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Duke Undergrads Sink Their Teeth into Evolution Research

Undergraduates Ben Schwartz (left) and Amalia Cong (center) have spent the past year studying enamel evolution in the labs of Christine Wall (right) and Greg Wray (not pictured).

Undergraduates Ben Schwartz (left) and Amalia Cong (center) have spent the past year studying enamel evolution in the labs of Christine Wall (right) and Greg Wray (not pictured).

By Erin Weeks

The evolution of thick tooth enamel helped turn our species into hard food-chomping omnivores, and two undergraduates are taking a bite out of research to unravel how that happened. Amalia Cong and Ben Schwartz are building on the work of a recent paper that identified precisely where in the human genome natural selection worked to give our species thick tooth enamel. The original study looked only at the potential role of four genes with a known role in tooth development — so now the team is broadening their scope.

“They’re really excited to expand out and push the envelope on new genes,” said Christine Wall, associate research professor of evolutionary anthropology and one of the authors of the paper, along with professor of biology Greg Wray.

Cong and Schwartz arrived in the Wall and Wray labs last summer through a special research session at Duke, the Howard Hughes Vertical Integration Partners (VIP) Program. For ten weeks, they received a crash course in primate evolutionary genomics.

“They had very little time, and the progress they made was astounding,” Wall said. “The success that they had is really a testament to how hard they worked. This has developed into their own research.”

“We’ve begun to expand our tooth enamel gene analysis to include proteins in conjunction with the RNA in order to gain a more holistic understanding of the evolutionary differences that exist between chimpanzees and humans,” Schwartz said. He will continue to work in the lab through this summer, turning the work into a senior thesis.

“One of our goals was to look at the relative expression of these few genes,” Schwartz said, which they’ve done by comparing tooth development in primates of different ages. “Our results correlated very heavily with known functions of these genes in other animals, such as rats.”

The experience has given both students a taste for research, which they hope to continue doing after graduating from Duke. Cong, who hails from a small city outside of Toronto, will be attending dental school in the fall, while Baltimore native Schwartz is interested in pursuing a joint MD/PhD.

Grad Student Solves 30-Year-Old Physics Problem

By Erin Weeks

Sometimes an age-old question just needs a fresh set of eyes.

That was the case in Duke’s physics department, where a graduate student and professor recently resolved a calculating dilemma that has vexed computational physicists for decades.

Emilie Huffman, second year PhD student in physics

Emilie Huffman, second year PhD student in physics

Emilie Huffman is a second-year PhD student from Charlotte, North Carolina. Last spring she began working with Shailesh Chandrasekharan, an associate professor and the director of graduate studies in physics, on what’s known as a sign problem.

Chandrasekharan is a theoretical nuclear and particle physicist who specializes in solving sign problems, which arise when one uses certain computational algorithms to calculate the behavior of large numbers of particles called fermions.

“Almost all the matter we know of are made with fermions,” Chandrasekharan said. “As building blocks of matter, it’s very important to be able to do calculations with them.”

But calculations of such complexity get tricky, and sign problems make it easy for wrong results to surface.

“It’s a very broad problem that affects almost all fields of physics involving quantum mechanics with strong correlations, where Monte Carlo methods are essential to perform calculations,” Chandrasekharan said.

Some in the field have simply moved on since the 1980s, leaving interesting questions plagued by sign problems unexplored. Other scientists have found workarounds and approximations. Very few, including Chandrasekharan, have tried to figure out solutions through the years. Huffman began work to expand on one of her advisor’s solutions, involving a grouping concept called fermion bags, and apply them to a new class of problems.

“She finally figured out a nice formula,” Chandrasekharan said. “Although the formula is quite simple and elegant, I couldn’t guess it.”

“In physics, often there’s a truth, and if you’re hitting on the right truth, everything starts falling into place.” Chandrasekharan says that’s what happened when he began applying Huffman’s formula to a class of problems.

Their paper appeared recently in the journal Physical Review B’s Rapid Communications.

“Now that I have a solution, I can begin to apply it,” Huffman said. Starting with condensed matter physics, Huffman plans to apply her solution to various questions that have been stymied by sign problems. “I can use this solution to study properties of graphene,” she said, referring to the single-layer carbon that has been touted as the strongest material in the world. Many puzzles remain in the field, especially involving multi-layer graphene sheets.

Wherever she turns her attention next, it’s clear Huffman has a promising career ahead.

Citation: “Solution to sign problems in half-filled spin-polarized electronic systems,” Emilie Huffman and Shailesh Chandrasekharan. Physical Review B Rapid Communications, March 12, 2014. DOI: 10.1103/PhysRevB.89.111101.


