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.

Visibly Thinking about Undergrad Research

By Karl Leif Bates

Undergraduate research is kind of a big deal at Duke.

The grand finale of nearly 200 of this year’s undergrad projects was a giant poster session called “Visible Thinking,” hosted by the Office of Undergraduate Research Support  on April 22.

Happy and relieved students sharing posters at Visible Thinking 2014. (Megan Morr, Duke Photo)

Happy and relieved students sharing posters at Visible Thinking 2014. (Megan Morr, Duke Photo)

This annual showcase just keeps getting bigger, louder and more crowded, which is a great testament to the involvement of undergrads in all areas of Duke’s research enterprise.

The posters and proud students wearing their interview suits filled all the common areas of the first and second levels of the French Family Science Center on Tuesday and spilled into a few out-of-the-way corners as well.

“For many of the students this is the culmination of their four years, in which they’ve made that transition from student to scholar,” said Ron Grunwald, director of the URS office. “They’re no longer simply learning what other people have discovered, they’re discovering things on their own.”

Indeed, Rebecca Leylek wasn’t the least bit discouraged by having to check her experiment every six hours around the clock for days on end to see how the mice’s wounds were healing. The second phase of her project was a protocol she developed and got approval for and it didn’t have the six-hour part. She’s off to grad school at Stanford in immunology.

Ani Saraswathula, who co-chaired the Duke Undergraduate Research Society, apparently missed the deadline for getting his poster into the printed program, but his science on brain tumors was pretty awesome. He’s sticking around after graduation for an MD/PhD at Duke.

The new Bass Connections research teams brought nearly two dozen posters, showing off projects about energy, environmental health, art history, online education, cognitive development,  and decision-making.

And then, there was just an amazing assortment of stinky lemurs and pathogenic yeast and budding investigators talking curious faculty and students through amazing posters like this: Understanding the role of BNP signaling in pak-3 mediated suppression of synaptic bouton defects in spastin null Drosophila.

So, in addition to quizzing the young scientists about their findings, we thought we’d ask a few of them to recite their impressive poster titles from memory:

Send in the Nerds

By Karl Leif Bates

Yeah, we're a bit excitable.

Yeah, we’re a bit excitable.

Hoping to triumph where our men’s and women’s basketball teams fell short, the Duke faculty are in the Final Four of an alternative NCAA bracket based on academic publications that’s being run by Thomson Reuters.

Sure, it’s a gimmick to get people looking at Thomson Reuters’ powerful but somewhat pricey InCites citation database  — but we’re winning!

By the reckoning of the “Metrics Mania” bracket, Duke is squaring off in the final with Stanford in a contest of “normalized citation impact” of our scholarly work. (It’s a weighted average of citations per paper that controls for year published and subject area.)

Joining us in the Final Four are Harvard and Wisconsin — kudos to the Badgers for making it both ways! We’ve apparently already beat Wisconsin on the normalized citation business, so now it’s on to the Cardinal.

Previous rounds had us clobbering Mercer (cough) and Iowa on absolute number of citations and then squeaking past Michigan and NC State on percentage of documents cited.

The national champion will be announced Tuesday, after the basketball game, Thomson Reuters’ savvy PR operation says.

*** UPDATE – Tuesday, April 8 ***

Stanford was declared the winner.  We’re done talking about this. :-(

Metrics Mania – Research Analytics – Thomson Reuters

Jane Austen and Game Theory

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Attendees played Regency Era card games involving game theory before the talk

By Olivia Zhu

“It is a great deal better to choose than to be chosen.” –Jane Austen, in Emma.

Jane Austen — novelist, romantic, and social critic — can now add another title to her repertoire: game theorist.

This role has been bestowed upon her by Michael Chwe, a game theorist in the Department of Political Science at UCLA and author of the book Jane Austen, Game Theorist. Chwe claims that Austen acts as a social scientist by setting up a theoretical framework for game theory in her novels. In his talk to a lively crowd well-versed in Austen’s works on March 25th, Chwe explained Austen’s uncanny emphasis on choice, preference, and strategic thinking.

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Chwe’s illustration of Jane’s choices and commensurability analysis in Pride and Prejudice

According to Chwe, Austen does not attribute actions to random variables, but rather to careful consideration of all alternatives. For example, Fanny Price in Mansfield Park chooses to refuse Henry Crawford’s offer of marriage after weighing her options; she does so entirely out of personal preference. Similarly, a major tenet in game theory is that the individual chooses what she wants to do without much consideration past her own wishes. Chwe said that Austen places a criticism on game theory here, when Fanny’s uncle, Sir Thomas, chastises Fanny being selfish instead of marrying Henry for the family’s financial security.

Chwe also introduced the game theory concept commensurability, in which negative factors are literally subtracted from positive factors in a decision to produce a single number of utility. He stated that Austen’s language, including phrases such as “finely checkered” happiness, “two

Chwe's playful histogram of Elizabeth Bennet's quantification of emotion.

Chwe’s playful histogram of Elizabeth Bennet’s quantification of emotion.

pleasures, however unlike in kind,” and “on the whole, no cause to repine,” clearly illustrate Austen’s intent to quantify emotions for commensurability.

Finally, Chwe pointed out the bounty of strategic thinking, another element of game theory, present in Austen’s novels. Austen does not portray calculation as unnatural or cold, he says. She mentions the word “scheme” 126 times, “contrive” 54 times, “foresight” 49 times, and “calculate” 41 times. Her strong, female characters often pride themselves on their ability to anticipate others’ actions.

Chwe concluded that though there is no direct evidence that Austen infused game theory into her novels, she clearly explores the concept of choice in her work.

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

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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.

Aphasia: Acceptance, Hope, Purpose

By Sonal Gagrani

Imagine having a head full of things to say, but not being able to articulate them. This is the life of Carl McIntyre.

AphasiaPosterSouth21

courtesy of aphasiathemovie.com

There is a three-hour window of opportunity after the initiation of a stroke in which it can be effectively treated. However, when a stroke hit Carl McIntyre, those three hours passed before he could be safely withdrawn from danger. His ability to speak and understand became heavily impaired, a condition known as aphasia. In order to raise awareness of this condition that affects not only him, but almost 40% of the people who suffer a stroke, he starred as himself in a film called Aphasia. Carl McIntyre came himself to speak at Duke for Brain Awareness Week following a screening of his film.

BAW logoAphasia is a group of communication disorders that affect the language centers of the brain causing impairments in speech, speech comprehension, reading and writing. It tends to arise with damage of some part of the brain, often due to a stroke, brain tumors, or neurodegenerative diseases.

McIntyre expressed powerfully that, “what happens to one, happens to two.” The aphasia affects not only him but his entire family. Life felt as if it was over, loving was difficult; he felt “trapped inside of his head.” Having a reservoir full of thoughts that he was unable to empty due to this inability to communicate could be eternally frustrating. Aphasia patients often are cognitively intact, but have trouble expressing what they want to say. McIntyre occasionally used a whiteboard to write down words he was struggling to say or stumbled on the first sounds of words.

Carl McIntyreBut rather than letting the aphasia control the way that he lived, McIntyre worked hard to restore his language capabilities and spread awareness of the challenges that inflicted individuals must face. Most importantly, McIntyre expressed the importance of keeping hope.

He explained that the first step to having a positive outlook on his condition was to accept the “old Carl was dead.” The next was to keep hope that his life could continue as normal as possible – that the condition would not impair his lifestyle. Last, he expressed the importance of having a sense a purpose by picking up hobbies and not losing all meaning in life. Carl strives to have a strong sense of self despite the adversities he and his family has had to face and inspires others to understand and do just this.