuqua School of Business also spent some time with the PBS crew, but it doesn't appear that her segments survived the editing process. You can see what they talked about on the show's blog, however.

The series airs locally on WUNC at 8 p.m. on Jan. 6, 13 and 20. The local PBS affiliate is also doing added programming and a special website.

The National Science Foundation, which underwrote some of the program, prepared this short webcast interview with Alda and the show's producers shortly before the holidays. (46 Minutes)