Copper Nanowires Now Match Performance of Leading Competitor

Images of the first and last stages (intermediate photo excluded) of the copper nanowire growth as seen through a transmission electron microscope. Interestingly, though not visible here, the nanowires are pink. (Photo: Shengrong Ye)

Images of the first and last stages of the copper nanowire growth as seen through a transmission electron microscope. Interestingly, though not visible here, the nanowires are pink. (Photo: Shengrong Ye)


By Erin Weeks

Copper nanowires are one step closer to becoming a low-cost substitute for the transparent conductor in solar cells, organic LEDs and flexible, electronic touch screens. A team at Duke has succeeded in making transparent conductors from copper nanowires that are only 1% less transparent than the conventional material, indium-tin oxide (ITO).

Copper is 1000 times more abundant and 100 times cheaper than indium, the main ingredient in ITO, but for years copper nanowires have lagged behind in terms of transmittance.

Assistant chemistry professor Benjamin Wiley’s lab has fixed that — simply by changing the aspect ratio, or the proportion of length to diameter, of the nanowires. The findings were reported recently in the journal Chemical Communications.

“We finally have something competitive with ITO in terms of performance, and we got there by increasing the nanowire aspect ratio,” Wiley said.

Using a special growth solution, Wiley’s lab can “sprout” the nanowires in under half an hour and at normal atmospheric pressure. Further tweaking the synthesis, the team was able to prompt the nanowires to grow long and uniform in diameter, instead of tapered and baseball bat-shaped, which have lower aspect ratios.

The paper also includes the images of copper nanowire growth as observed in real time, the first time such observations have been published.

Still, at least one kink remains before the nanowire technology will be attractive for commercial production. The copper nanowires are susceptible to corrosive oxidation, which Wiley’s team has tried to remedy by coating the nanowires with materials like nickel. Unfortunately, a nickel coating reduces the transparency of the nanowire films.

“So now we’re trying to figure out ways to protect the nanowires without decreasing the performance,” Wiley said. “We’re focused on getting the same performance, but having more stability.”

Citation: “A rapid synthesis of high aspect ratio copper nanowires for high-performance transparent conducting films.” Shengrong Ye, Aaron Rathmell, et al. Chemical Communications, March 11, 2014. DOI:10.1039/c3cc48561g.

Managing a Lab: The Parts You Won't Learn in Class


Panelists (L-R) Sally Kornbluth, Jessica Monserrate, Mohamed Noor and Susan Smith (Photo: David Steinbrenner)

By Erin Weeks

For many researchers in training, making it as a scientist involves the dream of one day running their own lab. But becoming the head of a laboratory takes far more than research chops — you’ve got to have serious people skills, too.

A March 13 panel called “Managing a Lab: Insights from Academia and Industry” advised an auditorium of Duke postdocs and PhD students on how to meet the management challenges they may face one day as principal investigators (PI). “Effective lab management can be as crucial to career success as the research itself,” the description for the session read.

Sally Kornbluth, Vice Dean for Basic Sciences at Duke Medicine and Duke’s provost-elect, drew from her own experience as a PI as she walked the audience through the nitty-gritty of building a lab from the ground up.

“The lab takes on the style of the PI,” she said. The job of the lab head is to set its scientific direction, obtain grant money and hire the right people.

PIs have to make decisions about what kind of leader they want to be — how accessible do they want to be? How will they motivate their lab members? How will they deal with difficult personnel situations? Some of these questions will be determined by the lead scientist’s personality, Kornbluth said, but others may require trial and error to figure out.

The panel, put on by the Office of Postdoctoral Services, included three other lab managers representing both academia and industry: Mohamed Noor, professor and chair of the biology department; Jessica Monserrate, a scientist at Bayer CropScience and former Duke postdoc; and Susan Smith, a scientific investigator at Stiefel and also former Duke and Duke Med postdoc.

The speakers fielded questions reflecting anxieties about the work climate many students and postdocs will soon enter, in which grant budgets are shrinking and PI positions are highly competitive. But the audience also asked evergreen questions about careers in science, like how to keep up lab morale and balance research with family life.

“Choose your spouse very wisely,” Kornbluth said, drawing laughs.

Sally Kornbluth, Duke's soon-to-be Provost, talks about managing a lab. The talk will be available online soon.

Sally Kornbluth, Duke’s soon-to-be provost, talks about managing a lab (Photo: David Steinbrenner). The talk will be available online soon.

Sign Up For Datafest 2014 to Work on Mystery Big Data


Heads up Duke undergrads and graduate students — here’s an opportunity to hang out in the beautifully renovated Gross Hall, get creative with your friends using big data and compete for cash prizes and statistics fame.

Datafest, a data analysis competition that started at UCLA, is in its third year in the Triangle. Every year, a mystery client provides a dataset that teams can analyze, tinker with and visualize however they’d like over the course of a weekend. Think hackathon, but for data junkies.

“The datasets are bigger and more complex than what you’ll see in a classroom, but they’re of general interest,” said organizer Mine Çetinkaya-Rundel, an assistant professor of the practice in the Duke statistics department. “We want to encourage students from all levels.”

Last year’s mystery client was online dating website eHarmony (you can read about it here), and teams investigated everything from heightism to Myers-Briggs personality matches in online dating. In 2012, the dataset came from Kiva, the  microlending site.

This year’s dataset provider will be revealed on the first day of Datafest. Sign up ends this Friday, March 7, Monday, March 10, so assemble your team and register here!


New Fossil Cache Hints at Human Ancestry

By Erin Weeks

In October 2013, three South African cavers made a discovery that may change our understanding of human origins.

Just 25 miles outside Johannesburg lies the Cradle of Humankind, a World Heritage Site marked by limestone caves, in which decades of research have unearthed an abundance of early hominin remains. Five years ago, the caves yielded a new species, Australopithecus sediba, whose classification has divided the anthropology community. And as recent months have shown, the Cradle of Humankind holds many more secrets.

At the bottom of one cave complex, past a fissure just eight inches wide, the cavers discovered what looked like hominin fossils lying undisturbed in soft dirt. The findings triggered a frenzy of activity, as researchers scrambled to assemble a team to investigate the promising fossils. One member was Duke paleoanthropologist Steve Churchill, who discussed his work on A. sediba and the new, as-of-yet unclassified fossils last week in a lecture on campus called “The 2-Million-Year-Old Boy.”

The research tents at the Rising Sun excavation site in South Africa (Photo: Steve Churchill)

The research tents at the Rising Sun excavation site in South Africa (Photo: Steve Churchill)

The National Geographic Society provided emergency funding for a three-week endeavor dubbed the Rising Star Expedition, which has been chronicled online by scientist Lee Berger (the blog has great pictures of the caves and fossils).

In those marathon three weeks, the team catalogued 1,200 fossils. By comparison, Churchill explained, 65 years of excavation yielded just 400 and 500 hominin fossils, respectively, in two nearby sites.

At first, the team hoped they might have a full skeleton from one individual on their hands–but as the expedition progressed, they realized that the fossils came from 12 to 20 different individuals.

Perhaps most fascinating is what researchers haven’t found at Rising Star: other animals. At most sites in the Cradle of Humankind, hominin knucklebones and teeth are scattered indiscriminately among antelope and leopard fossils. Researchers may never know why so many primates, yet nothing else, were preserved in Rising Star’s remote chambers, but it’s clear the assemblage formed under conditions very different than those of the nearby cave sites.

A peek inside the science tent. All of the equipment for the three-week expedition had to be hauled out to the cave site. (Photo: Steve Churchill)

A peek inside the science tent. All of the equipment for the three-week expedition had to be hauled out to the cave site. (Photo: Steve Churchill)

Where these primates belong on the hominid family tree is another lightning-rod question the team is working to answer. The age of the fossils is currently unknown, but there are indications they may fall into the time range in which early members of the genus Homo were first beginning to arise. If so, they may help to upend current theory, which holds that our Homo forebears evolved in East Africa rather than present-day South Africa.

Whatever the final word on their taxonomy, it’s clear the Rising Star fossils will lead to anthropological insights for years to come.

The Catastrophic Origins of Our Moon

This still from a model shows a planet-sized object just after collision with earth. The colors indicate temperature. (Photo: Robin Canup)

This still from a model shows Earth just after collision with a planet-sized object. The colors indicate temperature. (Photo: Robin Canup)

By Erin Weeks

About 65 million years ago, an asteroid the size of Manhattan collided with the Earth, resulting in the extinction of 75% of the planet’s species, including the dinosaurs.

Now imagine an impact eight orders of magnitude more powerful — that’s the shot most scientists believe formed the moon.

One of the leading researchers of the giant impact theory of the moon’s origin is Robin Canup, associate vice president of the Planetary Science Directorate at the Southwest Research Institute. Canup was elected to the National Academy of Sciences in 2012, and she’s also a graduate of Duke University — where she returned yesterday to give the fifth Hertha Sponer Lecture, named for the physicist and first woman awarded a full professorship in science at Duke.

According to the giant impact hypothesis, another planet-sized object crashed into Earth shortly after its formation 4.5 billion years ago. The catastrophic impact sent an eruption of dust and vaporized rock into space, which coalesced into a disk of material rotating around Earth’s smoldering remains (see a very cool video of one model here).  Over time, that wreckage accreted into larger and larger “planetesimals,” eventually forming our moon.

Physics professor Horst Meyer took this photo of Robin Canup, who was his student as an undergraduate,

Robin Canup (Photo: Horst Meyer, who taught Canup as an undergrad at Duke)

Scientists favor this scenario, Canup said, because it answers a number of questions about our planet’s unusual lunar companion.

For instance, our moon has a depleted iron core, with 10% instead of the usual 30% iron composition. Canup’s models have shown the earth may have sucked up the molten core of the colliding object, leaving the dust cloud from which the moon originated with very little iron in it.

Another mystery is the identical isotopic signature of the moon and the earth’s mantle, which could be explained if the two original bodies mixed, forming a hybrid isotopic composition from the collision.

Canup’s models of the moon’s formation help us understand the evolution of just one (albeit important) cosmic configuration in our galaxy. As for the rest out there, she says scientists are just beginning to plump the depths of how they came to be. Already, the models show “they’re even crazier than the theoreticians imagined.”

Touring the Planet's Most Powerful Gamma Ray Source

By Erin Weeks

When students pass by its unassuming building along Circuit Drive, many have no idea the world’s most intense gamma ray laser lies tucked away in the heart of Duke’s campus.

The Duke Free Electron Laser Laboratory, or DFELL, attracts physicists from across the country to study everything from nuclear security to the death of stars. Gamma rays are the most energetic members of the electromagnetic spectrum, and they can tell us a great deal about physics at the nuclear level. Cosmic events, like massive star collapse, produce high gamma radiation, but few natural sources exist on earth — so DFELL provides a window into the dense and infinitesimal world of the atomic nucleus. A group of students organized by Duke’s Society of Physics Students recently toured the lab to learn more. All photos were taken by Jonathan Lee.


DFELL’s gamma rays are generated by the collision of electron beams with photons racing around a large, oval storage ring, like a race track. Here, half the group gathers next to the straight leg of the oval’s left side.


Physics professor Ying Wu, the associate director for accelerators & light sources at DFELL, explains how electrons colliding with photons are like bowling balls crashing into an oncoming train. At left, you can see the red magnets that help guide the beams.


Though hidden to onlookers, this room houses a cavity mirror that helps to steer the beam of electrons with incredible precision. Even minute vibrations can knock the laser beam out of alignment, so the mirror assembly sits on reinforced concrete with shock absorbers.


Behold the Blowfish. This detector system boasts 88 “spines,” which can precisely measure what happens when intense gamma rays excite a nucleus, causing it to spit out particles. The spines are comprised of liquid-scintillator cells, which produce photons triggered by radiation, and photomultiplier tubes, which convert the photons to electrical signals.


“Blowfish’s goal in life is to make precision measurements of photonuclear reaction cross-sections,” says Grayson Rich, a graduate student at UNC who studies nuclear and neutrino physics at DFELL with Duke professor Phil Barbeau. Blowfish’s proximity to DFELL’s gamma rays “allows for really rigorous evaluation of theories for how nuclear systems behave.”

Four Things You May Not Know about Ecologist E.O. Wilson

By Erin Weeks

Edward O Wilson Red Hills, Aalabama  2010 by Beth Maynor Young 6x9_0

(Photo: Beth Maynor Young)

Edward O. Wilson is one of the most renowned living biologists, the world’s foremost authority on ants, and for a little while at least, a member of the Duke faculty.

Wilson is on campus teaching the first of an annual course, part of a recent partnership between the E.O. Wilson Biodiversity Foundation and Duke’s Nicholas School of the Environment. Feb. 11, he spoke to a sold-out auditorium about “The Diversity of Life,” a lecture that was equal parts awe-inspiring facts, humorous anecdotes from a life in science and call to arms for future generations.

Here are four things the audience learned last night about E.O. Wilson.

1. He’s dabbled in dreams of Jurassic Park. When asked what he thought of de-extinction, the plan to resurrect vanished species using their DNA, Wilson enumerated all the reasons why the efforts may be futile: we have only genetic shreds; the appropriate habitat may be gone; we can’t produce breeding populations from limited DNA.

But then he paused. “I’ll tell you frankly,” he said, “I’d like to see a mammoth.”

2. He made his first scientific discovery as an adolescent. An eye permanently damaged in a fishing accident led the young Wilson to his interest in ants, which he could view up close. One day in his native Alabama, he discovered a ferocious mound-building species he’d never seen before. He didn’t recognize it then, but those were among the first of the destructive red fire ants that would soon invade the entire Southeast, causing billions of dollars of economic and medical damage.

3. The man is 84 and still going strong. Professor Wilson closed his talk with a passage from his newest book, arriving in April, called “A Window on Eternity: A Biologist’s Walk Through Gorongosa National Park.” He’s written two dozen other books, including a foray into fiction at age 80 (the novel, called Anthill, won him the 2010 Heartland Prize for fiction).

4. The future is in nematodes. Or fungi. Or Archaea. Throughout the talk, Wilson reiterated his hopes for young scientists to become the cataloguers and guardians of Earth’s immense biological diversity. Only a fraction of the planet’s estimated species of nematodes, fungi and Archaea are known to science, and “these little things run the world,” he said.

The need for “-ologists” has never been greater, he said.

(Photo: Jared Lazarus)

(Photo: Jared Lazarus)

VIEW THE ENTIRE TALK (YouTube, 1:10 with introductions)


Adventures in Sanitation and Synthetic Poop

Assembling an anaerobic digestion toilet in Eldoret, Kenya (Photo: Marc Deshusses)

Assembling an anaerobic digestion toilet in Eldoret, Kenya (Photos: Aaron Forbis-Stokes, Deshusses Lab)

By Erin Weeks

Marc Deshusses spends a lot of time thinking about toilets.

A professor of civil and environmental engineering at Duke, Deshusses studies and designs technologies to treat contaminated soil, air and water — and save lives in the process.

An estimated 2.6 billion people across the globe lack access to a safe way of disposing of human waste. Poor sanitation spreads waterborne and diarrheal diseases, contributing to the deaths of over half a million children a year.

“The problem is huge,” Deshusses said last week in a talk (watch it here) describing two of his lab’s recent projects to improve the sanitation crisis. “We’re trying hard, we’re working on our solutions, and we’re trying to make a dent in this massive problem.”

One of those solutions-in-progress is a low-tech anaerobic digester, a toilet system that relies on biogas (produced by bacteria when they break down the human waste) and a simple biogas-powered heater to sterilize the treated waste. Deshusses wanted the digester to be cheap and easy to assemble, so one prototype even included a heater made from an aluminum coffee canister and a tomato soup can.

But before Deshusses’ team could deploy the technology in the field, they had to test it in the lab. And to do that, without having to handle real (somewhat dangerous) sewage, they turned to a synthetic pee-and-poo product developed for NASA.

NASA cares deeply about this issue because the logistics of dealing with waste in space are even trickier than on earth. The Duke team tinkered with a recipe for synthetic poop, adapting a formula for “simulated human feces” published in 2006 by NASA-funded researchers. The chemical composition of human waste varies from person to person, but the imitation poop needed to achieve the right nitrogen content, salts content, and chemical/biochemical oxygen demand, all of which impact how bacteria will break the waste down. Deshusses’ lab mixed up vats of the ingredients below, which include some surprising candidates.

A recipe for human waste: from L-R (top row), yeast, polyethylene glycol, psyllium (a soluble fiber), miso, oleic acid; (bottom row) calcium chloride, potassium chloride, sodium chloride, cellulose, water.

A recipe for syn-poo: from L-R (top row), yeast, polyethylene glycol, psyllium (a soluble fiber), miso, oleic acid; (bottom row) calcium chloride, potassium chloride, sodium chloride, cellulose, water.


The finished product, ready to be anaerobically digested

In the lab, the bacteria broke down the synthetic waste, producing enough biogas to power the heater, which in turn sterilized the small amount of leftover sewage. After confirming the technology worked, local partners helped the team deploy prototype digester toilets in three locations around Eldoret, Kenya last summer. Through trial and error there, they’re learning how to make the system even better, so they can roll out deployment in more locations.

See a movie from the Pratt School of Engineering:


“There’s not a silver bullet,” Deshusses said, but added, “anaerobic digestion is simple, it works, and it has potential.”

The heat exchange system sitting in front of the anaerobic digestion vat

No syn-poo here: the completed system (heat exchanger in foreground, anaerobic digestion vat in back) is ready for the real thing.

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